Re: [base] base/apache problems

[Jari Häkkinen]

Hi Richard,

You should type the name (or ip number) of the computer running your 
apache server in the address field of your web browser. If you followed 
the BASE installation instructions this is the same machine where you 
installed BASE.


Example:
Our demo server has the name base.thep.lu.se with the correspondiung ip 
number 130.235.95.158



Jari


[EMAIL PROTECTED] wrote:

Hi folks

This is a bit of a naive one but I've never run a webserver before and I'm
finding the apache manual a bit impenetrable. When the base installation guide 
says:

"Point your browser to your web server"

what does that actually mean. I assume I'm supposed to enter a path or an IP
address into my favourite web browser but what path or IP address. Excuse my
ignorance.

regards

Richard




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Re: [base] BASE 1.2.17b compilation error

[Jari Häkkinen]

Hm, this was a tricky one. What OS are you compiling on? A inital guess 
is that the compiler cannot find the definition for 'rlimit'.



Jari


Osvid wrote:

Hello,

I have some problems with the BASE 1.2.17b installation. When I run
"make install" I get these errors:

gcc -DHAVE_CONFIG_H -I. -I. -I../..-DJOBRUNNER_USER_UID=507
-DBASE_USER_UID=507 -Wall  -march=i686 -O3  -c -o jobRunner-jobRunner.o
`test -f 'jobRunner.c' || echo './'`jobRunner.c
jobRunner.c: In function `main':
jobRunner.c:96: parse error before `struct'
jobRunner.c:98: `cpulim' undeclared (first use in this function)
jobRunner.c:98: (Each undeclared identifier is reported only once
jobRunner.c:98: for each function it appears in.)
jobRunner.c:100: `rl' undeclared (first use in this function)
jobRunner.c:104: parse error before `long'
jobRunner.c:110: `ramlim' undeclared (first use in this function)
make[2]: *** [jobRunner-jobRunner.o] Error 1
make[2]: Leaving directory `/home/base/base-1.2.17/src/jobRunner'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/base/base-1.2.17/src'
make: *** [install-recursive] Error 1

What do you suggest me?

Thanks in advance!

Óscar D.

--
Óscar David Sánchez Jiménez
Telecommunications Engineer - Computer Science Ph.D. student
Grupo de Informática Médica
ITACA - BET (Bioingeniería, Electrónica y Telemedicina)
Universidad Politécnica de Valencia
Camino de Vera s/n E-46022 Valencia (Spain)


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Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
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Re: [base] MAGE-ML for ArrayExpress update, plug-ins

[Jari Häkkinen]

Hi Angela,


BASE plug-ins ... we are slowly working on getting the web page up 
again. Meanwhile we urge those of you who have plug-ins to send them to 
us through http://lev.thep.lu.se/trac/baseplugins



Jari

Angela Burr wrote:

Hi,

Our group has been using BASE for over a year and we have been eagerly awaiting
the completion of MAGE-ML creation corrections (so that MAGE-ML files created by
BASE are acceptable for ArrayExpress submission).  We have data in BASE that we
need to submit to ArrayExpress.  Would you please give an update on the progress
and possibly a timeline for when these changes will be incorporated into BASE
1.2.x?  We really appreciate all the work on this project, adding this function
in BASE will be very helpful.  


Also, when will more plug-ins be added to the new BASE plug-in development site?
Our group is interested in adding more analysis plug-ins to our BASE
installation and I'm sure that many BASE plugins have already been written.  We
would prefer not replicate the work if others have already written similar
plug-ins.  

Thank you for the updates in advance.  


Angela Burr
Center for Genomics and Bioinformatics
Indiana University, Bloomington


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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
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Re: [base] MAGE-ML for ArrayExpress update, plug-ins

[Jari Häkkinen]

Yes ... but probably after release. We have already assigned enough for 
us all to do, but this wil be added asap after Feb 23. There are more R 
related stuff to be implemented during the spring.



Jari

charles girardot wrote:

Hi Jari,

Could you make sure that the R dispatcher (AROMA BASE, by Henrik 
Bengtsson from Lund) continues to work in BASE 2.0


Thanks

Charles

On 16 janv. 06, at 13:40, Jari Häkkinen wrote:


Hi Angela,


BASE plug-ins ... we are slowly working on getting the web page up 
again. Meanwhile we urge those of you who have plug-ins to send them 
to us through http://lev.thep.lu.se/trac/baseplugins



Jari

Angela Burr wrote:


Hi,
Our group has been using BASE for over a year and we have been 
eagerly awaiting
the completion of MAGE-ML creation corrections (so that MAGE-ML files 
created by
BASE are acceptable for ArrayExpress submission).  We have data in 
BASE that we
need to submit to ArrayExpress.  Would you please give an update on 
the progress
and possibly a timeline for when these changes will be incorporated 
into BASE
1.2.x?  We really appreciate all the work on this project, adding 
this function
in BASE will be very helpful.  Also, when will more plug-ins be added 
to the new BASE plug-in development site?

Our group is interested in adding more analysis plug-ins to our BASE
installation and I'm sure that many BASE plugins have already been 
written.  We
would prefer not replicate the work if others have already written 
similar

plug-ins.  Thank you for the updates in advance.  Angela Burr
Center for Genomics and Bioinformatics
Indiana University, Bloomington
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se



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[base] BASE 2.0RC1 released

[Jari Häkkinen]

Hi all,

We have released BASE 2.0RC1.

You can access the release tar ball from http://base.thep.lu.se/base2. 
All available documentation regarding BASE 2.0 is available through the 
the BASE web site.


BASE 2.0 is a complete rewrite of BASE 1.2 in the Java programming 
language. RC1 has all basic functionality to support microarray 
experimentation but is not yet as feature rich as BASE 1.2.


Please send feedback through the mailing list.


Enjoy,

The Lund BASE team.


--
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se



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Re: [base] Anybody install BASE under Tomcat?

[Jari Häkkinen]

Hi,

There is no way to install BASE 1.2.17 (NOTE version number) since 1.x 
is based on PHP. However, BASE 2.0 is a complete rewrite in Java an runs 
with Tomcat. So, to run BASE in Tomcat you must switch to BASE 2.0.


BASE 2.0 inherently supports Affymetrix but the import plug-in for 
Ayffymetrix data is still to be written. This plug-in will appear as a 
part of the next milestone for BASE 2.0 
(http://lev.thep.lu.se/trac/base/roadmap).


More information on BASE 2.0 is available at http://base.thep.lu.se/base2/


Jari


Longfei Yu wrote:

Hi,

I am wondering if anybody tried to install BASE system under Tomcat?

I have done more implementation based on the BASE2.17, and it will 
support the Affymetrix experiment. I have added some more tables in the 
original database, so that the new system can extract the data from EXP, 
CEL, CHP file, and the user also can download all of them and DAT files 
for their experiment.


However, the new implementation is based on Java technology, and I run 
the Affymetrix part under Tomcat, and the original BASE under apache. 
But, I want to merge them together, and put them all under Tomcat.


I want to know if anybody did that successfully? If I want to run 
BASE2.17 under tomcat, what I need to do? Reinstall the BASE, or just 
copy the corresponding folds to Tomcat? Any suggestions will be appreciated.


Thanks a lot!

Best Regards,

Longfei



--
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se



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Re: [base] BASE 2.0 RC2 released

[Jari Häkkinen]

Hi,

We missed out on Affy support but it will appear very soon. Sorry about 
the slight delay. There is a requirement spec that I'll post later today.

Affymetrix in BASE1 has been done but I am not able to give any details 
about this. The migration from BASE 1 to 2 assumes a pristine 1.2.late 
version of the "official" database schema. This means that BASE1 Affy 
supporters need to modify the migration program to transfer data to BASE 2.

I think you should wait somewhat longer for Affy support in BASE2.


Cheers,

Jari


Steve Taylor wrote:
> Hi,
>> I am happy to announce that BASE 2.0 RC 2 is now available for download:
>> http://lev.thep.lu.se/trac/base/wiki/DownloadPage
>>
>> Installation instructions are available at the BASE2 home page:
>> http://lev.thep.lu.se/trac/base/wiki
> 
> It's good to see BASE2 is progressing! I notice Affy support is not in this 
> in this RC. Is there a set of requirements that details what we can expect 
> when this feature is implemented?
> 
> I am still unsure about if there is support for Affy in BASE1. I seem to 
> remember reading you can upload Affy data into BASE1 although functionality 
> is limited. Assuming this is possible... has anyone 
> got any experience in this and can point me to some documentation? Will the 
> migration tools migrate such data over if we were to proceed uploading to 
> BASE1? Or is it best to hold off a while longer 
> and wait for BASE2?
> 
> Thanks for any info,
> 
> Steve
> 
> 
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-- 
Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se


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Re: [base] BASE 2.0 RC2 released

[Jari Häkkinen]

I have added a summary of Affymetrix in BASE discussions to the 
subversion repository, 
http://lev.thep.lu.se/trac/base/browser/trunk/doc/affymetrix.txt

Among other things, this document outlines the current plan for 
Affymetrix support in BASE 2.


Jari


Jari Häkkinen wrote:
> Hi,
> 
> We missed out on Affy support but it will appear very soon. Sorry about 
> the slight delay. There is a requirement spec that I'll post later today.
> 
> Affymetrix in BASE1 has been done but I am not able to give any details 
> about this. The migration from BASE 1 to 2 assumes a pristine 1.2.late 
> version of the "official" database schema. This means that BASE1 Affy 
> supporters need to modify the migration program to transfer data to BASE 2.
> 
> I think you should wait somewhat longer for Affy support in BASE2.
> 
> 
> Cheers,
> 
> Jari
> 
> 
> Steve Taylor wrote:
>> Hi,
>>> I am happy to announce that BASE 2.0 RC 2 is now available for download:
>>> http://lev.thep.lu.se/trac/base/wiki/DownloadPage
>>>
>>> Installation instructions are available at the BASE2 home page:
>>> http://lev.thep.lu.se/trac/base/wiki
>> It's good to see BASE2 is progressing! I notice Affy support is not in this 
>> in this RC. Is there a set of requirements that details what we can expect 
>> when this feature is implemented?
>>
>> I am still unsure about if there is support for Affy in BASE1. I seem to 
>> remember reading you can upload Affy data into BASE1 although functionality 
>> is limited. Assuming this is possible... has anyone 
>> got any experience in this and can point me to some documentation? Will the 
>> migration tools migrate such data over if we were to proceed uploading to 
>> BASE1? Or is it best to hold off a while longer 
>> and wait for BASE2?
>>
>> Thanks for any info,
>>
>> Steve
>>
>>
>> ___
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>> basedb-users@lists.sourceforge.net
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>> [EMAIL PROTECTED]
> 

-- 
Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se


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Re: [base] BASE 2.0 RC2 released

[Jari Häkkinen]

Yesterday, I checked in a compilation of discussions regarding 
Affymetrix in BASE 2.0, 
http://lev.thep.lu.se/trac/base/browser/trunk/doc/affymetrix.txt, to the 
subversion repository. The development of the Affy support follows the 
plan outlined in this document. If you have any thoughts you'd line to 
share with us, please use the mailing lists or add comments through 
http://lev.thep.lu.se/trac/base/ticket/150


Cheers,

Jari

Jari Häkkinen wrote:
> Hi,
> 
> We missed out on Affy support but it will appear very soon. Sorry about 
> the slight delay. There is a requirement spec that I'll post later today.
> 
> Affymetrix in BASE1 has been done but I am not able to give any details 
> about this. The migration from BASE 1 to 2 assumes a pristine 1.2.late 
> version of the "official" database schema. This means that BASE1 Affy 
> supporters need to modify the migration program to transfer data to BASE 2.
> 
> I think you should wait somewhat longer for Affy support in BASE2.
> 
> 
> Cheers,
> 
> Jari
> 
> 
> Steve Taylor wrote:
>> Hi,
>>> I am happy to announce that BASE 2.0 RC 2 is now available for download:
>>> http://lev.thep.lu.se/trac/base/wiki/DownloadPage
>>>
>>> Installation instructions are available at the BASE2 home page:
>>> http://lev.thep.lu.se/trac/base/wiki
>> It's good to see BASE2 is progressing! I notice Affy support is not in this 
>> in this RC. Is there a set of requirements that details what we can expect 
>> when this feature is implemented?
>>
>> I am still unsure about if there is support for Affy in BASE1. I seem to 
>> remember reading you can upload Affy data into BASE1 although functionality 
>> is limited. Assuming this is possible... has anyone 
>> got any experience in this and can point me to some documentation? Will the 
>> migration tools migrate such data over if we were to proceed uploading to 
>> BASE1? Or is it best to hold off a while longer 
>> and wait for BASE2?
>>
>> Thanks for any info,
>>
>> Steve
>>
>>
>> ___
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>> basedb-users@lists.sourceforge.net
>> unsubscribe: send a mail with subject "unsubscribe" to
>> [EMAIL PROTECTED]
> 

-- 
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se



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[base] BASE2 and affymetrix

[Jari Häkkinen]

Yesterday, I checked in a compilation of discussions regarding 
Affymetrix in BASE 2.0, 
http://lev.thep.lu.se/trac/base/browser/trunk/doc/affymetrix.txt, to the 
subversion repository. The development of the Affy support follows the 
plan outlined in this document. If you have any thoughts you'd line to 
share with us, please use the mailing lists or add comments through 
http://lev.thep.lu.se/trac/base/ticket/150


Cheers,

Jari

-- 
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se



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Re: [base] bits and pieces...

[Jari Häkkinen]

Hi,

1) Charles and Kjell is working on MAGE-ML export for BASE 1.2.x, this 
is the only major development planned for BASE here in Lund. Charles and 
Kjell are dedicated on getting MAGE into 1.2.x so I assume the problems 
will be resolved. Here in Lund, Carl is the only developer involved in 
1.2.x, and will be fixing serious issues in 1.2.x after 2.0 release.

2) Someone else on this one?

3) We have no plans for BlueFuse data today, but if there is a demand to 
support BlueFuse data, it may become supported. Even better, we can help 
you get going if you would like to help the BASE community with BlueFuse 
data support.

4) Probably, but it is not in any of our target milestones. Our plan is 
to support most of the plug-ins available for 1.2.x also in BASE2.

5) Yes, I'll send you account details in another mail.


Jari


mark alston (IFR) wrote:
> Hi,
> 
> Various questions:
> 
> 1) Will you continue to develop BASE 1.2.X once BASE 2.0 is fully 
> functional? Or at least until the MAGE-ML export issue is sorted out?
> 
> 2) I have modified the database to handle BlueFuse data. I understand 
> that I WON’T be able to migrate my mongrel db to BASE2, but can I still 
> migrate it from 1.2.15 to say 1.2.17?
> 
> 3) I presume I can modify BASE2 to handle BlueFuse data, but are there 
> plans to include this functionality?
> 
> 4) Will I be able to connect BASE2 to GeneSpring as per 1.2.X?
> 
> 5) Can I have a username and password for the BASE2 demo site.
> 
> Regards,
> 
> Mark
> 
> **
> 
> Dr Mark Alston,
> 
> Computational Biologist,
> 
> Institute of Food Research,
> 
> Norwich Research Park, Colney,
> 
> Norwich NR4 7UA, UK.
> 
> Tel  +44 (0)1603 251432
> 
> e-mail  [EMAIL PROTECTED]
> 
> e-disclaimer at ___http://www.ifr.ac.uk/edisclaimer/_  
> 
> ___www.ifr.ac.uk_ <http://www.ifr.ac.uk>
> 
> ___www.foodandhealthnetwork.com_ <http://www.foodandhealthnetwork.com>
> 
> ** 
> 
> 
> 
> 
> ___
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
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Re: [base] BASE vs others

[Jari Häkkinen]

Hi,

here is answers from a BASE2 perspective.


David Waring wrote:
> I am looking for a database solution for the microarray facility at  
> Fred Hutchinson Cancer Center. We are a core facility with dozens of  
> users from labs around the Center and outside. I am looking carefully  
> at BASE, TM4, Longhorn, and maxdLoad2. I have a few questions about  
> BASE that would help me make this decision. Any feedback would be  
> very much appreciated.
> 
> Is BASE support for PostgreSQL as strong as support for MySQL?

In BASE2, we use Hibernate on top of the database layer. The simple 
answer is then that the database support depends on how well Hibernate 
support the different database flavours. We develop BASE 2 with MySQL as 
the database backend but do tests with PostgreSQL (and some others). 
There is one known issue with BASE2/PostgreSQL/Hibernate that awaits 
resolution from the Hibernate team.


> Can I get a detailed version of the schema? All I can find is a  
> general schema overview with tables listed but no  fields. The html  
> version of the schema description http:// 
> opensource.microarray.omrf.org/wiki/bin/view/BASE/DatabaseSchema is  
> apparently cut off or just was never finished.

This page may be out of date. For BASE 1.2.x refer to 
http://base.thep.lu.se/documentation.phtml

For BASE2 there is a lot of developer information, but no complete 
schema. Implementation details are given for most details of BASE2. See 
http://lev.thep.lu.se/trac/base/wiki/DeveloperInformation for more 
information.


> Are there tools for batch upload of data?  Particularly, I am looking  
> at the situation where our users have designed an experiment, and  
> hybridizations, we (the core lab) will perform the hybridization,  
> scan the array, run a spot analysis (GenPix) upload the data  
> (hopefully not using a web based interface one image at a time). We  
> will then perform standard normalizations / filters and need to get  
> all this into the database so that our users can analyze the data  
> later. I this a situation that BASE would be strong at?

For BASE 1.2.x there is a mass data import feature. For BASE2 the core 
supports batch upload of data but there is no UI for it yet.


> When will BASE 2.0 be ready for production?

The milestone for production ready BASE 2.0 is in the end of August, see
http://lev.thep.lu.se/trac/base/roadmap


> How many labs are currently using BASE?

Our estimate is that more than 100 labs use BASE 1.2.x, and there is 
already a handful users of BASE2.


> If you have any ideas about how the various alternatives stack up  
> please let me know. Be as technical as needed, I am an experienced  
> programmer and with lots of database experience.

I would go for BASE2, but then again, I am somewhat biased.


> Is there support for HUGE datasets like Tiling arrays? In these cases  
> we would not necessarily want to hold all of the results as  
> individual records but rather would want to hold the .cel files in  
> some structure so that our users could get to them for analysis using  
> other tools.

BASE 2.0 is supporting Affymetrix soon, so in principle Tiling arrays 
are possible. The "raw" data for Affy will be the .cel files, i.e. these 
will be used in subsequent analysis.


> Thanks
> 
> David

Thank you for you interest in BASE.


Jari



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Re: [base] Base2 upgrade

[Jari Häkkinen]

An upgrade in the sense of the installation document 
(http://base.thep.lu.se/chrome/site/doc/installation.html) is that a 
newer BASE 2.0 release is replacing an earlier BASE 2.0 release on a 
running server. This is NOT an upgrade of a BASE 1.2.x server to BASE 2.0.

When upgrading a live BASE 2.0 server with a newer release there is a 
known issue with PostgreSQL/Hibernate/BASE2.0. This issue makes upgrades 
between BASE 2.0 releases potentially unsafe. The problem is reported to 
the Hibernate developer team, and hopefully the issue will be resolved soon.

To perform a shift from BASE 1.2.x to BASE 2.0, a first time install of 
BASE 2.0 has to be performed, followed by an optional migration of data 
from BASE 1.2.17 to BASE 2.0.


Jari


David Waring wrote:
> In reading through the installation instructions I found the section  
> on performing the
> Upgrade of running BASE 2 installation
> 
> it says that this is not safe for PostgreSQL. What is the upgrade? Is  
> this necessary, and is it necessary if you are doing a brand new  
> installation?
> 
> David
> 
> 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se


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Re: [base] Plugin import: Configuration and use it

[Jari Häkkinen]

Sorry for the sluggish response time from the BASE team but we are all 
having vacation. We'll be back in full speed on August 7.

To your problem:

Change 'Reporter IDID' to 'Reporter ID\ID\'


Jari



Pablo Lemos Ochandio wrote:
> Hi David!!
> 
> Thanks again for the plugin, at this moment I am trying to import some data to
> BASE2 to understand how it works and later implement some plugins that I need.
> Your attach helps me at this point but now i need to upload these data (.gal
> and .gpr) to BASE2. The first error is fixed (a version problem). Now base2
> recognize my .gal file but returns me an error:
> 
> Error: Import failed on line 12: Item not found:
> Reporter[externalId=ID]
> 
> my plugin configuration is:
> 
> reporter map importer
> 
> Block  \Block\
> Column\Column\
> Data footer   
> Data header   Block\tColumn\tRow\tID\tName\tPCRcode\tDescription
> Data splitter \t
> HeaderATF\t1
> Ignore
> Max data columns  
> Meta grid X   
> Meta grid Y   
> Min data columns  
> Reporter ID   ID
> Row   \Row\
> Remove quotes false
> 
> 
> I see no place to indicate which is my ExternalID, although I can see this is
> a value that is expected from a reporter. I guess I am mixing up or forgetting
> things. May be you can help me out here.
> 
> Thanks a lot!!
> 
> 
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-- 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se


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Re: [base] Users Manual for BASE 2?

[Jari Häkkinen]

Hi,

The user manual for BASE 2 will become available during the fall. The 
manual will most probably be based on the BASE 1.2 user guide available 
from http://base1.thep.lu.se/documentation.phtml

Until a BASE 2 specific manual is ready you will have to resort to the 
old manual. The 1.2 manual is not optimal for BASE 2 but is usable to 
get going with 2.0 since most of the BASE 1.2 functionality is available 
in 2.0. Of course the look of the GUI has changed.

You can also use this mailing list for questions.


Jari


Jenny Drnevich wrote:
> Hello,
> 
> Any idea when the User's Manual for BASE 2 will be available? We're looking 
> for a microarray DB system, and I've gotten a trial account on the BASE 2 
> demo server, but it's hard to figure out how to get started on your own.
> 
> Thanks,
> Jenny
> 
> Jenny Drnevich, Ph.D.
> 
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
> 
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
> 
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: [EMAIL PROTECTED] 
> 
> 
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-- 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se


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Re: [base] demo server updates and presets Q's

[Jari Häkkinen]

Comments on the demo server only:

The current policy for the BASE 2 demo server updates is to update when 
a new release is made. The latest update was done last week October 18 
when 2.0.2 was made available for download. In cases when very important 
fixes are made we will probably update the server sooner (but also 
probably issue a new release at the same time).

Would you like to see this policy changed?


Cheers,

Jari


Lepp, Dion wrote:
> Hi all,
> 
>  
> 
> I was wondering how often the base2 demo server is updated ie. are the 
> changes shown in the Trac timeline reflected in the server immediately?
> 
>  
> 
> Secondly, I am having trouble understanding the “in current project” 
> preset, and the entire “active project” system for that matter.  What I 
> would expect is that when samples, hybs etc. are added, they will 
> automatically be associated with the active project.  If “In current 
> project” is then selected in the presets, only those samples, hybs, etc. 
> associated with the active will be displayed.  In my hands, setting the 
> active project or the “in current project” preset has no effect.  Could 
> someone please shed some light on this?
> 
>  
> 
> Thanks,
> 
>  
> 
> Dion
> 
>  
> 
> 
> Dion Lepp, M.Sc.
> Guelph Molecular Biology Research Unit
> Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada
> Telephone/Téléphone: 519-780-8090
> Facsimile/Télécopieur: 519-824-2600
> 93 Stone Road
> Guelph, Ontario
> N1H 2J8
> [EMAIL PROTECTED] 
> 
> 
> 
> 
> 
>  
> 
> Agriculture and Agri-Food Canada - Agriculture et Agroalimentaire Canada
> 
>  
> 
>  
> 
> 
> 
> 
> -
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> 
> 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
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[base] Changing CDF/CEL association (follow up posting)

[Jari Häkkinen]

If a CEL file is accidentally associated with an erroneous CDF file the 
association can be changed by selecting the problematic raw bioassay. 
Choose 'Edit...' from the properties tab and select '- none -' in the 
pull-down field for 'CEL file'. Click 'Save', redo edit, select a CEL 
file and make the proper association.

A mismatch between CDFs and CELs can be safeguarded against but this is 
currently an unresolved issue (http://base.thep.lu.se/ticket/372) in BASE.


Jari

-- 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se

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[base] BASE 2.1 released

[Jari Häkkinen]

Hello all,

The Lund BASE team is happy to announce that BASE 2.1 is now available 
for download: http://base.thep.lu.se/wiki/DownloadPage

Installation instructions and other documentation are available at the 
BASE 2 home page: http://base.thep.lu.se/

There are many improvements to BASE. The list of fixed issues and 
features can be browsed at 
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.1


The Lund BASE team.

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Re: [base] What plugins are part of the core installation of Base 2

[Jari Häkkinen]

Hi,

Plug-ins that comes with the core install are listed below. Many of the 
core plug-ins in BASE 2 are supporting core functionality such as 
imports and exports whereas some other are analysis plug-ins.

There is one external (that is, non-core) plug-in available at 
http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress for 
normalization of Affymetrix experiments.


Cheers,

Jari


The list of all 22 available core plug-ins in BASE 2.1 with a short 
description. I'll add them to http://base.thep.lu.se

* Base1PluginExecuter - This plug-in simulates the plug-in runner from 
Base 1.2 to enable old plug-ins to be executed.

* Bioassay set file exporter - Supported formats:
+ Tab Delimited, Multiple Sample Files (TDMS Format) for use in MeV 
(available from http://www.tm4.org).
+ BASE 1.2.17 BASEFile format export will be delivered in 2.1.1 shortly.

* Formula intensity calculator - Calculate intensities from raw data 
creating an initial root bioassay set. The intensities are calculated 
using Formula objects registered for the experiment's raw data type. 
Thus, the functionality of this plugin can be extended by adding more 
formula objects to the database.

* Help texts exporter - Exports a client applications help texts to a 
XML-file. The help tests can later be imported by the corresponding 
import plug-in.

* Help texts importer - Import of help texts from a XML-file to BASE.

* JEP extra value calculator - Calculates extra values for a bioassay 
set using expressions entered by the user.

* JEP filter plugin - Filtering of one bioassay set, creating a new 
bioassay set with fewer spots in it. The filter is based on expressions 
entered by the user. The functionality of this plugin is very flexible.

* JEP intensity transformer - Transforms the intensities of a 
bioassayset using expressions entered by the user.

* Normalization: Lowess - This is an efficient java implementation by 
Johan Enell of the LOWESS algorithm. It provides intensity-based 
normalization. The window size is the only smoothness parameter 
available in this implementation. The higher it is, the smoother the 
function will be. Tweaking the other two parameters allows you to gain 
performance at the price of a small precision loss. The default values 
are usually good. For more info on LOWESS: Cleveland WS, Devlin SJ: 
Locally weighted regression: an approach to regression analysis by local 
fitting. J Am Stat Assoc 1988, 83:596-610. Yang YH, Dudoit S, Luu P, Lin 
DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a 
robust composite method addressing single and multiple slide systematic 
variation. Nucleic Acids Res 2002, 30:e15.

* Normalization: Median ratio - This normalizer scales the intensities 
in such a way that their geometric mean (sqrt(i1 * i2)) is kept constant 
but the median of their ratios (i1/i2) is shifted to 1. The normalizer 
lets you exclude a percentage of the highest and lowest intensities as 
well as all spots with at least one intensity below a fixed value.

* Plate importer - Import of plates from a simple flat file.

* Plate mapping exporter - Export of plate mappings, which maps the 
coordinates of one or more source plates to coordinates on one or more 
destination plates.

* Plate mapping importer - Import of plate mappings, which maps the 
coordinates of one or more source plates to coordinates on one or more 
destination plates.

* Plugin configuration importer - Export of plug-in configurations to an 
XML-file. The plugin configurations can later be imported by the 
corresponding import plug-in.

* Plugin configuration exporter - Import of configuration for a BASE 
plugin from an XML-file.

* Print map importer - Import of array design from a print map file.

* Raw data importer - Import of raw data from a simple text file.

* Reporter importer - Import of reporters from a simple flat file.

* Reporter map importer - Import features to an ArrayDesign from a 
simple flat file.

* Simple export - Export all lists (in the GUI) as tab-separated text 
files or as XML.

* Spot images creator - Converts a full-size scanned image into smaller 
preview jpg images for each individual spot.

* ZIP file unpacker - Plug-in to unpacks a zip file on the BASE file 
system. Useful for upload of many files at once. Supports zip and jar files.


Paddy Tighe wrote:
> Hi,
> Am currently running base 1.2.17, looking at installing Base 2.0 – what 
> plugins are part of the core install  - I can’t seem to find this listed 
> on the Base site?
> 
> Regards
> 
> Paddy
> 
> This message has been checked for viruses but the contents of an 
> attachment may still contain software viruses, which could damage your 
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> permitted by UK legislation.
> 
> 
> 
> 
> 

Re: [base] 2 questions about Plugin configuration

[Jari Häkkinen]

Nicklas Nordborg wrote:
> Emmanuel Courcelle wrote:
>> Hello
>> Now using Base 2.1...
>>
>> I am trying to configure the "Raw Data importer " plugin, to upload and 
>> parse
>> genepix-type files.
>>
>> 1/ Pb configuring this plugin
>> --
>>
>> I click Plugin/Configuration/New
>> -configuration name: bla bla
>> -Raw DataType: Genepix
>> -Next
>> -Test with file/Select some uploaded file/Parse the file
>>
>> Then I get an error: "Start of data couldn't be found. Please try again 
>> with different settings."
>> In the window with the data file, I search the line marked Block Column 
>> Raw a.s.o., (it is the nb 30 for me),
>> I have a box marked 'Unknown': I choose in the list "Data header", I 
>> click and this fills up the field Data header regexp
>>
>> I then click again on "Parse the File", this produces THE SAME error: I 
>> tried with some other (simpler) regular expressions, same behaviour:
>> am I doing anything wrong ?
> 
> I don't think so. It seems strange that it can't find the data the 
> second time you click on "Parse the file" button. I really don't know 
> why that is happening. Most of our test data files are Genepix files 
> and we have not had any problems with them. I am thinking that maybe 
> something gets trunkated or there is a problem with different types of 
> linebreaks. Can you send me a few lines from a file with this problem? 
> If should be enough with one line of data. If your headers have 
> sensitive information please remove them as well.

I noticed a similar problem as Emmanuel. I choose a "data header" line 
and tried to parse the file. It did not work so I only used the first 
part of the regexp created by the wizzard. This solved the problem for 
me and the wizzard could parse the file. I'll try to see if I can 
reproduce this problem and report back later.

Cheers,

Jari


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Re: [base] how to import reporters ?

[Jari Häkkinen]

The reporter import button does appear because there is no plug-in 
configured for import of reporters. You need to create a configuration 
for the "Reporter importer" plug-in. We have compiled a getting started 
document that outlines the first steps with BASE 2, 
http://base.thep.lu.se/chrome/site/doc/user/getting_started.html


Jari

Emmanuel Courcelle wrote:
>> As I wrote in the previous mail:
>>The columns are numbered from 0 so the
>>file we have been testing on the "Rgn R²" column should be column
>>number 32 and the mapping to use \32\.
>>
>> I counted twice, but of course you should check that it is correct.
>>
>>   
> Sorry, you're right
>> You have to import reporters before you can import raw data. The error 
>> message means that there is no reporter with external ID=SMa1894 in the 
>> database.
>>   
> 
> OK
> Sorry for the probably stupid question, but how do I import reporters ?
> I tried the Reporters screen, but I found only buttons labelled New 
> Delete New reporterl list Export, there is no import button...
> 



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[base] Browser compatibility

[Jari Häkkinen]

Hi all,

We have previously decided to only support Firefox and Internet Explorer 
due to lack of resources. If someone is prepared to perform Safari 
testing we could add reasonable fixes into BASE to resolve Safari issues.

Is there someone out there who is willing to become a Safari/BASE tester.


The list of BASE team supported browsers is short:

Firefox production releases 2 or later.
Internet Explorer 7 or later.


Jari

-- 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se


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Re: [base] long term future and support for BASE2

[Jari Häkkinen]

Hi,

This is a fair question. We are four people involved in the BASE project 
as programmer in more or lesser degree (Nicklas and Martin are full time 
employed to work on BASE). We also have a close collaboration with the 
Oncology Department here in Lund and they also put effort in BASE (1 and 
2) progress.

The software part of BASE crew is funded until the end of 2009. BASE is 
an essential part of the core service at the microarray facility here at 
Lund University so we expect to be supporting BASE at least during this 
time. What happens beyond 2010 depends on so many things...

So, jump on to BASE and help us make the software better.


Cheers,

Jari


Micha Bayer wrote:
> Hi,
> 
> This is a non-technical question, for a change.
> 
> We are about to make a fairly long-term commitment to BASE as our
> microarray platform and were wondering what the future looks like for
> BASE, in terms of support and funding (we're talking the next few years
> rather than months here). 
> 
> This is obviously an issue with all open source projects, and I 'm sure
> BASE is no exception. I guess many other users may be in the same boat
> -- no-one wants the support for their system to suddenly dry up, and
> then to have to migrate their data to something else.
> 
> It would be good if someone could shed some light on this. 
> 
> Thanks
> 
> Micha
> 
> ==
> Dr Micha M Bayer
> Bioinformatics Specialist
> Genetics Programme
> The Scottish Crop Research Institute
> Invergowrie
> Dundee
> DD2 5DA
> Scotland, UK
> Telephone +44(0)1382 562731 ext. 2309
> Fax +44(0)1382 562426
> http://www.scri.sari.ac.uk/MichaBayer.htm
> =
>  
> 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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> DISCLAIMER:
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Re: [base] bioassays inheriting sample annotations in BASE 2

[Jari Häkkinen]

We have added this as a ticket, http://base.thep.lu.se/ticket/449. The 
migration program will perform the inheritance automatically. Thank for 
pointing this out.


Jari


Bob MacCallum wrote:
> Now I have data imported from BASE 1.2, I find that the sample annotations are
> not available in the bioassays or bioassaysets unless I go in and edit each
> bioassay and tell it to inherit the annotations from the samples.
> 
> Ideally I would like the migration script to do this for me, or to be able to
> edit all the bioassays in one go using the GUI.
> 
> Does anyone have any experience with this?  Are there some docs on this I
> didn't read?  The default behaviour in BASE 1 (to propagate the sample
> annotations through to the bioassays) seemed sensible to me.
> 
> cheers,
> Bob.
> 

-- 
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
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Re: [base] Offline files

[Jari Häkkinen]

The zip up-loader is meant to be used for uploading bulks of files, and 
is working well. For retrieving files from the server there is no batch 
support.


Jari


Bob MacCallum wrote:
> 
> Nicklas Nordborg writes:
>  > Giovanni Coppola wrote:
>  > > Hi everybody,
>  > > I have two questions:
>  > > 1) is there a way to download images or raw data files in batches?
>  > 
>  > No.
> 
> yes but there is a zip file unpacker (in BASE 2)
> 
> I haven't used it, but doesn't this cut down on the GUI clicking if you want
> to upload a lot of files?
> 
> At some point, someone will come up with a bulk loader which will
> batch/bulk/mass upload files *and* create/annotate/link the data objects (I'm
> not volunteering, yet...)
> 
>  > 
>  > > 2) while I was trying that (to download more than one file at once),  
>  > > in the 'Files and Directories' tree, I accidentally moved Offline  
>  > > some files, and now I don't seem able to download them anymore. Is  
>  > > there a way to restore them in the Primary position?
>  > 
>  > They have been deleted from the server. You have to upload them again.
>  > 
>  > /Nicklas
>  > 
>  > 
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Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
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Re: [base] Offline files

[Jari Häkkinen]

Hi all,

Just a thought, I think the best choice to trigger a large import like 
this is to create a plug-in instead of adding extra tabs to the file 
browser. The plug-in should start by requesting the zip file/directory 
to import. If the zip file is not already uploaded the user will have an 
opportunity to upload it. After choosing the zip file/directory the 
plug-in could start its import and creation of necessary items.

The above is fairly straightforward already today and the new code would 
start at import/creation of necessary items.

This will yield very little (or no) changes to the core and the plug-in 
should probably be started from the experiment listing page. This will 
of course change the experiment list jsp (a import tab is needed).

In my naive view this will only affect a jsp and a new plug-in is needed.


Jari

dominic oyeniran wrote:
>  
> 
> 
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Micha Bayer
> 
> Hi Micha,
> 
> 
>> I have just finished writing one. The user uploads a zip file, a new
> directory is created in the user's raw data directory (with >the same name
> as the zip file) and the files are then unzipped in there. They are then
> imported one by one as new 
>> RawBioAssay objects and at the end a new Experiment is created that has all
> these hanging off it. At the moment it only 
>> works for non-Affy data though. 
> 
> 
>> To do this I had to hack the BASE source (plugin wasn't possible as far as
> I can tell), and I am always reluctant to do that 
>> sort of thing because of versioning/upgrade issues (i.e. having to repeat
> this every time a new version is out). I have 
>> modified >the JSP page that controls the menus and inserted a new item
> there, and added a couple of JSP pages myself that >provide the UI for all
> this. 
> 
>> I did some more detailed testing yesterday and things worked fine but it's
> all still pretty raw and probably full of bugs. I am 
>> happy to share the code with others though, or even make it a full
> contribution to BASE if people are happy with it (perhaps >after it has been
> gone over by some of the BASE team). I also think the exception handling
> needs more work probably. 
> 
> 
> Base 2 has plans to have tab2mage import (importing experiments and
> associated files) see Ticket #338  on base2 trac
> http://base.thep.lu.se/ticket/338 system, and your zip file loader would
> certaily help to in importing experiments from repositories and doing other
> interesting stuff. We have this on our do list and would certainly
> appreciate if you can share the code with us to help in this process.
> 
> Also, do you have plans to extend the functionality to non-affy data too?
> 
> Thanks and hope to read from you.
> 
> Dominic
> 
> 
> 
> 
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-- 
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se


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Re: [base] Offline files

[Jari Häkkinen]

Ah, even better ;-)


Nicklas Nordborg wrote:
> Jari Häkkinen wrote:
>> Hi all,
>>
>> Just a thought, I think the best choice to trigger a large import like 
>> this is to create a plug-in instead of adding extra tabs to the file 
>> browser. The plug-in should start by requesting the zip file/directory 
>> to import. If the zip file is not already uploaded the user will have an 
>> opportunity to upload it. After choosing the zip file/directory the 
>> plug-in could start its import and creation of necessary items.
>>
>> The above is fairly straightforward already today and the new code would 
>> start at import/creation of necessary items.
>>
>> This will yield very little (or no) changes to the core and the plug-in 
>> should probably be started from the experiment listing page. This will 
>> of course change the experiment list jsp (a import tab is needed).
> 
> No change is needed to the jsp. The new plugin will be detected and an 
> "Import" button will appear.
> 
> /Nicklas
> 
> 
> 
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-- 
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se


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Re: [base] Offline files

[Jari Häkkinen]

Micha Bayer wrote:
> Hi Jari,
> 
> That sounds perfectly reasonable when you put it like this, but I was put off 
> going down that route by a post to the list from Nicklas 
> (http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg00228.html)
>  where he says that it is best to not use a plugin to do this because of 
> interface issues (whatever they are).

I think Nicklas was thinking about very interactive plug-ins.

> Personally, I think a plugin would be far better than what I have done -- if 
> I was to persist with my solution I would have to modify the BASE source 
> every time a new version comes out.

Our belief is that basically no modification to BASE is needed if one 
creates a import plug-in that creates all needed items automatically 
(using information from files of course). Trouble starts when 
communication is needed from the user after plug-in start. The plug-in 
system allows for communication just before a plug-in is started (at 
least was design like this, I suppose one can tweak user interaction 
with the plug-in but thats out of this topic).

> I also think that batch import *is* a high priority thing for most users, 
> whether they have a pile of legacy data or not. Most biologists I know would 
> probably rather spend a solid period doing labwork, and then process a whole 
> bunch of experiments in a oner. I also think it is a nonsense to have a human 
> doing boring, repetitive stuff -- computers are there to do that. Why waste 
> your time on something that a for loop can do. So perhaps the dev team should 
> reconsider this. 

I agree, I think it is an important issue as well. However, we think 
that we work on many other important issues already. We are mainly 
working on core stuff and hoping that others contribute with things that 
can be written as plug-ins. You are already doing this, and 
unfortunately you were pushed in the wrong direction.

> I am just talking to my boss about code ownership issues but I can probably 
> offer up my stuff one way or another, and people can then either cannibalise 
> it and turn it into a plugin, or adopt it (or a modified version) into the 
> core etc etc -- happy with any solution that makes others benefit from my 
> blood sweat and tears shed . :-)
> 

Dominic would probably benefit from your code and through him the code 
will probably end up in the BASE repository. Contributions are welcome 
and we consider all of them for inclusion the the BASE code base.


> Cheers
> 
> Micha
> 

Cheers,

Jari


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Re: [base] Offline files

[Jari Häkkinen]

>> here:
>> http://wiki.vectorbase.org/vectorbase/index.php/MicroarrayExperiments
>> (look for the example file links) but note that the BASE-specific
>> parameters
>> (protocols, raw file parsers, array designs, etc) are configured by the
>> user
>> in an interactive process before the upload.  Our bulk loader is also
>> 2-channel only...
>>
>> I have a feeling that the Tab2MAGE parser could be adapted into a BASE 2
>> bulk
>> loader somehow, although I think all Tab2MAGE code is Perl.
>>
>> I think MAGE-TAB is something we could get the average bench scientist to
>> provide (with a little help MGEDifying the annotations).  So far every
>> experiment I have loaded has come with some kind of spreadsheet (each one
>> in a
>> different format of course), so the leap to MAGE-TAB is not so great.
>>
>> Ok, enough from me...
>>
>>
>>
>>
>> Micha Bayer writes:
>>  >
>>  >
>>  > > -Original Message-
>>  > > From: [EMAIL PROTECTED] [mailto:basedb-
>> users-
>>  > > [EMAIL PROTECTED] On Behalf Of Nicklas Nordborg
>>  > > Sent: 29 November 2006 14:40
>>  > > To: BASE ML
>>  > > Subject: Re: [base] Offline files
>>  > >
>>  > > Jari Häkkinen wrote:
>>  > > > Hi all,
>>  > > >
>>  > > > Just a thought, I think the best choice to trigger a large import
>> like
>>  > > > this is to create a plug-in instead of adding extra tabs to the
>> file
>>  > > > browser. The plug-in should start by requesting the zip
>> file/directory
>>  > > > to import. If the zip file is not already uploaded the user will
>> have an
>>  > > > opportunity to upload it. After choosing the zip file/directory the
>>  > > > plug-in could start its import and creation of necessary items.
>>  > > >
>>  > > > The above is fairly straightforward already today and the new code
>> would
>>  > > > start at import/creation of necessary items.
>>  > > >
>>  > > > This will yield very little (or no) changes to the core and the
>> plug-in
>>  > > > should probably be started from the experiment listing page. This
>> will
>>  > > > of course change the experiment list jsp (a import tab is needed).
>>  > >
>>  > > No change is needed to the jsp. The new plugin will be detected and
>> an
>>  > > "Import" button will appear.
>>  > >
>>  > > /Nicklas
>>  >
>>  > So what interface would I have to implement for this to happen, if I
>> were to turn my code into a plugin?
>>  >
>>  > If it's not too much work I might consider doing this, that would be
>> much better.
>>  >
>>  > Cheers
>>  >
>>  > Micha
>>  >
>>  > ==
>>  > Dr Micha M Bayer
>>  > Bioinformatics Specialist
>>  > Genetics Programme
>>  > The Scottish Crop Research Institute
>>  > Invergowrie
>>  > Dundee
>>  > DD2 5DA
>>  > Scotland, UK
>>  > Telephone +44(0)1382 562731 ext. 2309
>>  > Fax +44(0)1382 562426
>>  > http://www.scri.sari.ac.uk/MichaBayer.htm
>>  > =
>>  >
>>  >
>>  >
>>  > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>> _ _
>>  >
>>  > DISCLAIMER:
>>  >
>>  > This email is from the Scottish Crop Research Institute, but the views
>>  > expressed by the sender are not necessarily the views of SCRI and its
>>  > subsidiaries.  This email and any files transmitted with it are
>> confidential
>>  > to the intended recipient at the e-mail address to which it has been
>>  > addressed.  It may not be disclosed or used by any other than that
>> addressee.
>>  > If you are not the intended recipient you are requested to preserve
>> this
>>  > confidentiality and you must not use, disclose, copy, print or rely on
>> this
>>  > e-mail in any way. Please notify [EMAIL PROTECTED] quoting the
>>  > name of the sender and delete the email from your system.
>>  >
>>  > Although SCRI has taken reasonable precautions to ensure no viruses are
>>  > present in this email, neither the Institute nor the sender accepts any
>>  > responsibility for any viruses, and it is your responsibility to scan
>>

Re: [base] Offline files

[Jari Häkkinen]

der.  For example, I would like all objects created and
>  > > linked,
>  > > from samples (with annotations) right up to raw bioassays (grouped into 
> an
>  > > experiment as Micha does, ideally).  Obviously to do this you need to
>  > > specify
>  > > the relationships between all the samples, annotations, dyes, hybs, data
>  > > files, but that could easily end up being as much work as manually 
> loading
>  > > the
>  > > data ;-)
>  > > 
>  > > Therefore you have to make compromises; the main one being that you treat
>  > > every sample/extract/etc in exactly the same way (same protocols, same
>  > > amounts, same labels, same array design).  This would probably work for
>  > > most
>  > > people - but let's discuss it anyway...
>  > > 
>  > > One issue with the bulk loader I wrote for BASE 1 is that if your
>  > > experiment
>  > > involves a dye swap for one biological replicate, the bulk loader will
>  > > label
>  > > each extract with both dyes for *all* replicates (leaving you with unused
>  > > labelled extracts after linking to the hybs).
>  > > 
>  > > One quite low cost way to define your experiment for a bulk loader is
>  > > Tab2MAGE
>  > > (soon to be MAGE-TAB, see
>  > > http://www.biomedcentral.com/1471-2105/7/489/abstract ) - although it
>  > > feels
>  > > strange to say this because I have been *exporting* Tab2MAGE from BASE 
> 1.2
>  > > rather than importing it.  The input files for our bulk loader are
>  > > specified
>  > > here:
>  > > http://wiki.vectorbase.org/vectorbase/index.php/MicroarrayExperiments
>  > > (look for the example file links) but note that the BASE-specific
>  > > parameters
>  > > (protocols, raw file parsers, array designs, etc) are configured by the
>  > > user
>  > > in an interactive process before the upload.  Our bulk loader is also
>  > > 2-channel only...
>  > > 
>  > > I have a feeling that the Tab2MAGE parser could be adapted into a BASE 2
>  > > bulk
>  > > loader somehow, although I think all Tab2MAGE code is Perl.
>  > > 
>  > > I think MAGE-TAB is something we could get the average bench scientist to
>  > > provide (with a little help MGEDifying the annotations).  So far every
>  > > experiment I have loaded has come with some kind of spreadsheet (each one
>  > > in a
>  > > different format of course), so the leap to MAGE-TAB is not so great.
>  > > 
>  > > Ok, enough from me...
>  > > 
>  > > 
>  > > 
>  > > 
>  > > Micha Bayer writes:
>  > >  >
>  > >  >
>  > >  > > -Original Message-
>  > >  > > From: [EMAIL PROTECTED] [mailto:basedb-
>  > > users-
>  > >  > > [EMAIL PROTECTED] On Behalf Of Nicklas Nordborg
>  > >  > > Sent: 29 November 2006 14:40
>  > >  > > To: BASE ML
>  > >  > > Subject: Re: [base] Offline files
>  > >  > >
>  > >  > > Jari Häkkinen wrote:
>  > >  > > > Hi all,
>  > >  > > >
>  > >  > > > Just a thought, I think the best choice to trigger a large import
>  > > like
>  > >  > > > this is to create a plug-in instead of adding extra tabs to the
>  > > file
>  > >  > > > browser. The plug-in should start by requesting the zip
>  > > file/directory
>  > >  > > > to import. If the zip file is not already uploaded the user will
>  > > have an
>  > >  > > > opportunity to upload it. After choosing the zip file/directory 
> the
>  > >  > > > plug-in could start its import and creation of necessary items.
>  > >  > > >
>  > >  > > > The above is fairly straightforward already today and the new code
>  > > would
>  > >  > > > start at import/creation of necessary items.
>  > >  > > >
>  > >  > > > This will yield very little (or no) changes to the core and the
>  > > plug-in
>  > >  > > > should probably be started from the experiment listing page. This
>  > > will
>  > >  > > > of course change the experiment list jsp (a import tab is needed).
>  > >  > >
>  > >  > > No change is needed to the jsp. The new plugin will be detected and
>  > > an
>  > >  > > "Import" button wil

Re: [base] Offline files

[Jari Häkkinen]

Yes, there is a problem with spammers of trac environments. We have 
changed the ticket reporting system to require authentication (details 
on the baseplugins wiki). For BASE and Proteios this has fixed the 
problem of ticket spam (at least for now), so hopefully the ticketing 
system will stay clean.


Jari


Micha Bayer wrote:
>> -Original Message-
>> From: [EMAIL PROTECTED] [mailto:basedb-users-
>> [EMAIL PROTECTED] On Behalf Of Jari Häkkinen
>> Sent: 30 November 2006 15:42
>> To: BASE ML
>> Subject: Re: [base] Offline files
>>
>> There is a possibility to get access to the subversion repository and
>> trac environment just for this kind of stuff. Check out
>> http://baseplugins.thep.lu.se Trac environment allows for discussions
>> about the importer through the ticketing system.
> 
> I just looked at the ticketing system on the plugins page and it looks like 
> it's been majorly vandalized by spammers. Is this email based?
> 
> Someone might want to take a look at this.
> 
> Cheers
> 
> Micha
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> 
> DISCLAIMER:
> 
> This email is from the Scottish Crop Research Institute, but the views 
> expressed by the sender are not necessarily the views of SCRI and its 
> subsidiaries.  This email and any files transmitted with it are confidential 
> to the intended recipient at the e-mail address to which it has been 
> addressed.  It may not be disclosed or used by any other than that addressee.
> If you are not the intended recipient you are requested to preserve this 
> confidentiality and you must not use, disclose, copy, print or rely on this 
> e-mail in any way. Please notify [EMAIL PROTECTED] quoting the 
> name of the sender and delete the email from your system.
> 
> Although SCRI has taken reasonable precautions to ensure no viruses are 
> present in this email, neither the Institute nor the sender accepts any 
> responsibility for any viruses, and it is your responsibility to scan the 
> email 
> and the attachments (if any).
> 
> 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se


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[base] BASE 2.1.1 released

[Jari Häkkinen]

A new minor release is available for download at 
http://base.thep.lu.se/wiki/DownloadPage

A list of fixed item is available here 
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.1.1&order=id


Jari

-- 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se


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Re: [base] Delay before starting plugin

[Jari Häkkinen]

Hi,

In base.config, change the line

jobqueue.internal.checkinterval  = 30

30 is the polling time in seconds.


Jari


Emmanuel Courcelle wrote:
> Hello
> When I click to start a plugin, the system waits a certain amount of 
> time (tipycally 1 mn).
> Why is there such a delay ? Is it possible to shorten it ?
> 
> Please note the machine is not particularly loaded, I am alone (for now) 
> working with Base.
> 


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Re: [base] walk thru

[Jari Häkkinen]

Hi,

There is a getting started document available at
http://base.thep.lu.se/chrome/site/doc/user/index.html


Jari


Gabe Dagani wrote:
> Greetings,
> 
>Has anyone created a simple walkthru for setting up a simple experiment,
> uploading GPR, GPS, TIFF files into a project and doing some analysis?
> 
> I am just a beginner and the manual is outdated for base 2.0.
> 
>thanks - Gabe
> 

-- 
Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se

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Re: [base] Add new plates

[Jari Häkkinen]

A list of all core plug-ins with sample configuration files (also for 
plate importer) is available at 
http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html


Jari

Nicklas Nordborg wrote:
> Audrey Bihouee wrote:
>> Hi everybody,
>>
>> A little question in BASE 2 : I'm very suprised because I can't find 
>> anywhere where you can add a new plate "de novo".
>> In the plate page, only "Merge" is available. But how could you merge 
>> plates if you don't have any plates at all  ?
>> In the plate type page, I can add a new plate type but I can't add 
>> associated plates.
> 
> You have to use the "Import" function to import plates. You will need a 
> file that contains the reporter ID for each well coordinate. The file 
> may contain multiple plates. For an example see the test file that we use:
> http://base.thep.lu.se/browser/trunk/src/test/data/test.plate96.import.txt?format=raw
> 
> If you don't have an "Import" button on the Array LIMS->Plates page you 
> must first define a file format(=plugin configuration) from the 
> Administrate -> Plugins -> Configurations page.
> 
> See the "Getting started" documentation 
> (http://base.thep.lu.se/chrome/site/doc/user/getting_started.html) for 
> more information about how to create plugin configurations.
> 
> /Nicklas
> 
> 
>> Thanks for help.
>> Audrey
>>
> 
> 
> -
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
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[base] BASE 2.2 released.

[Jari Häkkinen]

Hi all,

We are happy to announce the release of BASE 2.2. You can download BASE 
from http://base.thep.lu.se/wiki/DownloadPage

This release contains many new feature and fixes. A list of fixed and 
added features in 2.2 is found by clicking on this beast: 
http://base.thep.lu.se/query?status=new&status=assigned&status=reopened&status=closed&milestone=BASE+2.2&order=id


Enjoy,

The Lund BASE Team


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Re: [base] Database schema limbo--schema version=28

[Jari Häkkinen]

I have successfully upgraded from 2.1.2 to 2.2. This is of course not 
exactly the same upgrade as Chris.


Jari


Nicklas Nordborg wrote:
> Chris Wiita wrote:
>> I attempted a update to Base2.2 from a 2.1.1 installation.  Executing 
>> updatedb.sh worked until the "Updating database" step:
> 
> I really don't know why this is happening. The error message says 
> something about "Discriminator: 0" but we never use a 0, only the values 
> 1, 2, 3 and 4, which have the following meaning:
> 
>   1 = Biosource
>   2 = Sample
>   3 = Extract
>   4 = Labeled extract
> 
> Can you check the "BioMaterials" table and check if any row have a value 
> in the "discriminator" column that is not in the 1-4 range?
> 
> If there are such values they must be changed to one of the above. Then 
> we have to ask the question how they got there in the first place.
> 
> If there are only 1-4 the error message complaining about 
> "Discriminator: 0" is a bit confusing and is something that we need to 
> investigate further to see if we can reproduce the error.
> 
> Another option is to manually change the schema version to 29, but then 
> you will not get the changes between 28 and 29. Luckily, this change 
> doesn't involve any changes to the database. It only recalculates the 
> remaining quantity of all biomaterials since a bug may have caused them 
> to be incorrect. See ticket #466: http://base.thep.lu.se/ticket/466
> 
> I don't think it was a good idea to run the update script from an 
> earlier version. I really don't know if that might have messed things up 
> more or not. I'll add a ticket to make sure that the update script 
> checks the schema version and doesn't execute if it is too high. In any 
> case it is good that the main program does the check and refuses to 
> start since it can lead to incorrect data beeing inserted into the 
> database.
> 
> It is not possible to revert back to an earlier version. You can only do 
> this if you have made a backup of the database.
> 
> /Nicklas
> 
>> --
>> [75%]   Updating database...
>> [87%]   --Updating schema version: 28 -> 29...12:06:13,579 ERROR 
>> Update:1150 - updateToSchemaVersion29: FAILED
>> net.sf.basedb.core.BaseException: Object with id: 1 was not of the 
>> specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData 
>> (Discriminator: 0)
>> at 
>> net.sf.basedb.core.HibernateUtil.loadList(HibernateUtil.java:1355)
>> at 
>> net.sf.basedb.core.Update.updateToSchemaVersion29(Update.java:1105)
>> at net.sf.basedb.core.Update.updateDatabase(Update.java:504)
>> at net.sf.basedb.install.InitDB.main(InitDB.java:69)
>> Caused by: org.hibernate.WrongClassException: Object with id: 1 was not 
>> of the specified subclass: 
>> net.sf.basedb.core.data.MeasuredBioMaterialData (Discriminator: 0)
>> at org.hibernate.loader.Loader.getInstanceClass(Loader.java:1444)
>> at 
>> org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1275)
>> at org.hibernate.loader.Loader.getRow(Loader.java:1197)
>> at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:568)
>> at org.hibernate.loader.Loader.doQuery(Loader.java:689)
>> at 
>> org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224)
>> at org.hibernate.loader.Loader.doList(Loader.java:2211)
>> at 
>> org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2095)
>> at org.hibernate.loader.Loader.list(Loader.java:2090)
>> at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:375)
>> at 
>> org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:338)
>> at 
>> org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:172)
>> at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1121)
>> at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
>> at 
>> net.sf.basedb.core.HibernateUtil.loadList(HibernateUtil.java:1351)
>> ... 3 more
>>
>> [90%]   Database update failed: Object with id: 1 was not of the 
>> specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData 
>> (Discriminator: 0)
>>
>>
>> net.sf.basedb.core.BaseException: Object with id: 1 was not of the 
>> specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData 
>> (Discriminator: 0)
>> at 
>> net.sf.basedb.core.HibernateUtil.loadList(HibernateUtil.java:1355)
>> at 
>> net.sf.basedb.core.Update.updateToSchemaVersion29(Update.java:1105)
>> at net.sf.basedb.core.Update.updateDatabase(Update.java:504)
>> at net.sf.basedb.install.InitDB.main(InitDB.java:69)
>> Caused by: org.hibernate.WrongClassException: Object with id: 1 was not 
>> of the specified subclass: 
>> net.sf.basedb.core.data.MeasuredBioMaterialData (Discriminator: 0)
>> at org.hibernate.loader.Loader.getInstanceClass(Loader.java:1444)
>> at 
>> org.hibernate.loader.Loader.instanceNotYetLoaded(L

Re: [base] Database schema limbo--schema version=28

[Jari Häkkinen]

e(Update.java:504)
> at net.sf.basedb.install.InitDB.main(InitDB.java:69)
> Caused by: org.hibernate.WrongClassException: Object with id: 2 was not 
> of the specified subclass: 
> net.sf.basedb.core.data.MeasuredBioMaterialData (Discriminator: 1914725632)
> at org.hibernate.loader.Loader.getInstanceClass(Loader.java:1444)
> at 
> org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1275)
> at org.hibernate.loader.Loader.getRow(Loader.java:1197)
> at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:568)
> at org.hibernate.loader.Loader.doQuery(Loader.java:689)
> at 
> org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224)
> at org.hibernate.loader.Loader.doList(Loader.java:2211)
> at 
> org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2095)
> at org.hibernate.loader.Loader.list(Loader.java:2090)
> at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:375)
> at 
> org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:338)
> at 
> org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:172)
> at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1121)
> at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
> at 
> net.sf.basedb.core.HibernateUtil.loadList(HibernateUtil.java:1351)
> ... 3 more
> 
> 
> -keith
> 
> 
> Jari Häkkinen wrote:
>> I have successfully upgraded from 2.1.2 to 2.2. This is of course not 
>> exactly the same upgrade as Chris.
>>
>>
>> Jari
>>
>>
>> Nicklas Nordborg wrote:
>>   
>>> Chris Wiita wrote:
>>> 
>>>> I attempted a update to Base2.2 from a 2.1.1 installation.  Executing 
>>>> updatedb.sh worked until the "Updating database" step:
>>>>   
>>> I really don't know why this is happening. The error message says 
>>> something about "Discriminator: 0" but we never use a 0, only the values 
>>> 1, 2, 3 and 4, which have the following meaning:
>>>
>>>   1 = Biosource
>>>   2 = Sample
>>>   3 = Extract
>>>   4 = Labeled extract
>>>
>>> Can you check the "BioMaterials" table and check if any row have a value 
>>> in the "discriminator" column that is not in the 1-4 range?
>>>
>>> If there are such values they must be changed to one of the above. Then 
>>> we have to ask the question how they got there in the first place.
>>>
>>> If there are only 1-4 the error message complaining about 
>>> "Discriminator: 0" is a bit confusing and is something that we need to 
>>> investigate further to see if we can reproduce the error.
>>>
>>> Another option is to manually change the schema version to 29, but then 
>>> you will not get the changes between 28 and 29. Luckily, this change 
>>> doesn't involve any changes to the database. It only recalculates the 
>>> remaining quantity of all biomaterials since a bug may have caused them 
>>> to be incorrect. See ticket #466: http://base.thep.lu.se/ticket/466
>>>
>>> I don't think it was a good idea to run the update script from an 
>>> earlier version. I really don't know if that might have messed things up 
>>> more or not. I'll add a ticket to make sure that the update script 
>>> checks the schema version and doesn't execute if it is too high. In any 
>>> case it is good that the main program does the check and refuses to 
>>> start since it can lead to incorrect data beeing inserted into the 
>>> database.
>>>
>>> It is not possible to revert back to an earlier version. You can only do 
>>> this if you have made a backup of the database.
>>>
>>> /Nicklas
>>>
>>> 
>>>> --
>>>> [75%]   Updating database...
>>>> [87%]   --Updating schema version: 28 -> 29...12:06:13,579 ERROR 
>>>> Update:1150 - updateToSchemaVersion29: FAILED
>>>> net.sf.basedb.core.BaseException: Object with id: 1 was not of the 
>>>> specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData 
>>>> (Discriminator: 0)
>>>> at 
>>>> net.sf.basedb.core.HibernateUtil.loadList(HibernateUtil.java:1355)
>>>> at 
>>>> net.sf.basedb.core.Update.updateToSchemaVersion29(Update.java:1105)
>>>> at net.sf.basedb.core.Update.updateDataba

Re: [base] [base-announce] BASE 2.2 released.

[Jari Häkkinen]

Hi all,

We are not so happy anymore. We have removed BASE 2.2 from the download 
page. We are working on the upgrade problem.

If you are planning to upgrade to 2.2 anyway you MUST make a backup 
before upgrading, however our recommendation is to wait until 2.2.1 is 
released.

We are sorry about this serious flaw in BASE 2.2.


Cheers,

Jari


Jari Häkkinen wrote:
> Hi all,
> 
> We are happy to announce the release of BASE 2.2. You can download BASE 
> from http://base.thep.lu.se/wiki/DownloadPage
> 
> This release contains many new feature and fixes. A list of fixed and 
> added features in 2.2 is found by clicking on this beast: 
> http://base.thep.lu.se/query?status=new&status=assigned&status=reopened&status=closed&milestone=BASE+2.2&order=id
> 
> 
> Enjoy,
> 
> The Lund BASE Team
> 
> 
> -
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier.
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> ___
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> [EMAIL PROTECTED]
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-- 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
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[base] Bug fix release 2.2.1 is available now

[Jari Häkkinen]

Hi all,

We are eager to announce the release of BASE 2.2.1. You can download 
BASE from http://base.thep.lu.se/wiki/DownloadPage

This release does not contain the database upgrade that was not working 
in 2.2. We have also added a check making it impossible to make a 
"backwardsupgrade", i.e., reverting to an earlier version using the 
update script. This is of course only available from now on so be 
careful with the older releases.

Of course, all the nice things that was added to 2.2 is still there. A 
list of fixed and added features in 2.2 is found by clicking on this 
beast: 
http://base.thep.lu.se/query?status=new&status=assigned&status=reopened&status=closed&milestone=BASE+2.2&order=id


Enjoy,

The Lund BASE Team
-- 
Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se

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Re: [base] 1.2 plugins

[Jari Häkkinen]

Hi Steve,

BASE 1.2 plug-ins can be made to run in BASE 2. I have not tried to get 
a 1.2 plug-in to run in BASE 2 myself yet, but Johan Enell is doing the 
major coding for the BASE 1 plug-in executer.

TMEV is already in BASE 2.2 If you click the third icon in the bioassay 
set view of an experiment you will initiate MeV. MeV is running as an 
Java web start application, and the bioassay set is automatically loaded 
at MeV start. You'll have to accept the certificate. You can perform 
analysis in MeV but the results cannot (currently) be stored back to 
BASE but saving to the local disk works.

I forgot to add our customized version of MeV to BASE-hacks page. I'll 
add the code to BASE-hacks.


Cheers,

Jari


Steve Taylor wrote:
> Hi,
> 
> Can anyone confirm if it is possible to run BASE 1.2 plugins reliably in BASE 
> 2+? I noticed on the web site it says:
> 
> "Plug-ins created for BASE 1.2 can be made to work in BASE 2 using the 
> Base1PluginExecuter plug-in (this is still in development phase)."
> 
> Also is TMEV planned to be integrated into BASE2? On
> 
> http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html
> 
> it says:
> 
> "MeV is a versatile microarray data analysis tool, incorporating 
> sophisticated algorithms for clustering, visualization, classification, 
> statistical analysis and biological theme discovery, 
> http://www.tm4.org. We use a modified version of MeV and provide information 
> about the changes at http://trac.thep.lu.se/tracs/BASE-hacks.";
> 
> but the link doesn't work.
> 
> Thanks for any advice,
> 
> Steve
> --
> Medical Sciences Division
> Weatherall Institute of Molecular Medicine/Sir William Dunn School
> Oxford University
> 
> 
> -
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-- 
Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se

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Re: [base] 1.2 plugins

[Jari Häkkinen]

Sorry, unfinished sentence ...

Jari Häkkinen wrote:
> Hi Steve,
> 
> BASE 1.2 plug-ins can be made to run in BASE 2. I have not tried to get 
> a 1.2 plug-in to run in BASE 2 myself yet, but Johan Enell is doing the 
> major coding for the BASE 1 plug-in executer.

... Johan should be able to give some pointers.


> TMEV is already in BASE 2.2 If you click the third icon in the bioassay 
> set view of an experiment you will initiate MeV. MeV is running as an 
> Java web start application, and the bioassay set is automatically loaded 
> at MeV start. You'll have to accept the certificate. You can perform 
> analysis in MeV but the results cannot (currently) be stored back to 
> BASE but saving to the local disk works.
> 
> I forgot to add our customized version of MeV to BASE-hacks page. I'll 
> add the code to BASE-hacks.
> 
> 
> Cheers,
> 
> Jari
> 
> 
> Steve Taylor wrote:
>> Hi,
>>
>> Can anyone confirm if it is possible to run BASE 1.2 plugins reliably in 
>> BASE 2+? I noticed on the web site it says:
>>
>> "Plug-ins created for BASE 1.2 can be made to work in BASE 2 using the 
>> Base1PluginExecuter plug-in (this is still in development phase)."
>>
>> Also is TMEV planned to be integrated into BASE2? On
>>
>> http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html
>>
>> it says:
>>
>> "MeV is a versatile microarray data analysis tool, incorporating 
>> sophisticated algorithms for clustering, visualization, classification, 
>> statistical analysis and biological theme discovery, 
>> http://www.tm4.org. We use a modified version of MeV and provide information 
>> about the changes at http://trac.thep.lu.se/tracs/BASE-hacks.";
>>
>> but the link doesn't work.
>>
>> Thanks for any advice,
>>
>> Steve
>> --
>> Medical Sciences Division
>> Weatherall Institute of Molecular Medicine/Sir William Dunn School
>> Oxford University
>>
>>
>> -
>> Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to share your
>> opinions on IT & business topics through brief surveys-and earn cash
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> 

-- 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se

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Re: [base] 1.2 plugins

[Jari Häkkinen]

Hi Steve,

Yes, we are planning to save the analysis made in TMEV back to BASE. The 
deadline for this feature to be included to BASE is not set yet. We have 
one guy assigned for this task but he has other things to do before he 
can start on TMEV.

I have started to transfer our hacks on TMEV code to the BASE-hacks trac 
pages, http://trac.thep.lu.se/trac/basehacks/. Currently the TMEV source 
code is there with modifications to the build.xml file to make it 
compile on my Mac (and hopefully on other Unix like environments). I'll 
try to add the changes in a few days (time permitting).


Cheers,

Jari


Steve Taylor wrote:
> Hi Jari,
> 
>> BASE 1.2 plug-ins can be made to run in BASE 2. I have not tried to get 
>> a 1.2 plug-in to run in BASE 2 myself yet, but Johan Enell is doing the 
>> major coding for the BASE 1 plug-in executer.
>>
> 
> Look forward to hearing about it.
> 
>> TMEV is already in BASE 2.2 If you click the third icon in the bioassay 
>> set view of an experiment you will initiate MeV. MeV is running as an 
>> Java web start application, and the bioassay set is automatically loaded 
>> at MeV start. You'll have to accept the certificate. You can perform 
>> analysis in MeV but the results cannot (currently) be stored back to 
>> BASE but saving to the local disk works.
>>
> 
> That sounds excellent. Are there plans to write the TMEV analysis results 
> back to the server and be able to visualise the analysis workflow in BASE in 
> the usual way? This would be a really good way of 
> capturing and keeping all the data in one place. I realise it may require 
> some more hacking of TMEV but it would be a fantastic feature...
> 
>> I forgot to add our customized version of MeV to BASE-hacks page. I'll 
>> add the code to BASE-hacks.
>>
>>
> 
> 
> Ok thanks.
> 
> Steve
> 
> 
> 
>> Cheers,
>>
>> Jari
>>
>>
>> Steve Taylor wrote:
>>
>>> Hi,
>>>
>>> Can anyone confirm if it is possible to run BASE 1.2 plugins reliably in 
>>> BASE 2+? I noticed on the web site it says:
>>>
>>> "Plug-ins created for BASE 1.2 can be made to work in BASE 2 using the 
>>> Base1PluginExecuter plug-in (this is still in development phase)."
>>>
>>> Also is TMEV planned to be integrated into BASE2? On
>>>
>>> http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html
>>>
>>> it says:
>>>
>>> "MeV is a versatile microarray data analysis tool, incorporating 
>>> sophisticated algorithms for clustering, visualization, classification, 
>>> statistical analysis and biological theme discovery, 
>>> http://www.tm4.org. We use a modified version of MeV and provide 
>>> information about the changes at http://trac.thep.lu.se/tracs/BASE-hacks.";
>>>
>>> but the link doesn't work.
>>>
>>> Thanks for any advice,
>>>
>>> Steve
>>> --
>>> Medical Sciences Division
>>> Weatherall Institute of Molecular Medicine/Sir William Dunn School
>>> Oxford University
>>>
>>>
>>> -
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>>
> 
> 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
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Re: [base] Error running RMAExpress plug-in

[Jari Häkkinen]

Hi,

I think that you forgot to import reporter (probeset) information before 
running the plug-in, i.e., there is a probeset in the .cel files that 
does not exist in the reporter table.


Jari


Cris wrote:
> Hi all,
> 
> I am trying to run the RMAExpress plug-in to import Affymetrix data, but 
> I get the following error:
> 
> net.sf.basedb.core.BaseException: Unable to import root bioassay.
> at se.lu.thep.affymetrix.RMAExpress.storeResult (RMAExpress.java:424)
> at se.lu.thep.affymetrix.RMAExpress.run(RMAExpress.java:307)
> at 
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88)
> at net.sf.basedb.core.InternalJobQueue$JobRunner.run 
> (InternalJobQueue.java:420)
> at java.lang.Thread.run(Thread.java:595)
> 
> I successfully installed and run the RMAExpressConsole, so I have no 
> clue of where is the problem.
> 
> I'm running BASE in a Linux FC6 with MySQL.
> 
> Thanks a lot for any help.
> 
> 
> --
> Cristiane Rocha
> Laboratorio de Genetica Molecular
> Faculdade de Ciencias Medicas - Unicamp
> Brasil - 55 - 19- 3521-8956
> 


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[base] BASE 2.2.2 released.

[Jari Häkkinen]

Hi all,

A new bug fix release is available for download from 
http://base.thep.lu.se/wiki/DownloadPage

Issues resolved in this release are listed here, 
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.2.2


Happy BASEing,

The Lund BASE team.


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Re: [base] Unexpected exit of RMAExpress sub-process

[Jari Häkkinen]

Hi,

You have probably forgotten to import the reporters for the Affymetrix 
chip you are using.

This is an issue waiting to be fixed, http://base.thep.lu.se/ticket/435


Cheers,

Jari


[EMAIL PROTECTED] wrote:
> dears,
> while trying to set 'new root bioassay set' i get this error:
> 
> Unexpected exit of RMAExpress sub-process. Return value: 126
> 
> with stack trace
> java.io.IOException: Unexpected exit of RMAExpress sub-process. Return  
> value: 126
> at se.lu.thep.affymetrix.RMAExpress.runRMAExpress(RMAExpress.java:362)
> at se.lu.thep.affymetrix.RMAExpress.run(RMAExpress.java:306)
> at  
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88)
> at  
> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420)
> at java.lang.Thread.run(Thread.java:595)
> 
> please let me know if you know..
> thanks!!
> sergio
> 
> 
> 
> This message was sent using IMP, the Internet Messaging Program.
> 
> 
> -
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-- 
Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se

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Re: [base] Affymetrix Format

[Jari Häkkinen]

There is no support for ddt or cab. Currently only cdf and cel files are
supported by the Affymetrix plug-ins. Annotation files (.csv) are used for
uploading probeset (reporter in BASE language) information.

The issue of supporting ddt and cab files is an import and a plug-in
issue. There are two ways to solve this:

i) Write code that treats the file in a proper way and submit the solution
to the developer team (preferred route ;-) ).

ii) Submit a ticket through http://base.thep.lu.se explaining what you'd
like to see wrt to ddt and cabs.


Note, to include ddt and cab support to BASE, the file formats must be
open, that is we must be able to read them without proprietary
non-distributable code.


Cheers,

Jari

Joel Masciocchi wrote:
> Hi
>
> I would know if it's possible to use dtt or cab format with BASE ?
>
> Regards
>
> --
> Joel Masciocchi
> Engineer of Bioinformatics Service Line
> CRS4 - Bioinformatics
> Loc. Pixina Manna Edificio 3 Pula 09010 (CA), Italy
>
>
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Re: [base] Base Lowess normalization program

[Jari Häkkinen]

Hi,

I assume you are referring to the BASE 2 implementation of lowess. The 
lowess plug-in is a part of the BASE core and is available in source 
form in the source package downloadable from the base web site. You can 
browse the code at 
http://base.thep.lu.se/browser/trunk/src/plugins/core/net/sf/basedb/plugins/LowessNormalization.java

We have no reported issues with the plug-in but we have not tested 244k 
arrays. It may be out of memory issues, can you check the logs for 
messages related to the problem.


Jari


George Wu wrote:
> Dear All:
> 
> I am using Base Lowess program to normalize my Microarray data. But seems it
> works with my small dataset input (e.g. 44k-probe records). But it doesn't
> work with my big data input file (e.g. 244K-probe array). 
> 
> So does Lowess have data file size limitation? If so, how can I fix it? By
> the way, I only have the executable? Is there any way I could get source
> code?
> 
> Thank you very much,
> 
> George
> 


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Re: [base] Base Lowess normalization program

[Jari Häkkinen]

If you are using the BASE 1 implementation of lowess the source is 
available in directory base-1.2.17/plugins/src/normalizers/. You can 
douwnload the latest BASE 1.2.17b source from http://base1.thep.lu.se/ 
(select 'Download BASE' in the left margin).

You cannot directly run the BASE 2 implementation of the lowess plug-in 
outside the BASE 2 application. Doing this requires changes to the code, 
and the header you present will not be valid. If you want to use lowess 
as a stand alone tool you should go for the BASE 1.2 implementation.


Cheers,

Jari

George Wu wrote:
> 
> Thanks, Jari. The problem happened with Base 1 version. We set up your
> lowess as standalone version so that we can run command like: cat input.txt
> | lowess > output.txt on Solaris unix. 
> 
> In input file, we used header like the following. Can we use the same header
> format to run your BASE2 Java version? If not, could you provide a header
> sample? 
> 
> Thanks,
> George
> 
> 
> BASEfile
> section lowess settings
> fit_fraction0.33
> min_x_step  0.1
> n_iter  4
> %
> 
> section assays
> count   2
> columns id  name
> annotationColumns
> %
> 1   temp
> 
> section spots
> columns positionreporterassayData
> assayFields intensity1  intensity2
> assays  1
> %
> 0   1   12761491
> 1   1   2096790
> 2   1   11465017
> 
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Jari
> Häkkinen
> Sent: Thursday, May 03, 2007 8:35 AM
> To: BASE ML
> Subject: Re: [base] Base Lowess normalization program
> 
> Hi,
> 
> I assume you are referring to the BASE 2 implementation of lowess. The 
> lowess plug-in is a part of the BASE core and is available in source 
> form in the source package downloadable from the base web site. You can 
> browse the code at 
> http://base.thep.lu.se/browser/trunk/src/plugins/core/net/sf/basedb/plugins/
> LowessNormalization.java
> 
> We have no reported issues with the plug-in but we have not tested 244k 
> arrays. It may be out of memory issues, can you check the logs for 
> messages related to the problem.
> 
> 
> Jari
> 
> 
> George Wu wrote:
>> Dear All:
>>
>> I am using Base Lowess program to normalize my Microarray data. But seems
> it
>> works with my small dataset input (e.g. 44k-probe records). But it doesn't
>> work with my big data input file (e.g. 244K-probe array). 
>>
>> So does Lowess have data file size limitation? If so, how can I fix it? By
>> the way, I only have the executable? Is there any way I could get source
>> code?
>>
>> Thank you very much,
>>
>> George
>>
> 


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Re: [base] Base and webservices

[Jari Häkkinen]

Hi,

there is sample code available at 
http://baseplugins.thep.lu.se/wiki/se.lu.thep.webservices_clients that 
runs against the demo server. The code is written in Perl and R. The 
Perl can be used as a script or used to get BASE/R connectivity from an 
R environment.


Jari


Nicklas Nordborg wrote:
> Emmanuel Courcelle wrote:
>> Hello
>>
>> Just to have some information about the future: Are there any plans to 
>> use some or all functionalities of BASE through some web service ?
>>
>> Do you have some documentation about this, is there anything already 
>> running (even experimental) ?
> 
> We have been experimenting with this in a separate branch.
> http://base.thep.lu.se/browser/branches/webservices
> 
> It is possible to login and list your Affymetrix experiments and 
> download the CEL and CDF files associated with each raw bioassay.
> There is no documentation about this exception what you can get from 
> reading the source code.
> 
> I don't think the entire BASE API will be exposed through webservices. 
> Webservices require a coarser API to make it usable. Right now we are 
> waiting for more use cases in order to be able to start working on that API.
> 
> /Nicklas
> 
> 
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-- 
Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se

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[base] BASE 2.3 released

[Jari Häkkinen]

We are happy to announce the yesterday release of BASE 2.3.

This is mainly a documentation release with some minor enhancements to 
the actual code. Fixed items can be browsed at 
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.3

The new documentation is linked to from http://base.thep.lu.se and 
covers 200 pages (and there are many more pages to be written).

Please send us feedback on the documentation, and of course on features 
in BASE that misbehaves.


Happy BASEing,

The Lund BASE team.


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[base] BASE 2.3.1 released

[Jari Häkkinen]

Hi all,

Our best BASE so far is available for download at 
http://base.thep.lu.se/wiki/DownloadPage


Happy BASEing,

The Lund BASE team


-- 
Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se

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Re: [base] Unable to import root bioassay

[Jari Häkkinen]

Hi,

You have probably not imported all probeset into the reporter table. 
Please make sure that ALL reporters are imported, that is check that the 
  number of imported and updated reporters match the number of probesets 
in the affychip you use.


Cheers,

Jari


[EMAIL PROTECTED] wrote:
> Dear All:
> 
> I have some trouble to launch my experiment analysis thus I send you
> the error message which appears
> 
> 
> Name  Run plugin: RMAExpress plug-in
> Description
> Priority  5 (1 = highest, 10 = lowest)
> StatusError: Unable to import root bioassay.
> Percent complete
> 
>100%
> Created   2007-06-15 15:20:53
> Started   2007-06-15 15:21:26
> Ended 2007-06-15 15:21:42
> Serverbiobase.crs4.org
> PluginRMAExpress plug-in
> Configuration - none -
> 
> 
> net.sf.basedb.core.BaseException: Unable to import root bioassay.
> at se.lu.thep.affymetrix.RMAExpress.storeResult(RMAExpress.java:424)
> at se.lu.thep.affymetrix.RMAExpress.run(RMAExpress.java:307)
> at  
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88)
> at  
> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420)
> at java.lang.Thread.run(Thread.java:595)
> 
> 
> 
> Could somebody say me what is wrong?
> I am using BASE 2.2.2
> and mysql  Ver 14.12 Distrib 5.0.27, for redhat-linux-gnu (i686) using  
> readline 5.0
> thanks
> 
> 
> This message was sent using IMP, the Internet Messaging Program.
> 
> 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
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[base] BASE 2.3.2 released

[Jari Häkkinen]

The new release is available for download from 
http://base.thep.lu.se/wiki/DownloadPage

The new release addresses issues with the Base1PluginExecutor, see 
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.3.2 for 
details on the fixes.


Happy BASEing,

The Lund BASE team


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Re: [base] Error: Table 'base2dynamic.D2Spot' doesn't exist

[Jari Häkkinen]

Hi Sergio,

We are looking in to this problem but have difficulty to reproduce the 
error. We have tested the plier plugin with apt v1.6. Are you using the 
latest apt release (1.8)? (Do 'apt-probeset-summarize --version' to get 
the version information.)

Do you get a new (visible) node in the analysis tree in BASE after 
running the plugin?

We would be happy if we could move this discussion to the ticket related 
to this issue. Add comments to http://baseplugins.thep.lu.se/ticket/73 
but remember to login as base/base to add comments.


Cheers,

Jari


Nicklas Nordborg wrote:
> Sergio Contrino wrote:
>> dear nicklas,
>> thank you for the prompt answer and apologies for the lack of info.
>> here the info requested.
>> thank you
>> sergio
>>
>> i am running a test base 2.3.2 on mysql 5.1.14-beta (i must apologies 
>> again, i was thinking to be running on the reccomended 5.0)
>>
>> the stack (as in base report) is
> 
> I think I partly know what is happening. There are two problems, the 
> first causing the second.
> 
> 1. The Plier plugin is creating a root bioassayset but is never 
> inserting any data to it. If no data is inserted, then the missing table 
> isn't created.
> 
> 2. Before everything is committed to the database the root bioassayset 
> tries to count the number spots that has been inserted. This fails 
> because the table isn't there and there is no check if it exists at this 
> place.
> 
> Number 2 is a bug in the BASE core and should be easy to fix. This will 
> be included in the 2.4 release in about two weeks.
> 
> Why number 1 is happening is hard to tell. The Plier plug-in seems to 
> execute without errors. Maybe there is something wrong with the output 
> from the the 'apt-probeset-summarize' program. In that case, the plug-in 
> will just ignore it and continue without inserting any data. I guess the 
> developer of the Plier plug-in knows more about this...
> 
> I'll add a ticket to the BASE plug-ins site about #1.
> 
> /Nicklas
> 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se

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[base] web services branch is patched and is working again

[Jari Häkkinen]

Hi,

Due to some unknown reasons merges from the main development trunk to 
the web services branch has failed. The web service branch is now up to 
date and should work properly. Please report any problems through the 
mailing list.


Jari


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Re: [base] Should I use BASE 1.2.17 or go to BASE 2.4

[Jari Häkkinen]

Hi,

You should definitely go with BASE 2.4. 2.4 will be released on Monday 
20. No delay is expected.

Happy BASEing,

Jari


Diana Bernal wrote:
> Dear Jari,
>  
> I will re-start using BSE.  I tried for a little while a year ago and I 
> used BASE 1.2.17. Now That I will start again from scratch should I 
> install BASE 2.4 or should I keep BASE 1.2.17.  What is your advice?.  
> Thankyou a lot. 
>  
> Best regards,
>  
> Diana Bernal
> 
> */Jari Häkkinen <[EMAIL PROTECTED]>/* escribió:
> 
> Hi Sergio,
> 
> We are looking in to this problem but have difficulty to reproduce the
> error. We have tested the plier plugin with apt v1.6. Are you using the
> latest apt release (1.8)? (Do 'apt-probeset-summarize --version' to get
> the version information.)
> 
> Do you get a new (visible) node in the analysis tree in BASE after
> running the plugin?
> 
> We would be happy if we could move this discussion to the ticket
> related
> to this issue. Add comments to http://baseplugins.thep.lu.se/ticket/73
> but remember to login as base/base to add comments.
> 
> 
> Cheers,
> 
> Jari
> 
> 
> Nicklas Nordborg wrote:
>  > Sergio Contrino wrote:
>  >> dear nicklas,
>  >> thank you for the prompt answer and apologies for the lack of info.
>  >> here the info requested.
>  >> thank you
>  >> sergio
>  >>
>  >> i am running a test base 2.3.2 on mysql 5.1.14-beta (i must
> apologies
>  >> again, i was thinking to be running on the reccomended 5.0)
>  >>
>  >> the stack (as in base report) is
>  >
>  > I think I partly know what is happening. There are two problems, the
>  > first causing the second.
>  >
>  > 1. The Plier plugin is creating a root bioassayset but is never
>  > inserting any data to it. If no data is inserted, then the
> missing table
>  > isn't created.
>  >
>  > 2. Before everything is committed to the database the root
> bioassayset
>  > tries to count the number spots that has been inserted. This fails
>  > because the table isn't there and there is no check if it exists
> at this
>  > place.
>  >
>  > Number 2 is a bug in the BASE core and should be easy to fix.
> This will
>  > be included in the 2.4 release in about two weeks.
>  >
>  > Why number 1 is happening is hard to tell. The Plier plug-in
> seems to
>  > execute without errors. Maybe there is something wrong with the
> output
>  > from the the 'apt-probeset-summarize' program. In that case, the
> plug-in
>  > will just ignore it and continue without inserting any data. I
> guess the
>  > developer of the Plier plug-in knows more about this...
>  >
>  > I'll add a ticket to the BASE plug-ins site about #1.
>  >
>  > /Nicklas
>  >
>  >
> -
>  > This SF.net email is sponsored by: Splunk Inc.
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>  > unsubscribe: send a mail with subject "unsubscribe" to
>  > [EMAIL PROTECTED]
> 
> -- 
> Jari Hakkinen, PhD
> Complex Systems Division mailto:[EMAIL PROTECTED]
> Department of Theoretical Physics phone: +46 (0)46 2229347
> Lund University fax: +46 (0)46 2229686
> Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se
> 
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Re: [base] import of affymetrix data - which approach

[Jari Häkkinen]

Hi,

The plier and rmaexpress plug-ins calculates the probeset expression 
values using information from the cel/cdf files. The plugins are 
presented on the BASE plugin site 
http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix How the 
expression values are calculated is presented elsewhere (please follow 
links from the plugin website).

The raw data for Affymetrix is stored in the original cel files and is 
not stored in database tables like GenePix and other data. Affymetrix 
related expression data is not stored in the database tables until the 
creation of the first root bioassay set.

You do not need to create another affymetrix plugin if you are happy 
with the algorithms provided by plier and rmaexpress. However, if you 
need something else then you may need to write your own plugin (or help 
us improve the current affymetrix plugin).

You may want to change the extended-properties.xml, some information on 
this is available here, 
http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html

The problem with using CDFs in your array design is most likely related 
to missing reporters (probesets). Have you imported the reporters 
associated with the design (CDF)?

Please read the information provided in the plugin site and 
http://base.thep.lu.se/chrome/site/doc/user/getting_started.html (nice 
example on the workflow in BASE with references to Affymetrix data). 
And, of course, you can also use the mailing list.


Cheers,

Jari


Reha Yildirimman wrote:
> Hello,
> 
> like some other people I am trying to import data from affymetrix CEL 
> files.
> Searching the archive I have read that people use the RMAExpress and PLIER
> plugins. As far as I understood the plug-in extracts/calculates the 
> intensities but
> where are those data stored, since the associated raw data type for 
> affymetrix has
> no database table definition?
> Furthermore, are those intensities the stated MEAN values inside the CEL 
> file
> and are extracted intensities for each coordinate/probe or only for 
> probe sets ?
> 
> I have another approach and if that seems ineffective to you please drop 
> me a line!
> My approach is to change the affymetrix data type inside the 
> raw-data-type.xml
> from a simple file-definition to a database-definition like the other 
> data-types defined
> inside the xml.
> I added properties for the values:  MEAN (float), STDV (float), NPIXELS 
> (float)
> To be able to import data via a base-plugin from a CEL file each data 
> line has to have
> an association to a reporter - thus I added a column holding the 
> ProbeSet ID for each
> CEL file.
> 
> My problem is that when I associate a CDF file to an array design - 
> which I need for
> reference purpose - it states under Properties:
> 
> Features: Yes(0)
> 
> 
> This makes the raw data importer fail with:
> 
> Item not found: Feature[row=null, column=null, block=null, 
> metaGridX=null, metaGridY=null] on line 2
> 
> 
> If I take out the connection to the CDF - thus turning the Feature 
> property to No - the raw data importer works.
> How can I get around the problem without having to add to each line 
> inside the CEL file fake numbers for the features
> row, column, block, ...
> 
> Thanks alot in advance.
> 
> Best,
> 
> Reha
> 
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> 
> 
> 
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-- 
Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se

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[base] BASE 2.4 released

[Jari Häkkinen]

Hi all,

We are happy to announce BASE 2.4. The packages are added to the 
download area, http://base.thep.lu.se/wiki/DownloadPage

Please send feedback through the mailing lists.

Happy BASEing

The Lund BASE team

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Re: [base] BASE 2.4 on Windows

[Jari Häkkinen]

jesse paquette wrote:
> Hello all,
> 
> I'm currently going through the BASE 2.1 getting started document located at 
> (http://base.thep.lu.se/chrome/site/doc/user/getting_started.html).  I'm 
> running Windows XP, and there are a few things with BASE I've noticed that 
> aren't so compatible with my OS.
> 
> First, it's not to easy to create a symbolic link to the BASE www directory. 
>   My workaround is to copy the BASE "www" directory over to the Tomcat 
> "webapps" directory and rename it to "base2".

That's ok.


> Secondly, I'm trying to install the Affymetrix/RMAExpress/Plier plugin, and 
> I'm at the part that requires make to install the precompiled plugin into 
> the plugins directory.  I downloaded NMake for Windows, but I've got a 
> compile error.  Here's my command:

I am not sure about nmake compatibility with GNU make, gmake. You'd be 
better of with gmake but maybe it is not available for you.


> nmake BASEROOT="C:/Program Files/BASE/base-2.4.0" install-precompiled
> 
> The make error is this:
> 
> makefile(62) : fatal error U1036: syntax error : too many names to left of 
> '='
> 
> Line 62 in the makefile is:
> 
> BASEROOT ?= /usr/local/base
> 
> After trying a bunch of different things, I found that if I hard coded the 
> Makefile line to :
> 
> BASEROOT = "C:\Program Files\BASE\base-2.4.0"
> 
> and removed all of the '?' characters from the "?=" lines, NMake proceeded 
> until it encountered another problem.
> 
> "install is not recognized as an internal or external command, operable 
> program or batch file."
> 
> Poking around the rest of the Makefile yields a number of other non-Windows 
> commands.
> 
> My workaround: I just created the directories and moved the affymetrix.jar 
> file manually.  Will that be a problem?

No, problems at all. 'make install' simply creates the necessary 
directory structure and copies the jar to the requested directory.


> I'm really trying to avoid using CygWin or any other third-party 
> LINUX-emulating application, since going that route would mean that I should 
> probably just be installing BASE on a non-windows OS.
> 
> Jesse

Remember to place the plier and rmaexpress binaries in the same 
directory as you placed the jar file.


Was the above the only things you needed to do to get BASE to run on MS 
Windows?



Cheers,

Jari

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Re: [base] BASE 2.4 on Windows

[Jari Häkkinen]

jesse paquette wrote:
> Is there a problem with not using the permission model for the plugin?  I 
> don't have an 'Everyone' group set up yet.

No, there are no reported problems using the permission model.

The 'Everyone' group should be created when you install BASE, and it is 
more straightforward to share. The choice is yours.


Jari


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Re: [base] recompiling affymetrix plugin

[Jari Häkkinen]

You must use Java 1.5 or later, and soon we will require java 1.6.


Jari


Sergio Contrino wrote:
> dear base,
> i am trying to compile (with the distributed make) a slightly modified 
> (Plier.java) affy plugin (v 0.7) and i get a long (69) list of errors, 
> mostly
> 
> Syntax error, annotations are only available if source level is 5.0
> 
> any  suggestion? apologies if in the wrong list
> thanks
> sergio
> 
> 
> javac -cp /usr/local/base/www/WEB-INF/lib/BASE2Core.jar:.build 
> .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
> --
> 1. ERROR in .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 87)
>  @SuppressWarnings("unchecked")
>  ^
> Syntax error, annotations are only available if source level is 5.0
> --
> 2. ERROR in .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 92)
>  List errors = validateRequestParameters
>  
> The type List is not generic; it cannot be parameterized with arguments 
> 
> --
> 3. ERROR in .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 92)
>  List errors = validateRequestParameters
>   ^
> Syntax error, parameterized types are only available if source level is 
> 5.0
> --
> 4. ERROR in .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 110)
>  List rawBioAssays =
>  
> The type List is not generic; it cannot be parameterized with arguments 
> 
> --
> 5. ERROR in .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 110)
>  List rawBioAssays =
>   ^^^
> Syntax error, parameterized types are only available if source level is 
> 5.0
> --
> 6. ERROR in .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 111)
>  (List)request.getParameterValues("rawBioAssays");
>   ^
> The type List is not generic; it cannot be parameterized with arguments 
> 
> --
> 7. ERROR in .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 111)
>  (List)request.getParameterValues("rawBioAssays");
>^^^
> Syntax error, parameterized types are only available if source level is 
> 5.0
> --
> 8. ERROR in .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 112)
>  for (RawBioAssay rba : rawBioAssays)
>   ^^
> Syntax error, 'for each' statements are only available if source level is 
> 5.0
> --
> 9. ERROR in .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 123)
>  storeValue(job, request, nameParameter);
>   ^
> nameParameter cannot be resolved
> --
> 10. ERROR in 
> .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 124)
>  storeValue(job, request, experimentParameter);
>   ^^^
> experimentParameter cannot be resolved
> --
> 11. ERROR in 
> .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 125)
>  storeValues(job, request, rawBioAssaysParameter);
>^
> rawBioAssaysParameter cannot be resolved
> --
> 12. ERROR in 
> .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 135)
>  response.setError(e.getMessage(), Arrays.asList(e));
>   ^^
> The method asList(Object[]) in the type Arrays is not applicable for the 
> arguments (Throwable)
> --
> 13. ERROR in 
> .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 155)
>  List> parameters = new 
> ArrayList>();
>   ^^^
> Syntax error, parameterized types are only available if source level is 
> 5.0
> --
> 14. ERROR in 
> .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 155)
>  List> parameters = new 
> ArrayList>();
>   ^^^
> The type PluginParameter is not generic; it cannot be parameterized with 
> arguments 
> --
> 15. ERROR in 
> .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 155)
>  List> parameters = new 
> ArrayList>();
> 
> ^^^
> The type PluginParameter is not generic; it cannot be parameterized with 
> arguments 
> --
> 16. ERROR in 
> .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 155)
>  List> parameters = new 
> ArrayList>();
> 
> ^^^
> Syntax error, parameterized types are only available if source level is 
> 5.0
> --
> 17. ERROR in 
> .build/se/lu/thep/affymetrix/AbstractExternalBinaryPlugin.java
>   (at line 157)
>  experimentType = n

Re: [base] Base1PluginExecuter parameter xml

[Jari Häkkinen]

Why not use the clustering in the MeV plugin shipped with BASE?


Jari


Johan Enell wrote:
> Hj Bob,
> 
> The clustering from Base1 will not work in Base2. Or more precisely,  
> you will be able to run the plugin but you wont be able to se the  
> result. The visualization page in Base1 was a specific php page for  
> that plugin and we didn't want a solution like that in Base2.
> 
> 
> When you configure Base1 plugins you should always start of from a  
> base1 plugin configuration file. From the plugin page in Base1 you  
> will find an export link with each plugin. Use that file to configure  
> the Base1PluginExecuter.
> 
> /Johan
> 
> 
> 11 sep 2007 kl. 16.58 skrev Bob MacCallum:
> 
>> Hi,
>>
>> I was trying to find out if base1's hierarchical clustering would  
>> run under
>> base2 - and got to the point where I need to provide parameter  
>> settings as
>> XML.   I could spend an hour figuring this out by hand (e.g. from  
>> the examples
>> on the BASE2 demo server) but I'm convinced there's an easier way.   
>> I've
>> searched the plugin site for documentation.  Could someone help  
>> please?
>>
>> Since the hierarchical clustering isn't on the BASE2 demo server,  
>> does that
>> mean it doesn't work?
>>
>> We know that there won't be any display tools available in BASE2  
>> for this, but
>> we can work with the PNGs and assorted text files.
>>
>> many thanks,
>> Bob.


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Re: [base] Base1PluginExecuter parameter xml

[Jari Häkkinen]

a) I don't know how memory efficient MeV is but isn't memory always an 
issue when clustering?

b) But imagine a future where MeV actually stores data back to BASE! I 
think this may become doable as a part of the web services development 
in BASE 2.5.

I would like to go even further where users can perform a MeV clustering 
on the server side, and when the job finishes be able to look at the 
results using MeV. It should be possible to do by hacking the MeV code. 
Just making things clear, we are not working on this but I just wanted 
to plant an idea for BASE/MeV development.


Cheers,

Jari


Bob MacCallum wrote:
> I knew someone was going to ask that...
> 
> Because
> 
> a) I tried it and get out-of-memory errors on a 1GB Mac clustering a
>relatively modest experiment (12 hybs x 20k spots).  We will have users in
>developing nations with much less computing power than that.
> 
> b) Anything done in MeV is not stored for eternity in the BASE analysis tree
>for future reference.
> 
> c) We will need/write something similar to clust_*.phtml supplied with BASE1,
>and the PNGs from this plugin will work fine for us.
> 
> cheers,
> Bob.
> 
> Jari Häkkinen writes:
>  > Why not use the clustering in the MeV plugin shipped with BASE?
>  > 
>  > 
>  > Jari
>  > 
>  > 
>  > Johan Enell wrote:
>  > > Hj Bob,
>  > > 
>  > > The clustering from Base1 will not work in Base2. Or more precisely,  
>  > > you will be able to run the plugin but you wont be able to se the  
>  > > result. The visualization page in Base1 was a specific php page for  
>  > > that plugin and we didn't want a solution like that in Base2.
>  > > 
>  > > 
>  > > When you configure Base1 plugins you should always start of from a  
>  > > base1 plugin configuration file. From the plugin page in Base1 you  
>  > > will find an export link with each plugin. Use that file to configure  
>  > > the Base1PluginExecuter.
>  > > 
>  > > /Johan
>  > > 
>  > > 
>  > > 11 sep 2007 kl. 16.58 skrev Bob MacCallum:
>  > > 
>  > >> Hi,
>  > >>
>  > >> I was trying to find out if base1's hierarchical clustering would  
>  > >> run under
>  > >> base2 - and got to the point where I need to provide parameter  
>  > >> settings as
>  > >> XML.   I could spend an hour figuring this out by hand (e.g. from  
>  > >> the examples
>  > >> on the BASE2 demo server) but I'm convinced there's an easier way.   
>  > >> I've
>  > >> searched the plugin site for documentation.  Could someone help  
>  > >> please?
>  > >>
>  > >> Since the hierarchical clustering isn't on the BASE2 demo server,  
>  > >> does that
>  > >> mean it doesn't work?
>  > >>
>  > >> We know that there won't be any display tools available in BASE2  
>  > >> for this, but
>  > >> we can work with the PNGs and assorted text files.
>  > >>
>  > >> many thanks,
>  > >> Bob.


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Re: [base] Error: Run Plugin: RMAExpress plug-in

[Jari Häkkinen]

Hi,

jesse paquette wrote:
> Hello,
> 
> I'm still trying to get through the 2.1 getting started document 
> (http://base.thep.lu.se/chrome/site/doc/user/getting_started.html).  
> Moving on to section 2d, "Analysing an experiment step I".  I'm getting 
> an error when I try to run the RMAExpress plug-in job.  The stack trace 
> is below.  I'm curious as to why the plug-in is looking for the 
> RMAExpressConsole application in the Tomcat temp directory.  I think 
> I've configured everything properly so far.  The RMAExpressConsole 
> application file is located in the same directory as the plug-in's 
> affymetrix.jar library.

What is the name of the RMAExpressConsole file. Is it with or without 
.exe extension. If it is without the extension can you please try to add 
the extension, and the other way around if it is with the extension.


> I've got about 100 raw .CEL files to load.  How's the batch import 
> functionality coming along?

Take a look at 
http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.Tab2MageImporter I think 
this should solve your batch import problem.


Cheers,

Jari


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[base] BASE 2.4.1 released

[Jari Häkkinen]

A new version of BASE is available for download at 
http://base.thep.lu.se/wiki/DownloadPage

Fixed issues are listed at 
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.4.1


The Lund BASE team


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Re: [base] procedure for obtaining normalized data

[Jari Häkkinen]

Hi,

I think this is a problem with negative and zero intensity values (due 
to FG-BG). You need to decide how to treat these intensities and the 
filter or modify these numbers. After resolving this, you can proceed as 
you describe.


Cheers,

Jari


Ana Conesa wrote:
> Hi
> 
> I am using BASE to store and analyze 2 color (GenePix) data from a
> costum cDNA array.
> I am addressing now the analysis of an experiment. I created a raw bioassay
> out of raw data files and I would like now to normalize. I am not sure
> which is the standard procedure to do this. At first I calculated FG-BG
> using the formula intensity calculator and then I tried to compute M
> values on the result as log2(ch1/ch2) with the idea of running lowess
> normalization on this result, but this is giving me a "value" error, so
> I guess this is not the way. Could anyone give me a bit of help on this
> Thanks a lot
> Ana
> 
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-- 
Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se

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[base] BASE 2.4.2 released

[Jari Häkkinen]

A new version of BASE is available for download at
http://base.thep.lu.se/wiki/DownloadPage

Fixed issues are listed at
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.4.2


The Lund BASE team


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[base] BASE 2.4.3 released

[Jari Häkkinen]

A new version of BASE is available for download at
http://base.thep.lu.se/wiki/DownloadPage

Fixed issues are listed at
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.4.3


The Lund BASE team


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Re: [base] 2.4.2 => 2.4.3 - any database schema change?

[Jari Häkkinen]

There is no need to delete the database between upgrade in a stable 
release of BASE. Please read 
http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.upgrade.html
 
for upgrading instructions.


Jari


Dave Hau wrote:
> 2.4.3 release followed closely after 2.4.2 release.  I would like to 
> upgrade from 2.4.2  to 2.4.3, but was just wondering if I could keep my 
> database and just copy the entire 2.4.3 www directory to my tomcat 
> server.  Preferably I would like to not have to nuke the entire database 
> this time around for the upgrade.  Is there a database script in the 
> base package I can do a diff on to see if there's been any schema 
> change?  I did a quick search and didn't find any.
> 
> Thanks and best regards,
> Dave Hau

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[base] BASE 2.4.4 released. Please read, important performance issue fixed in this release.

[Jari Häkkinen]

We are happy to announce the release of BASE 2.4.4.

As always you can find the latest release at 
http://base.thep.lu.se/wiki/DownloadPage for download.

This releases contains an important fix that resolves severe performance 
issues, cf. http://base.thep.lu.se/ticket/796. The code is now fixed but 
you will have to update your database, please read 
http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.upgrade.html
on how to update your database. We have not detected any data integrity 
problems related to this issue.

The script may take quite some time depending on your database size. Our 
BASE installation took almost 24h to fix, so patience is a virtue here. 
Remember to upgrade BASE before starting the upgrade script and kepp 
BASE shutdown until the script ends.

Happy BASEing,

The Lund BASE team


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Re: [base] Problems running Tab2Mage Importer, "NOT sufficient Disk Space"

[Jari Häkkinen]

Just for your information:

Dominic Oyeniran wrote:
> This is a known issue and has been documented here: 
> http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt.
> Please scroll to the usage section right after the installation section.

We prefer to use links to the more generic http://baseplugins.thep.lu.se 
since lev is merely the current host of the baseplugins (and base) and 
it may changes in the future. That is the above link should be a more 
archive safe 
http://baseplugins.thep.lu.se/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt
 


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Re: [base] Tab2Mage Importer has problemsfinding AnnotationTypeCvImporter

[Jari Häkkinen]

However, given the performance improvement you should go for 2.4.4

Jari


Nicklas Nordborg wrote:
> vegard nygaard wrote:
> 
>> When I briefly inspected what was created in BASE it looked OK despite the
>> error messages in the log. The "overview" tab for the experiment crashed
>> though, but it has done that for me a lot and may not be caused by the
>> tab2mage importer. Anyways here is the error message
>  >
>  >
>  > java.lang.NullPointerException
> 
> This has been fixed in the 2.4.4 release. See 
> http://base.thep.lu.se/ticket/803 for a manual workaround if you don't 
> want to upgrade.
> 
> /Nicklas


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Re: [base] migration from 1.2.16 to 2.3.2

[Jari Häkkinen]

Select 'Download BASE' at http://base1.thep.lu.se/ and download version 
1.2.17b. Follow the instructions in the package to upgrade from 1.2.16 
to 1.2.17b

The 1.2.20/21 is a reference to the underlying database schema version 
and not the BASE application version. It is a little bit confusing.


Jari


Spollen, William G. wrote:
> We installed and used BASE 1.2.16 a few years ago and now want to 
> migrate the data to BASE 2.3.2 on another machine. The migration script 
> we found on the web did not work.  After looking around it appears I am 
> to upgrade first to version 1.2.20 or 21, but we cannot find any such 
> version at SourceForge.  Where can I find this version?
> 
>  
> 
> Thanks
> 
>  
> 
> Bill


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Re: [base] migration from 1.2.16 to 2.3.2

[Jari Häkkinen]

Thanks Bob, I forgot to mention that in my post. I am in the process of 
releasing 2.4.5 which actually removes one line of debug code that makes 
BASE sleep for 5 seconds in many queries! Wait till the new package that 
will appear soon.


Jari


Bob MacCallum wrote:
> Hi Bill,
> 
> Since you will have to rerun the analysis steps again in BASE2 (these are not
> migrated yet to my knowledge) you will find that the latest release (2.4.4)
> does it all many times quicker (although I haven't got round to upgrading from
> 2.4.2 yet...)
> 
> So it would be worth the hassle upgrading your 2.3.2 to the latest and
> greatest.  I guess you can do that pre- or post-migration though.
> 
> cheers,
> Bob
> 
> Jari Häkkinen writes:
>  > Select 'Download BASE' at http://base1.thep.lu.se/ and download version 
>  > 1.2.17b. Follow the instructions in the package to upgrade from 1.2.16 
>  > to 1.2.17b
>  > 
>  > The 1.2.20/21 is a reference to the underlying database schema version 
>  > and not the BASE application version. It is a little bit confusing.
>  > 
>  > 
>  > Jari
>  > 
>  > 
>  > Spollen, William G. wrote:
>  > > We installed and used BASE 1.2.16 a few years ago and now want to 
>  > > migrate the data to BASE 2.3.2 on another machine. The migration script 
>  > > we found on the web did not work.  After looking around it appears I am 
>  > > to upgrade first to version 1.2.20 or 21, but we cannot find any such 
>  > > version at SourceForge.  Where can I find this version?
>  > > 
>  > >  
>  > > 
>  > > Thanks
>  > > 
>  > >  
>  > > 
>  > > Bill
>  > 
>  > 
>  > -
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-- 
Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden  http://www.thep.lu.se

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[base] BASE 2.4.5 available for download

[Jari Häkkinen]

A new version of BASE is available for download at
http://base.thep.lu.se/wiki/DownloadPage

This release contains one fix removing a debug sleep statement. Server 
performance is improved when upgrading to this release.

The Lund BASE team


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Re: [base] regular expression and wildcards

[Jari Häkkinen]

Nicklas Nordborg wrote:
> vegard nygaard wrote:
>> "F633 Median" not working but giving a funny error message: Error: For input
>> string: ""F633 MEdian"" on line..., (The E's in the input has been
>> uppercased!)
> 
> That is because string like '1.23e-2' are not recognised as numbers 
> unless the 'e' is first converted to a capital 'E'.


That is, Java cannot handle scientific notation properly (cf. 
http://base.thep.lu.se/changeset/3703)


Jari

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Re: [base] regular expression and wildcards

[Jari Häkkinen]

I moved it to the BASE core ticketing system as 
http://base.thep.lu.se/ticket/811

Jari


Nicklas Nordborg wrote:
> vegard nygaard wrote:
>> Thanks for quick answers.
>>
>> I would like column mappings to support wildcards or regular expressions.
>> Not a big thing, but I took the liberty to add it as a ticket.
>> Implement it if it is cheap and when you have time.
> 
> You added it to the wrong site. It is a BASE core issue. It has nothing 
> to with the plug-ins on the BASE plug-ins site.
> 
> /Nicklas


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Re: [base] Getting started with BASE2.4

[Jari Häkkinen]

Are you logged in as with administrator privileges? Only users with 
administrator privileges are allowed to use the Reporter map importer 
and thus configure it. There is no need to create this plug-in it comes 
with pre-installed with BASE.


Jari


Diana Bernal wrote:
> 
> Dear BASE staff, I am strating to set up BASE 2.4. I have followed the 
> BASE 2.1 - User documentation: Getting started. I was able to configure 
> the /Reporter importer/ , now I should configure the /Reporter map 
> importer/ . However I can't find it. Shoul I create a new plug-in for 
> the /Reporter map importer/, if so how do I create a new plug-in?. 
> Thankyou very much. Diana Bernal


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Re: [base] Java memory error

[Jari Häkkinen]

We cannot recreate this problem. We have used the CDF importer on BASE 
2.5.0beta and 2.4.5 with no problems. One difference may be that we use 
jobagents (i.e., running jobs in a different thread than the core BASE 
application) but we did not experience any failures prior to switching 
to jobagents.

We even tried to give the jobagent 2GBs of memory to play with without 
any problems.

So ... we have no clue on what is going on. Are you able to do anything 
with your BASE? You are running a pure non-tampered BASE installed 
according to the installation instructions?

Can you please send us the information from the about button, 
configuration tab.


Jari


matthew lange wrote:
> The cdf file mentioned in my original post is called HG-U133_Plus_2.cdf, 
> and is downloadable from Affymetrix.  It is 97 MB.
> 
> Here is the Stack trace provided through the BASE CDF ProbeSet Importer 
> (not using the custom reporter importer here, just the generic one that 
> comes with base), accessible from the array design page, as "verify 
> Reporters" link.
> 
> Thanks a bunch for your help.  Let me know if I can be more specific.
> 
> Kind Regards,
> 
> matthew
> 
> 
> java.lang.OutOfMemoryError: Java heap space
> at java.lang.String.substring(String.java:1770)
> at java.lang.String.subSequence(String.java:1803)
> at java.util.regex.Pattern.split(Pattern.java:993)
> at java.lang.String.split(String.java:2103)
> at java.lang.String.split(String.java:2145)
> at affymetrix.gcos.cdf.CDFFileData.readTextProbeSets(Unknown Source)
> at affymetrix.gcos.cdf.CDFFileData.readTextFormat(Unknown Source)
> at affymetrix.gcos.cdf.CDFFileData.open(Unknown Source)
> at affymetrix.gcos.cdf.CDFFileData.read(Unknown Source)
> at affymetrix.fusion.cdf.FusionCDFData.read(Unknown Source)
> at net.sf.basedb.core.Affymetrix.checkIfReportersExists(Affymetrix.java:416)
> at 
> net.sf.basedb.plugins.CdfFileReporterImporter.importFromCdf(CdfFileReporterImporter.java:460)
> at 
> net.sf.basedb.plugins.CdfFileReporterImporter.run(CdfFileReporterImporter.java:183)
> at 
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:89)
> at 
> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421)
> at java.lang.Thread.run(Thread.java:595)
> 
> 
> 
> On Dec 3, 2007 11:02 PM , *Nicklas Nordborg* <[EMAIL PROTECTED] 
> > wrote:
> 
> 
> 
> -- Forwarded message --
> From: *Nicklas Nordborg* <[EMAIL PROTECTED]
> >
> Date: Dec 3, 2007 11:02 PM
> Subject: Re: [base] Java memory error
> To: BASE ML  >
> Cc: Joseph Fass < [EMAIL PROTECTED]
> >, [EMAIL PROTECTED]
> 
> 
> 
> Matthew Lange wrote:
>  > I am using the latest Base, and trying to load an initial data
> set.  My
>  > initial effort was to modify the reporter importer to load some affy
> 
> Why have you modified the reporter importer? What modifications have you
> made? The regular reporter importer can import Affymetrix csv files
> without problems. The hard part may be to come up with regular
> expressions that works. Sample configurations can be downloaded from
> 
> http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html
> 
> 
> 
> 
>  > probes from a csv file.  This worked fine for a small list, but
> as the
>  > list approached >500 individuals, I started receiving out of memory
> 
> What do you mean with "individuals"? We regularly test with importing
> 5+ reporters/probesets. It works fine with 500MB memory with room to
> spare.
> 
>  > errors from the Java Heap...and even brought Tomcat to its knees on a
>  > couple of occassions.  As a workaround, I uploaded the an 80ish
> MB CDF
>  > file from Affy, which contains the array design.  This went in fine.
>  > Then I tried to use the feature that allows me to import
> reporters from
>  > the CDF file--again Java OOM errors, and tomcat whining.
> 
> We use the Affymetrix Fusion SDK for reading CDF files. I don't know
> about the memory requirements. I think the binary format uses less
> memory since data is read from the file at demand. If the file is in
> text format everything is parses and stored in memory. The biggest test
> file we have is ~40MB text format. Memory usage stays below 100MB while
> parsing that file.
> 
> 
>  > We have given Tomcat 2GB to play with, and this seems like it
> should be
>  > more than enough.  Are there known issues with this utility that I
>  > should be aware of, or is there a rule-of-thumb to follow when
>  > allocating memory to tomcat, based on the size of files that need
> to be
>  > parsed?  Or maybe another memory 

[base] BASE 2.5 released

[Jari Häkkinen]

Hi all,

We are happy to announce the release of BASE 2.5. The packages are added 
to the download area, http://base.thep.lu.se/wiki/DownloadPage

Please send feedback through the mailing lists.

Happy BASEing


The Lund BASE team

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[base] BASE 2.5.1 released

[Jari Häkkinen]

A new version of BASE is available for download at
http://base.thep.lu.se/wiki/DownloadPage

Fixed issues are listed at
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.5.1


The Lund BASE team

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Re: [base] APT version 0.2 released

[Jari Häkkinen]

Nice work. I've successfully tested the apt-summarize plug-in. I do not 
have any genotype data so I have to leave that for someone else to test.

I miss a short description of the two plug-ins. How to use them and what 
to expect from them. Specifically the genotyoe plug-in requires some 
additional files (or one file). Is the chrx file alwasy the same for a 
given .cdf (array design in BASE speak)? If yes, maybe we should extend 
array design to also store the chrx file for seamless use. Also, should 
there be more than one Affy raw data type, one for expression and 
another for snp?

Jim Collet made an inquiry about support for 'apt-cel-extract' to the 
mailing list in the beginning of this year. How do we proceed to get 
this algorithm (and others) into the APT plug-in set?


Cheers,

Jari


Robin Andersson skrev:
> Hi all,
> 
> A plugin package for execution of the Affymetrix Power Tools 
> apt-probeset-summarize and apt-probeset-geneotype are available for 
> download from:
> http://madr.lcb.uu.se/browser/plugins/se/uu/lcb/APT/tags/0.2
> 
>  From this repository you can download a precompiled jar file or the 
> source code. See the INSTALL file for instructions. This package is a 
> suggested replacement of the affymetrix package including the Plier and 
> RMAExpress plugins.
> 
> Robin

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Re: [base] APT version 0.2 released

[Jari Häkkinen]

Regarding different Affymetrix type (snp and expression)

BASE 2.5 has implemented support for something called platform and 
variants to support different type of chips within a platform (see 
http://base.thep.lu.se/chrome/site/latest/html/userdoc/platforms/platforms.html).
 
In this case we have Affymetrix as platform and the variants could be 
'affymetrix' (for expression chips) and 'snp'. I think the 'affymetrix' 
variant cannot be changed since it is already used by the core. What 
variants are required is really up to the plug-in creator but in the 
current APT plug-in two are needed. I think it is wise to discuss these 
new features with the BASE core programmers before starting on platforms 
and variants for APT.

There is a parallel to this with the Illumina platform which we are 
working on here in Lund. We decided to add the Illumina support as an 
external plug-in, 
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina. The Illumina 
platform also have different variants and the variants required by the 
plug-in are created as a part of the plug-in installation. The plug-in 
is not ready yet but you can follow the progress through the plug-in site.

We are going to try the Affymetrix snp support of the APT plug-in here 
and will report our experiences with the Affy snp back to you. We'll 
probably also have some ideas on platforms and variants for you to when 
you switch to BASE 2.5.


Cheers,

Jari

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Re: [base] BASE2 backups

[Jari Häkkinen]

Hi,

We are working on a backup scheme here in Lund. We'll send a note when 
we have something that at least works. Then we can all improve our 
backup strategy ;-)

Why use svn? Do you need to track changes to files? For the userfiles 
directory a simple rsync should be fine, it is incremental (transfers 
only changes).


Cheers,

Jari


Bob MacCallum skrev:
> Hi all,
> 
> Does anyone have any genius solutions for backing up BASE2?  We're trying to
> get a major production server online and obviously backups would be quite
> useful.
> 
> I can do what we already do for BASE1: periodic full mysqldump and rsync of
> BASE's filestore to an off-site location.  That approach only allows me to
> restore to the latest full dump (to keep db and files in sync).
> 
> I wonder if subversion could be used to manage the "userfiles" directory
> in BASE2? (i.e. commit new files to svn at the same time as a mysqldump was
> done).  I suspect this is a heavier workload than svn was designed for.
> 
> A more incremental approach to backing up the db would be useful when we are
> in the tens/hundreds of gigs.  Maybe a slave mysql server?  Could that work
> reliably between two distant sites?
> 
> Any ideas?
> 
> cheers,
> Bob.
> 
> 

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Re: [base] upgrading BASE without restarting tomcat

[Jari Häkkinen]

I have no help on upgrading BASE without restarting tomcat but we are 
running several BASE server instances on one machine. Each BASE instance 
runs in their own tomcat instance . This allows us to change and update 
BASE servers independently of each other. Maybe this helps you? I can 
give you more information on  how to setup this if  you think it helps you.


Cheers,

Jari


Bob MacCallum wrote:
> I just opened a feature suggestion ticket on the subject of being able to
> upgrade base without restarting tomcat.  Currently it seems this is not
> possible, at least with my skills and knowledge.  The official base guidelines
> are to restart tomcat.
> 
> http://base.thep.lu.se/ticket/971
> 
> Maybe you know better?  Any nuggets of wisdom gladly received on the ticket
> page or mailing list.
> 
> cheers,
> Bob.
> 

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Re: [base] upgrading BASE without restarting tomcat

[Jari Häkkinen]

You only need port 80 (I think, see more below), the different servers 
are connected through different directories:

http://base2.thep.lu.se/demo
http://base2.thep.lu.se/base2

To get this going is simply creating a proper apache/tomcat connector 
configuration, and setting up tomcat. Internally this is done through 
different port numbers that isn't exposed outside of the server. I do 
not think the firewall interferes with these ports (need to be checked).


Jari


Bob MacCallum wrote:
> Thanks Jari.
> 
> That might be an option, although we don't have many ports open to the outside
> world (only 80 and 8080) and would like to stick with 80.  I assume your
> tomcat instances are on separate ports?
> 
> I haven't tried tomcat 6 yet.  Will do so if this matter becomes urgent (at
> the moment it would just be a luxury).
> 
> cheers,
> Bob.
> 
> Jari Häkkinen writes:
>  > I have no help on upgrading BASE without restarting tomcat but we are 
>  > running several BASE server instances on one machine. Each BASE instance 
>  > runs in their own tomcat instance . This allows us to change and update 
>  > BASE servers independently of each other. Maybe this helps you? I can 
>  > give you more information on  how to setup this if  you think it helps you.
>  > 
>  > 
>  > Cheers,
>  > 
>  > Jari
>  > 
>  > 
>  > Bob MacCallum wrote:
>  > > I just opened a feature suggestion ticket on the subject of being able to
>  > > upgrade base without restarting tomcat.  Currently it seems this is not
>  > > possible, at least with my skills and knowledge.  The official base 
> guidelines
>  > > are to restart tomcat.
>  > > 
>  > > http://base.thep.lu.se/ticket/971
>  > > 
>  > > Maybe you know better?  Any nuggets of wisdom gladly received on the 
> ticket
>  > > page or mailing list.
>  > > 
>  > > cheers,
>  > > Bob.
>  > > 
>  > 
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Re: [base] Luminex data

[Jari Häkkinen]

There is support for Illumina using the Illumina plug-in package, 
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina. Illumina is 
bead-based and maybe a similar package can be created for Luminex? So, 
BASE supports bead based data but luminex is currently not directly 
supported.


Jari


david vilanova wrote:
> Hello,
> Are there any plans to support luminex expression data based on beads ?
> The overall workflow for tracking the samples is the same, the only think
> that change is that instead of usign arrays, it would be beads.
> 
> If not , do you knwo of any available lims system for beads ?
> 
> 
> 
> 
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Re: [base] Which import plugins are available in BASE?

[Jari Häkkinen]

> Good Morning All,
> 
> I have a lot of Affymetrix array data that I would like to analyze together.
> The zip that contains these files is very big and I can't upload it to 
> BASE to use Batch Data Importer to import it into my experiment.

There is a known issue with files larger than 2GB, 
http://base.thep.lu.se/ticket/841

Is your file larger than 2GB? There is a thread related to this issue, 
http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg01464.html 
The resolution in this thread did not help the original poster but it 
might help you.


> It would  be beautiful if were possible to add to an experiment raw 
> bioassays that uses the same Array Design used by existing raw bioassays.
> Are there any plans to implement such a feature?


There is the batch data importer, 
http://baseplugins.thep.lu.se/wiki/uk.ac.scri.batchimporter, that you 
already refer to above. Also, there is the tab2mage importer, 
http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.Tab2MageImporter, but I 
think it is still immature.

We may have a look at the batch data importer in the future to see if we 
can improve and customize it for our core facility needs. However, I 
cannot give any time projections for this work.

In principle the current batch data importer should be usable even if 
smaller than 2GB files are used for data upload. Split the zip-file to 
reasonable size, use the plug-in. This will create a lot of raw 
bioassays and assign them to the experiment you selected to import from.


Jari

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Re: [base] lowess normalisation

[Jari Häkkinen]

Hi Bob,

We are looking into the issue. It looks like the BASE2 version of lowess 
is flawed. We are testing and reading publications to make sure that we 
make a proper fix. We already have a fix for the problem but want to 
make sure that we don't create new bugs. We plan to release a 2.7.2 ASAP 
with the fix.

Thank you for reporting this issue to us.


Jari


Bob MacCallum wrote:
> I've done some more tests on the lowess problem.
> 
> Please refer from now on to our development server:
> 
> http://base.vectorbase.org:8080/base2dev/
> Experiment: "Male vs. female (Koutsos et al., 2007)" 
> 
> I ran the base1 lowess plugin and got a very different result compared to the
> base2 plugin.  The base1 plugin results look correct to me.  The base2
> correction factor plots do not look at all right to me.
> 
> Can anyone hazard a guess as to if this is a bug or are the default parameters
> not suitable for my data?
> 
> Due to time pressures I think I'm going to have to switch all our analysis
> over to use the base1 plugin.
> 
> many thanks,
> Bob.
> 
> Bob MacCallum writes:
>  > 
>  > Has anyone had problems with the Lowess analysis plugin?
>  > 
>  > To me it looks like it is overcorrecting.  Where a M/A plot
>  > is largely below the zero line before normalisation, it ends
>  > up largely above it afterwards.
>  > 
>  > I'm using default values (including 0 for block group size).
>  > Default values were always fine in BASE1.
>  > 
>  > You can look for yourself with the guest login at
>  > http://fungen.vectorbase.org/base2
>  > 
>  > Experiment "Male vs. female (Koutsos et al., 2007)" is a good
>  > small example.
>  > 
>  > I don't see a recent ticket on this (I have not upgraded in
>  > a few months).
>  > 
>  > cheers,
>  > Bob.
>  > 
>  > 
>  > -- 
>  > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
>  > Division of Cell and Molecular Biology | Imperial College London |
>  > Phone +442075941945 | Email [EMAIL PROTECTED]
>  > 
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Re: [base] lowess normalisation

[Jari Häkkinen]

The problem is now being fixed, http://base.thep.lu.se/ticket/1077. 
Unfortunately this problem affects all versions of BASE2 and everyone 
are recommended to upgrade to the future 2.7.2 (or later).

The problem is localized and 2.7.2 will be released later today or at 
latest tomorrow. More details on the issue will follow in the 
announcement of the new release.


Cheers,

Jari


Bob MacCallum wrote:
> Has anyone had problems with the Lowess analysis plugin?
> 
> To me it looks like it is overcorrecting.  Where a M/A plot
> is largely below the zero line before normalisation, it ends
> up largely above it afterwards.
> 
> I'm using default values (including 0 for block group size).
> Default values were always fine in BASE1.
> 
> You can look for yourself with the guest login at
> http://fungen.vectorbase.org/base2
> 
> Experiment "Male vs. female (Koutsos et al., 2007)" is a good
> small example.
> 
> I don't see a recent ticket on this (I have not upgraded in
> a few months).
> 
> cheers,
> Bob.
> 
> 

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[base] BASE 2.7.2 released. Important bug fix included!

[Jari Häkkinen]

Hi all,

We have released BASE 2.7.2. The release includes important bug fixes
in the LOWESS plug-in shipped as a part of the BASE package. Some
other improvement are also included in the release.

It is highly recommended at all BASE installations where LOWESS is
used as a part of their analysis in BASE are upgraded to this
release. More details on the LOWESS problem is given below.

Note, we have not found any problems with the BASE1 lowess
implementation and analysis made with BASE1 lowess in BASE1 or BASE2
are still valid.

More information about the changes in 2.7.2:
http://base.thep.lu.se/query?milestone=BASE+2.7.2&group=resolution

Download from:
http://base.thep.lu.se/wiki/DownloadPage


We regret any inconvenience that the LOWESS bug may have caused,

The Lund BASE team



Text copied from the installation/upgrade chapter of the BASE
documentation, 
http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.upgrade.html

Bug in the LOWESS plug-in affecting BASE version 2.0 -- 2.7.1

This release fixes a serious bug in the LOWESS plug-in shipped as a
part of the BASE package. The bug is found in all BASE versions
between 2.0 and 2.7.1, and has caused incorrect normalization values
to be calculated. All data that has been normalized with the BASE2
LOWESS plug-in prior to BASE 2.7.2 should be considered invalid and
needs to be re-normalized with the fixed version. Downstream analysis
steps that has used the incorrectly normalized data also needs to be
redone. For more information about the bug see
http://base.thep.lu.se/ticket/1077

BASE 2.7.2 includes a utility for finding all experiments/bioassay
sets that includes data normalized with the LOWESS plug-in. An
administrator can use this utility to extract a list of all
experiments/bioassay sets that needs to be fixed. The utility can also
tag the name of the found experiments/bioassay sets with FIX LOWESS to
make it easier to find data that needs to be fixed.

The utility can't see any difference between data normalized with the
old version and the fixed version. It will simply report all data that
has been normalized with the LOWESS plug-in. Only use the utility a
single time right after the upgrade to BASE 2.7.2.

The utility is a command line program that should be executed on the
BASE application (web) server.

cd /bin
./onetimefix.sh lowess_warn -u  -p  -f

We recommend running the utility as the root user. The -f option is
optional. If it is included the found experiments/bioassay sets are
tagged with FIX LOWESS, otherwise only a list with the information is
generated.

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Re: [base] Plotting data from separate Bioassay sets against each other

[Jari Häkkinen]

The plotting in BASE is somewhat rudimentary and may sometime feel 
inadequate. However to create an impressive plot tool is a whole project 
   itself. If someone knows of a free plot tool it may be possible to 
integrate it to BASE in a similar fashion as MeV is integrated. Of 
course, this is lot of work and someone needs to volunteer to do the 
work. In the meantime, your plot can be realized with the current BASE 
using a plug-in available for download at the BASE plug-in site.

Download and install 
http://baseplugins.thep.lu.se/wiki/se.lu.onk.MergeBioAssay The plug-in 
will allow you to merge the bioassays to two averaged bioassays. These 
can the be merged another round with the same plug-in using the "ratio 
of ratio" average method. After the second merge you'll have one 
bioassay usable with the plot tool; plot ch1 vs ch2! Simple, isn't it!

I have not tested the above myself but it should work :-) I'll try it 
myself one day when I have time.

Other ways to move forward is to create the bioassayset containing your 
assays, export the matrix and use another plotting tool. Sometimes one 
have to accept the fact that one tool cannot do everything ... or write 
and share your own tool.


Cheers,

Jari


Jan Torleif Pedersen wrote:
>  Well I have one dataset - 10 control animals and another dataset 10
> treated animals each run on a single chip - so one bioassay set for each
> set of ten animals - now I just wanted to plot the average normalised
> signal in the control vs the average normalised signal in the treated
> group. Fairly common and trivial thing I should think. - But again -
> maybe there is something about the workflow that I do not properly
> understand ?
> 
> Jan
> 
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Nicklas
> Nordborg
> Sent: Friday, August 22, 2008 2:00 PM
> To: BASE ML
> Subject: Re: [base] Plotting data from separate Bioassay sets against
> each other
> 
> Jan Torleif Pedersen wrote:
>> Hi Nicklas,
>>
>> Well that is a clea answer. Does that mean I will have to merge all my
> 
>> data into a single raw datafile in order to be able to plot it within 
>> Base ?
> 
> You would end up with a single dataset and I don't understand how this
> would improve things. The plot functionality in BASE works on a single
> spot at a time. For example, you can plot ch1 against ch2 or M against
> A, etc.
> 
> 
> /Nicklas
> 
> 
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Re: [base] BASE 2.8 has been released

[Jari Häkkinen]

Hi,

I just uploaded a new version of the spreadsheet to the wiki. I think 
you should use that one instead. Some column names have changed so if 
you have created configurations for the previous sample file you need to 
update the configurations. The changes are from Array design and down to 
rawbioassays.


Jari


Bob MacCallum wrote:
> Dear Nicklas et al.,
> 
> This is fantastic news.  I am testing the new import plugin(s) now.
> 
> I have imported the documentation/demo spreadsheet into Google Docs and shared
> it to everyone here (so if you have no openoffice and no google account you
> can still read it):
> http://spreadsheets.google.com/ccc?key=pRS68LZhEttbUTcTRpn1EKw&hl=en
> 
> So far it's working great.  I've got biosources, samples and extracts all
> linked properly.
> 
> Is the protocol lookup always name-based?  Or can that be done with internal
> IDs (note to everyone: these can now be display in the list view).  It's
> working fine for me with the name, by the way.
> 
> Would it be trivial to have an option for "use project's default protocols"?
> 
> Would it also be possible to have the file parsing configuration saved
> somehow?
> 
> many thanks for this excellent advance.
> 
> cheers,
> Bob.
> 
> Nicklas Nordborg writes:
>  > Hello all,
>  > 
>  > We are happy to announce the release of BASE 2.8. This is major release
>  > adding several new features. One of the most important is a bunch of 
>  > batch import/update plug-ins that makes it possible to import data for 
>  > hundreds of items with a lot less effort than before. More information 
>  > about the batch import functionality is available in the documentation: 
>  > 
> http://base.thep.lu.se/chrome/site/latest/html/userdoc/import/import_data.html#import_data.batch
>  > 
>  > For a complete list of changes, see:
>  > http://base.thep.lu.se/query?status=closed&milestone=BASE+2.8
>  > 
>  > As usual, the program can be downloaded from:
>  > http://base.thep.lu.se/wiki/DownloadPage
>  > 
>  > Installation/upgrade instructions:
>  > 
> http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.html
>  > 
>  > /Nicklas
>  > 
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Re: [base] batch import/edit experiment items

[Jari Häkkinen]

When I was trying all these new imports I always work in one project. 
After importing the RasBioAssays, I simply select all rawbioassays in 
that project and create an experiment from the tab. And you get all 
rawbioassays automatically in that experiment.

If you have attached raw data files to your rawbioassays and are running 
affymetrix you should be set to create a root bioassayset immediately. 
No manual import is needed.


Jari


Nicklas Nordborg wrote:
> Well, we had to stop somewhere. Our use cases include importing hundreds 
> of samples, extracts, etc. down to raw bioassays, everything put into a 
> single (or at least only a few) experiments. Since the raw data import 
> also has to be done manually for each raw bioassay, we didn't see any 
> real benefit for importing experiments.
> 
> There is no technical limitation.
> 
> /Nicklas
> 
> Bob MacCallum wrote:
>> Hello,
>>
>> I was wondering why there is not an Experiment item importer, just like all
>> the other new importers?
>>
>> I was hoping to use it to create a bunch of experiments which all contain
>> details of the same publication.  (Export all columns from list view of
>> "master" experiment, duplicate row N times, change names, import data again.)
>>
>> Is there a technical reason, or did you not think there was a valid reason 
>> for
>> anyone to use it?
>>
>> cheers,
>> Bob.
>>
>> Bob MacCallum writes:
>>  > 
>>  > I've just loaded a 60-hyb Affy experiment on our production server using 
>> the
>>  > new import plugins.  Everything worked fine!  No RSI!
>>  > 
>>  > The only thing I am having to do manually is inherit biosources to raw
>>  > bioassays.  This is easy enough to do on the experiment page (shift click 
>> on
>>  > raw bioassay names).
>>  > 
>>  > great work BASE people!
>>  > 
>>  > thanks,
>>  > Bob.
>>  > 
>>  > 
>>  > -- 
>>  > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
>>  > Division of Cell and Molecular Biology | Imperial College London |
>>  > Phone +442075941945 | Email [EMAIL PROTECTED]
>>  > 
>>  > -
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> 
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Re: [base] How to connect to FTP server

[Jari Häkkinen]

Hi,

In ftp/config.xml the  tag there is a port property set to 
2121. I think this sets the port number. See 
http://baseplugins.thep.lu.se/browser/extensions/net.sf.basedb.ftp/trunk/ftp-config.xml#L29


Jari


Pawel Sztromwasser wrote:
> Hi all,
> 
> I have just upgraded to the latest BASE 2.8.2 and installed the base-FTP 
> server. Everything went smoothly, but I have one, little silly question: 
> how do I connect to the server? what is the address?
> 
> I have tried various combinations of the host name where BASE is 
> installed (with and without port number) and haven't managed to connect. 
>   I couldn't find anything in the ftp-config.xml and docs either. What 
> am I missing?
> 
> All the best,
> Pawel
> 
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Re: [base] Users can't login in

[Jari Häkkinen]

Hi,

Is there any information in the logs?


Jari


david vilanova wrote:
> Hello,
> I have upgrade from 2.7.0 to 2.8.2. Only the root login is allowed to
> connect. The rest of the users get a permission denied. I have tried to
> change the password to those users but they can't login anymore ??
> 
> Any idea what's wrong ??
> 
> 
> 
> 
> 
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> 
> 
> 
> 
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Re: [base] high-throughput transcriptome sequencing data

[Jari Häkkinen]

Hi Bob,

Sorry for not commenting your thoughs on storing sequencing data in 
BASE. We have discussed it here and will be looking into it later. This 
will become an issue for us also since we have sequencing equipment 
generating huge quantities of data. So far we are only getting friendly 
with the new machine.

I think we should add your thoughts to a ticket for further discussions. 
I hope we can be more active on this issue later this autumn. How urgent 
is this issue for you?

Regarding SNP-data and other arrays with huge quantities of information. 
We have decided to avoid storing this sort of data in the database 
tables, it would probably cripple BASE. We have prepared BASE during the 
last releases for storing raw data in files instead of the raw tables, 
and also to store data in files also when analysing the data, i.e. in 
the analysis tree. However, there is no plug-ins that take advantages of 
these new features but they will appear.

We are not currenlty working with Affymetrix SNP data wrt BASE. However, 
we now have the Affymetrix platform available at our department and may 
soon face the challenges of getting that data into BASE (it has not been 
decided to store that data in BASE yet). Maybe the Uppsala people has 
something on this, http://madr.lcb.uu.se/ ?

On our side we are interested in getting Illumina SNP data into BASE and 
have slow progress towards realising it but we expect that to appear 
during the winter. We are supposed to write a specification on how we 
want to see this in BASE but there is very little written so far.

If you are getting confused when I talk about experimental equipment at 
our department it is natural. I am at the Dept. of Oncology now but I am 
still using my old mailing address in this list.


Cheers,

Jari

Bob MacCallum wrote:
> Hi again.
> 
> Any thoughts on this (see below) at all?  Please reply off-list if you are
> feeling shy.
> 
> I'd also like to raise some general questions about scalability.
> 
> 1. Is anyone working on an Affymetrix SNP plugin?
> 
> 2. Is anyone doing anything with tiling arrays?
> 
> I realise that archiving the .CEL files is no problem.  Using BASE to run
> analysis programs on those files is possible through plugins.  But storing
> per-feature data in the analysis tables is going to break, when you have
> millions of features, right?
> 
> cheers,
> Bob.
> 
> Bob MacCallum writes:
>  > 
>  > I'm just thinking out loud about how to incorporate high throughput
>  > transcriptome sequencing data into BASE.  It's some way off, but I'm 
> assuming
>  > that it will be cheap and quantitative enough to replace arrays at some 
> point
>  > during the renewal period of our project (2009-2014).
>  > 
>  > 1. Create an "array design" with all genes of interest (ideally this would 
> be
>  >the largest set possible, e.g. known genes + predicted genes of all
>  >qualities, perhaps even predicted genes from the new sequence data).  
> The
>  >layout would be fictitious, of course (what's the minimum one can get 
> away
>  >with?).
>  > 
>  > 2. Create a rawbioassay to correspond to each sequencing run.
>  > 
>  > Then *one* of 3a/b/c for each sequencing run/rawbioassay:
>  > 
>  > 3a. Outside BASE, align the new sequences to genome or transcript sequences
>  > and calculate "intensities" for each gene on the "array design" and 
> dump
>  > into a tab delimited raw data file.  Attach that file to the 
> rawbioassay
>  > and import numeric data as usual.
>  > 
>  > 3b. Upload the text file of sequences to the raw bioassay's "data file".
>  > Create a BASE plugin to do the the alignment and quantification as in 
> 3a,
>  > and load the numeric data into the database.
>  > 
>  > 3c. Similar to 3b, but calculate the intensities at the "create root 
> bioassay"
>  > step, similar to the Affymetrix RMA plugin.
>  > 
>  > 4. continue with analysis as normal.  biosources, samples etc can be 
> linked to
>  >the bioassay too, of course.
>  > 
>  > I guess a new raw data type (for "Generic" platform) would have to be
>  > created for 3a (and 3b?) but that's not difficult.
>  > 
>  > Is it possible to go with 3a, but also attach the sequence file to the raw
>  > bioassay (or scan?) - something like keeping tiff files for scans?  Just 
> for
>  > documentation purposes.
>  > 
>  > Any thoughts from the community or developers?
>  > 
>  > cheers,
>  > Bob.
>  > 
>  > -- 
>  > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
>  > Division of Cell and Molecular Biology | Imperial College London |
>  > Phone +442075941945 | Email [EMAIL PROTECTED]
>  > 
>  > -
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>  > htt

Re: [base] high-throughput transcriptome sequencing data

[Jari Häkkinen]

There is a cc field for tickets. This will generate email to the listed 
mail addresses when the ticket changes but the drawback is that the mail 
addresses are visible for everyone.


Jari


Nicklas Nordborg wrote:
> Bob MacCallum wrote:
>> Is there any way for me to subscribe to this ticket (get email updates when
>> changed)?
> 
> If you have a RSS enabled mail client/browser/other program, you can use 
> the "RSS feed" link at the bottom of that page.
> 
> /Nicklas
> 
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Re: [base] BASE on OS X server

[Jari Häkkinen]

Hi all,

You should definitely go for 10.5. I am working with BASE on my 10.5 
equipment MacBook Pro and it is performing well. As Emil pointed out the 
installation document really tells you the story of getting BASE running.

Details on software other than BASE:

I have installed a Java-6beta for Mac
#~> java -version
java version "1.6.0_07"
Java(TM) SE Runtime Environment (build 1.6.0_07-b06-153)
Java HotSpot(TM) 64-Bit Server VM (build 1.6.0_07-b06-57, mixed mode)

I am running tomcat-6.0.16 downloaded from the tomcat web site.

I run MySQL 5.something installed with 'port'. Go to 
http://www.macports.org/ and download the port dmg, install it, issue 
'sudo port install mysql5'. Tomcat-6 is not provided through port yet.

And, then I just followed the install instructions with the below 
amendment. I should say known amendments since I am recalling my 
installation procedure from memory.

In preparation for 2.9 you should actually set default character 
encoding to UTF-8 for your database. This will be a requirement from 2.9 
and later. Simply use these database creation steps:

MySQL:

CREATE DATABASE base2 DEFAULT CHARACTER SET utf8;
CREATE DATABASE base2dynamic DEFAULT CHARACTER SET utf8;

Postgres:
createdb --owner db_user --encoding UTF8 base2


Good luck and welcome to BASE,

Jari


Emil Lundberg wrote:
> Hi,
> 
> We've been running BASE on Mac hardware for a few years and the 
> installation process is pretty straightforward (these days :-).  We are 
> not, however, currently up to the versions requiring Java 6 (our 
> production system is still on 10.4 though this is due to change 
> anydayrealsoon), so I can only speculate on that. Following the BASE 
> installation guide works really well AFAIK, although it really help if 
> you know what you are doing...
> 
> http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.installation.html
>  
> 
> 
> Some OS X pointers below. We can go into detail if need be, but I don't 
> want to start lecturing on stuff you already know ;-)
> 
> If you have access (or an upgrade path to) an OSXS 10.5/Intel/64-bit 
> setup, please go ahead and use it, as the versions of mysql and tomcat 
> are up to date and (likely) fresh enough to be used for BASE. Configure 
> and activate the MySQL and Tomcat (checkbox under Web) services in the 
> GUI and Bob's your uncle (sort of).
> 
> If you want to run it on older hardware (PPC or 32-bit), 10.5 still 
> helps. I do recall being told that BASE does not actually make use of 
> Java 6, it's just that they don't test on any older releases anymore, 
> but I'll let the BASE folks comment on that. You will have to "compile" 
> BASE yourself though (see docs above, but basically "ant package.bin" in 
> the source root, then follow the standard install instrux).
> 
> If you want to run it on 10.4, you will also have to install more 
> up-to-date versions of mysql and tomcat. We use the MacPorts system 
> (http://www.macports.org/), this highly recommended even if you don't 
> want to run BASE. Install 1.6 from the disk image, then add msql and 
> tomcat like so (add stuff under /opt/local):
> 
> $ sudo -s
> 
> # sudo port install mysql5 +server
> # sudo -u mysql mysql_install_db5
> # cp -p /opt/local/share/mysql5/mysql/my-huge.cnf 
> /opt/local/etc/mysql5/my.cnf
> # launchctl load -w /Library/LaunchDaemons/org.macports.mysql5.plist
> # mysqladmin5 -u root password "mysqlrootpassword"
> 
> # port install tomcat5
> # cp -p /opt/local/share/java/tomcat5/conf/setenv.local.sample \
> /opt/local/share/java/tomcat5/conf/setenv.local
> : edit setenv.local :
> export JAVA_JVM_VERSION=1.5
> JAVA_OPTS="-jvm server -Xms256m -Xmx1024m -Djava.awt.headless=true"
> # cp -p /opt/local/share/java/tomcat5/conf/tomcat-users.xml.sample \
> /opt/local/share/java/tomcat5/conf/tomcat-users.xml
> : edit tomcat-users.xml :
> 
> 
> 
> 
>  roles="admin,manager"/>
> 
> # tomcatctl restart
> 
> Further/up-to-date instructions (changing data root, creating the db's 
> etc) should be provided by the output of the "port install" commands. 
> N.B. MacPorts does not currently provide a tomcat6 port, but as with 
> Java, likely the latest 5.5 is OK (BASE guys?).
> 
> Best Regards & HTH,
> 
> Emil / [EMAIL PROTECTED]
> 
>> BASE looks like just what we need, but we have OS X servers, one 
>> running 10.4 and one running 10.5.  Has anyone succeeded in getting it 
>> running on either of these platforms, and does anyone have a recipe?  
>> I spent a little time on the 10.4 server today, but there seems little 
>> chance of me getting the 1.6 SDK and the relevant version of Tomcat 
>> working there.  Has anyone done it on 10.5?
>>
>> Thanks in advance.
>>
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