nd 3.9 versions are not making any major changes to the
> database so I think it should be possible to go directly from 3.7 to 3.9.
>
> /Nicklas
>
>
> On 2016-08-05 15:28, Bob MacCallum wrote:
> > Dear BASE guys,
> >
> > I got the error below with updatedb.sh
&
Dear BASE guys,
I got the error below with updatedb.sh
I've had a look at Update.java and I'm afraid the hibernate stuff is
outside my comfort zone...
Please could you let me any further information you need to diagnose?
cheers,
Bob
[72%]--Creating platforms...
[73%]--Creating news...
Thanks Nicklas,
Most awesome!
On Thu, May 12, 2016 at 12:02 PM, Nicklas Nordborg <
nicklas.nordb...@med.lu.se> wrote:
> On 2016-05-12 12:24, Bob MacCallum wrote:
> > Dear BASE developers,
> >
> > It's really great that Experiments can have annotations now (I kno
Dear BASE developers,
It's really great that Experiments can have annotations now (I know,
already for several years...).
Would it be possible to add these as configurable columns in Experiment
list view?
I can add the Trac ticket if you remind me privately of the login info.
many thanks,
Bob
-
Hi Nicklas et al,
Will there be a "Third generation" BASE paper we can cite any time soon?
Happy to continue to cite the 2009 paper but I was just wondering!
cheers,
Bob
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Want excitement?
Manually upgrade your production
Thanks Nicklas,
Sorry I hadn't seen the existing functionality - we will check it all out
and get back to you soon!
On Tue, Jun 24, 2014 at 12:42 PM, Nicklas Nordborg <
nicklas.nordb...@med.lu.se> wrote:
> On 2014-06-24 11:55, Bob MacCallum wrote:
> > Hi Nicklas et al,
&
Hi Nicklas et al,
Getting up to speed with BASE3 and NGS - so far all seems good - even
upgrading our own API code has gone smoother than I expected. Thanks!
A possible feature request for general discussion:
Would it be possible to have "placeholder" files in the BASE file system
which weren't
ut for some reason it has been
> overlooked. It should be easy enough to implement this, and I can
> probably fix this for the next (BASE 3.3) release.
>
> But for now, the importer will choke on anything that is not a "Field"
> line as described by http://www.ensembl.org
Hi all,
[mods please delete the mail I sent from my gmail account, or add me with
that account but with no delivery, thank]
Just upgraded from 2->3 and now trying out the NGS feaures. Quick question
about GTF import for array designs...
When doing array design->import the importer is complainin
ion!
On Tue, Oct 9, 2012 at 3:46 PM, Bob MacCallum
wrote:
> Getting closer - I have set up a custom dialect:
>
> package org.vectorbase.funcgen.hibernate;
> import org.hibernate.Hibernate;
> import org.hibernate.dialect.MySQLInnoDBDialect;
> import org.hibernate.dialect.fu
ike Nicklas has seen this before :-)
https://forum.hibernate.org/viewtopic.php?f=1&t=994753
I reckon I'll get it to work sooner or later.
cheers,
Bob.
On Tue, Oct 9, 2012 at 2:15 PM, Bob MacCallum
wrote:
> Hi Nicklas,
> Thanks very much for the quick reply. I am *so* close to getting
12:50 PM, Nicklas Nordborg wrote:
> On 2012-10-09 13:11, Bob MacCallum wrote:
>> Hi all,
>>
>> I'm trying to get a Reporter query from the BASE2.x API which is
>> basically "ORDER BY RAND(123)" - to get reproducible "random" order (I
>
Hi all,
I'm trying to get a Reporter query from the BASE2.x API which is
basically "ORDER BY RAND(123)" - to get reproducible "random" order (I
can explain *why* in another email if anyone cares to know).
I tried this
DataQuery repQuery =
net.sf.basedb.core.Reporter.getQuery();
repQuery.order(O
More feedback:
I've extensively used the "no column"->"use project default"
functionality, and I think it's logical to do it that way, but the
expression-based enhancement sounds like a good next step forward.
On Tue, Oct 25, 2011 at 1:01 PM, Nicklas Nordborg wrote:
> On 2011-10-25 09:45, Pawel
On Tue, Oct 25, 2011 at 12:16 PM, Nicklas Nordborg wrote:
> On 2011-10-25 09:22, Pawel Sztromwasser wrote:
>> Hi
>>
>> Working with the MageTab export I have noticed that it would be great to
>> have additional properties for experiments that could hold MGED Ontology
>> annotations, e.g. Experimen
On Tue, Sep 27, 2011 at 1:51 AM, Nicklas Nordborg wrote:
> On 2011-09-26 22:19, Bob MacCallum wrote:
>> Hi Nicklas et al,
>>
>> I've been scanning the 3.0 alfa documentation and have seen how
>> biomaterials are handled with respect next gen (with the new library
Hi Nicklas et al,
I've been scanning the 3.0 alfa documentation and have seen how
biomaterials are handled with respect next gen (with the new library
type).
However, I can't see how raw data and analysis works. Do the concepts
of reporters and array designs still apply? I'm happy to install and
Help, can anyone explain? In BASE 2.12.2pre I'm getting the following
exception thrown, despite the issue being addressed way back in 2.4
http://base.thep.lu.se/changeset/3703
http://base.thep.lu.se/ticket/743
net.sf.basedb.core.BaseException: For input string: "1.10E+03" on line
11 in file 'GSM4
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>
Another idea might be to use Javascript to highlight the
just-edited-with-shift-click list entry somehow. That would make it easier to
process a list in this way without missing an entry.
Nicklas Nordborg writes:
> Bob MacCallum wrote:
> > It's not possible to show inherited
net/sfu/www-adobe-com
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em" button
I don't know if it's easy to implement, but somehow the GUI would know that it
had come from a list view and display the buttons:
[first |<] [previous <] [next >] [last >|]
Many mail readers do this kind of thing.
It would be much appreciated if you could add
'AgeX' (or whatever)
create new floating point annotation Age
reannotate as necessary
delete AgeX annotations
delete AgeX annotation type
check experimental factors and inherited annots are still OK.
Also, does the Annotation importer handle units yet?
cheers,
Bob.
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; SourcForge Community
> >> SourceForge wants to tell your story.
> >> http://p.sf.net/sfu/sf-spreadtheword
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> >> basedb-users@lists.sourceforge.net
> &g
>
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&
oblem will go away, right?
(Because this other BASE instance doesn't need to run jobs.)
So actually the default protocols work perfectly from the bulk import plugins.
Sorry for any trouble!
Nicklas Nordborg writes:
> Bob MacCallum wrote:
> >
> > As an admin user, I creat
working properly yet.
The workaround is for me to add the protocols to the bulk import text file(s),
but I was hoping not to have to do this.
regards,
Bob.
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Phone +442075941945 | Email [E
Nicklas Nordborg writes:
> Bob MacCallum wrote:
> > For two colour designs, we usually only inherit from the "experimental"
> > biosource. (Explanation: an experimental samples might be annotated as
> > "Infected with E. coli", "Infected wi
(ch1) and which is control (ch2). BASE will later
choose one arbitrarily (in Experiment Explorer for example).
Could the rawbioassay importer have a "Biosource to inherit annotations
from" column?
cheers,
Bob.
--
lly, of course, 1 & 2 together.
Does anyone know a workaround?
many thanks,
Bob.
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Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442
Y"? Given some
recent developments in the schema and no indications in the main
documentation, I would appreciate some guidance.
many thanks,
Bob.
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Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial
Hi again,
I saved you the trouble of cutting and pasting to make a new ticket:
Handling short read transcript sequence data
http://base.thep.lu.se/ticket/1153
Is there any way for me to subscribe to this ticket (get email updates when
changed)?
cheers,
Bob.
--
Bob MacCallum | VectorBase
but there is very little written so far.
>
I'll see what we can do if/when we have some Affy SNP data in the coming
months. I imagine file-based analysis plugins are not too difficult to
implement.
many thanks again.
cheers,
Bob.
>
> Bob MacCallum wrote:
> > Hi again.
g 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 ou
rse.
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
docu
users (or perhaps webservices clients) on your
BASE instance you might find this is the explanation behind the site hanging
for your users.
cheers,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +44
w 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:
> >>
cate 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 plu
nice workaround, hadn't thought of that.
thanks!
Nicklas Nordborg writes:
> Bob MacCallum wrote:
> > Now that the GUI is maturing nicely (I love the auto-configure button for
> > setting the file parser column mappings, select all button for bioassays,
> > column
ithin the "select file to import" dialogue. At the moment it doesn't seem
possible and I have to interrupt my work flow to go to the file browser to
perform the replacement, then go back to the list view.
This has been bugging me for a while!
many thanks,
Bob.
--
Bob MacCallum |
assay 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 PROT
nged 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.,
> &g
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&g
; 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/base2de
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 end
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.
ut file it seems
to leave the existing annotations untouched. Is there a special "NULL" value
I can put in the input file?
cheers,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +
y use anyway: verify
annotations by showing them as columns in the list view, and I always press
the refresh button after the plugin has finished (like you do with the
analysis pipeline).
cheers,
Bob.
--
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Division of Cell a
://poi.apache.org/).
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iver com.mysql.jdbc.Driver (version 5.0)
Java runtimeJava(TM) SE Runtime Environment (1.6.0-b105), Sun Microsystems
Inc.
Operating systemLinux amd64 2.6.16.54-0.2.5-smp
Memory Total: 108.4 MB
Free: 22.6 MB
Max: 910.3 MB
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biosources, this would save a lot of GUI work
(prior to the MAGE-TAB importer being completed)
I could imagine project defaults would be suitable for some of the item
attributes, otherwise they could be empty of course.
many thanks,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Chr
e an optional flattened view in the
Files browser. Then the filters (removed,owned by others) could work on
everything at once.
While we are on the subject of a GUI wish-list: would a
"File->New->Biosource/Sample/Extract..." menu be of use to anyone?
At the moment one must go to th
239;13503038;w?http://sf.net/marketplace___
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Bob MacCallu
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 a
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 suggest
know better? Any nuggets of wisdom gladly received on the ticket
page or mailing list.
cheers,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED
as a workaround. Note/tip: if you need to provide a "shared"
directory for all users to read it has to be under /home/ and of course have
Everyone read/use permissions.)
I'm running 2.6.2pre (==2.6.1) on a pretty standard system.
cheers,
Bob
Nicklas Nordborg writes:
&g
o take ownership of these items?
many thanks,
Bob
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
--
,
Bob.
Nicklas Nordborg writes:
> Bob MacCallum wrote:
> > Thanks for all the ideas on this.
> >
> > re: userfiles/db sync, would this work..?
> >
> > backup:
> >
> > 1. mysqldump to date-stamp-named files
> > 2. rsync -arv /data/base2/file
excellent, thanks, will try that.
Nicklas Nordborg writes:
> Bob MacCallum wrote:
> > Hi,
> >
> > I'm trying to import some ChipSkipper data into BASE2.6. While configuring
> > the raw data importer I see that the files all have different column
>
ow if this works in BASE2.
Has anyone else run into this type of problem?
cheers,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL
Nicklas Nordborg writes:
> Bob MacCallum wrote:
> > deleted in BASE. I doubt these would interfere with the running of BASE
> > however. A small program could be written to delete any files that are not
> > known about by the db (unless there is already something t
rosoft
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ample), then backups could be made while
people still browsed
(or would mysqldump --lock-tables achieve basically the same thing?)
cheers,
Bob.
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orkload 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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Ah yes, I see this appears (in the expression builder) after I have made a
reporter list. Thanks.
Nicklas Nordborg writes:
> Bob MacCallum wrote:
> >
> > Also, can reporter lists be used in filter expressions in BASE2?
>
> Yes. They should show up in the expression
lists.sourceforge.net
> > unsubscribe: send a mail with subject "unsubscribe" to
> > [EMAIL PROTECTED]
> >
>
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paste/upload them into
BioMart. I could export a MEV or BASEfile but this would be overkill.
Also, can reporter lists be used in filter expressions in BASE2?
many thanks,
Bob
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Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial
ld make lots of reporter lists and do this (although I never actually
did).
many thanks,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
---
Thanks for this.
The "column restriction" formula type seems to work for me here.
Nicklas Nordborg writes:
> Bob MacCallum wrote:
> > Hi,
> >
> > Could someone just point me roughly in the direction of how
> > to save an analysis filter preset? I ca
stance, as this
saves a lot of hassle when upgrading BASE on our test server. For production
purposes we could figure out some way of maintaining different versions of
base.config (with jobqueue.internal.enabled = false) for all but the main web
instance.
cheers,
Bob.
--
Bob MacCallum |
ot only one result - no more duplication!
On starting one tomcat and BASE-related webapp again I still don't get
duplication.
I'll post back here again if we see duplication again and can recreate the
conditions. In the meantime, all seems OK again.
cheers,
Bob.
>
> /Nickla
Hi,
Could someone just point me roughly in the direction of how
to save an analysis filter preset? I can't seem to figure
it out myself...
many thanks,
Bob.
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Division of Cell and Molecular Biology | Imperial Co
p
Memory Total: 474.6 MB
Free: 238.2 MB
Max: 910.3 MB
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Phone +442075941945 | Email [EMAIL PROTECTED]
---
Hello BASEers
If I add two labeled extracts to a hyb (e.g. two colour array), there is only
one box for the "used" amount. Does this mean that hyb'ing different amounts
for each channel is not possible (in BASE)?
many thanks,
Bob.
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d you ever have two or more experimental factors that should not be
treated in this manner? I can't think of a scenario off the top of my head.
cheers,
Bob.
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Division of Cell and Molecular Biology | Imper
d a browser.
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> ==
>
>
> > -Original Message-
> > From: [EMAIL PROTECTED] [mailto:basedb-users-
> > [EMAIL PROTECTED] On Behalf Of Bob MacCallum
pping through log files to find problems? Stop.
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lution 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
> > t
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:
>
> >
&g
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,
> >>
>
can work with the PNGs and assorted text files.
many thanks,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +44
Problem temporarily solved!
"clear filter" in the view/presets menu clears the problem
(although I had previously cleared all the filters manually)
I forgot to mention that the error appears in a big red box
above the list table.
Bob MacCallum writes:
>
> Hi,
>
> I
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