Hi Shameera,
You need to email the Jar file to me or to [email protected]
The exercise page is now updated too -
http://biojava.org/wiki/Short_coding_exercise#Submission
Thanks for the question!
Regards,
Peter
On 28/03/2011 10:56, Shameera Rathnayaka wrote:
Hi Peter and Andreas,
I was able to check out the source using GIT.
I have already implemented the short coding exercise for 'Amino acids
physico-chemical properties calculation project' but as i noticed
there is not any link given to submit the assignment. I need to know
that where should i submit it , or do i have to submit it with my
project proposal?
Thanks in advance!
On Fri, Mar 25, 2011 at 9:11 PM, Andreas Prlic <[email protected]
<mailto:[email protected]>> wrote:
I removed the checkout instructions from the broken anonymus SVN
repository. The recommended way to check out the code is now via
github, either using SVN or GIT...
Andreas
On Fri, Mar 25, 2011 at 6:40 AM, Peter Troshin
<[email protected] <mailto:[email protected]>> wrote:
> Dear Shameera,
>
>>>>As i felt it is required some knowledge about BioSQL so is it
a good
>>>> point to start my next step????
>
> I am sorry but I do not see how BioSQL relates to this project.
Perhaps more
> explanation from your side would have helped me to see the
connection.
>
>>>>I have some problem with checkout and installing BioJava3
>
> Me too, I was unable to checkout the BioJava Live from
> svn://code.open-bio.org/biojava/biojava-live/trunk
<http://code.open-bio.org/biojava/biojava-live/trunk> due to the
following
> error
>
> " A socket operation was attempted to an unreachable host.
> svn: Can't connect to host 'code.open-bio.org
<http://code.open-bio.org>': A socket operation was
> attempted to an unreachable host. "
>
> However, a git read-only mirror
http://svn.github.com/biojava/biojava.git
> seems to work fine, at least I was able to checkout the project.
> So I'd suggest you to try that.
>
>>>>2. And i downloaded biojava3(v3.0.1) tar.gz and extracted it,
as in the
>>>> Biojava : started says i want to set the CLASSPATH variable as
>
> Have you downloaded biojava-all package from
> http://biojava.org/download/bj3.0.1/biojava3.0.1-all.tar.gz or
was this
> something else? I cannot really comment on that one, as I have
never tried
> this. I am coping this message to the BioJava list let’s see if
someone else
> is aware of any problems with this package.
>
>
> I hope this helps.
>
> Regards,
> Peter
>
>
> On 25/03/2011 04 <tel:25%2F03%2F2011%2004>:30, Shameera
Rathnayaka wrote:
>>
>> Sorry for the delay,
>>
>>
>> I went through some sources and got a basic understanding of
the project,
>> and I referred some links in the cookbook also.As i felt it is
required some
>> knowledge about BioSQL so is it a good point to start my next
step????
>>
>> I have some problem with checkout and installing BioJava3
>>
>> 1. I logged in using openid log in and tried to checkout via
Developer
>> SVN, but it is asking password for three times and then shows
"svn: Network
>> connection closed unexpectedly" then i used a USB modem but it
gives same
>> result.
>>
>> 2. And i downloaded biojava3(v3.0.1) tar.gz and extracted it,
as in the
>> Biojava : started says i want to set the CLASSPATH variable as
"export
>> CLASSPATH=/home/thomas/
>>
>>
biojava-live.jar:/home/thomas/bytecode.jar:/home/thomas/commons-cli.jar:/home/thomas/commons-collections-
>>
2.1.jar:/home/thomas/commons-dbcp-1.1.jar:/home/thomas/commons-pool-1.1.jar:."
>> </home/thomas> change according to my directory, in UNIX
Bourne-type shells,
>> but i couldn't find those .jar files in my directory.
>>
>> Thanks
>>
>>
>> On Tue, Mar 22, 2011 at 6:25 PM, Peter Troshin
<[email protected] <mailto:[email protected]>
>> <mailto:[email protected]
<mailto:[email protected]>>> wrote:
>>
>> Hi Shameera,
>>
>> >>>Yes as you said, equations are not the case. But i needed to
>> know will the equations be provided or not :)
>>
>> No one asks you to devise the equations yourself all you need is
>> to be able to read the paper and get the equation out of it.
>> Please note that this is YOUR project and a mentor is there to
>> help but not to provide everything for you. I think the
equations
>> are not hard to find besides if I just give you the
equations you
>> will not understand them thoroughly. As I said before you
need to
>> read the papers and by the source I meant the papers not the
>> source code. If this is something that sounds too hard for you
>> then, you may want to reconsider your decision contributing to
>> BioJava project. BioJava is not only about Java but about
Biology
>> as well. Ability and will to find the information you need is a
>> crucial for the success in any project.
>> In addition to it there are plenty of implementations for the
>> method that you set to implement. My advice to you would be to
>> Google for molecular weight, extinction coefficient, instability
>> index etc. I am sure you will find plenty of information on
these
>> topics.
>>
>> To get you started I am giving you the link to the software that
>> calculates half of the properties you need. There are
formulas and
>> plenty of documentation
http://expasy.org/tools/protparam-doc.html
>>
>> But please next time come back with a little more specific
questions.
>>
>> P.S. I do not envisage any GUI interfaces for the library
you want
>> to develop however, as a student you are free to propose this if
>> you think this would be of benefit to the project.
>>
>> Regards,
>> Peter
>>
>>
>> On 21/03/2011 17 <tel:21%2F03%2F2011%2017>
<tel:21%2F03%2F2011%2017>:32, Shameera Rathnayaka
>> wrote:
>>>
>>>
>>> Yes as you said, equations are not the case. But i needed
to know
>>> will the equations be provided or not :)
>>> And also i'm willing to see those equations. Could you please
>>> help me to find out those equations,
>>> then i could figure it out how to apply multi-threading
>>> technology to speed up the process.
>>>
>>> As i think i need to also develop a GUI except to the methods
>>> isn't it???
>>>
>>>
>>> <Also I believe that you are much better off reading the
sources and
>>> understanding how these things work>
>>>
>>> Yes now im referring to biojava source code . But im in a
little
>>> bit confusion about how to get a start and where the start
should
>>> be?
>>>
>>>
>>> On Mon, Mar 21, 2011 at 4:52 PM, Peter Troshin
>>> <[email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>> wrote:
>>>
>>> Hi Shameera,
>>>
>>>
>>> >>> As a
>>> starting point to
>>>
>>> the project i would like to know about the
>>>
>>>
>>>
>>> >>> Equations which are needed to these
>>> calculations, how
>>>
>>> can i get
>>>
>>>
>>>
>>> >>> those and more about the project.
>>>
>>> It is good that you are interested in the project.
>>> Did you try to find the formula yourself? I will be
happy to
>>> help you if you cannot find them, but really
>>> this must not be hard. Also I believe that you are much
>>> better off reading the sources and
>>> understanding how these things work than just have a
formula.
>>>
>>> Regards,
>>> Peter
>>>
>>>
>>> On 19/03/2011 17:22, Shameera Rathnayaka wrote:
>>>
>>> > hi,
>>>
>>>
>>>
>>> >
>>>
>>>
>>>
>>> > Im Shameera Rathnayaka, a third year Undergraduate
>>> of
>>>
>>> Department of
>>>
>>>
>>>
>>> > Computer Science and Engineering University of
>>> Moratuwa ,Sri
>>>
>>> Lanka.I
>>>
>>>
>>>
>>> > am interested in implementing "Amino acids
>>> physico-chemical
>>>
>>>
>>>
>>> > properties calculation" project as my GSOC 2011
>>> project.I
>>>
>>> have
>>>
>>>
>>>
>>> > previous experience in working with Java, MySql and
>>>
>>> Algorithms from
>>>
>>>
>>>
>>> > my university projects. As my most recent project i
>>> have
>>>
>>> developed a
>>>
>>>
>>>
>>> > visual navigation
>>>
>>>
>>>
>>>
>>> >
>>>
>>>
>>>
(XVisualNavigator<http://extensions.services.openoffice.org/en/project/XVN>)
>>>
>>>
>>>
>>> >
>>>
>>>
>>>
>>> >
>>> plugin for openoffice 3.2.1 using java. I am Currently
>>> working as an intern
>>> > at WSO2
>>>
>>> <http://wso2.com/?comwblink=menu>
>>> which is an open source
>>>
>>>
>>>
>>> > middle-ware development company.
>>>
>>>
>>>
>>> >
>>>
>>>
>>>
>>> > As a starting point to the project i would like to
>>> know about
>>>
>>> the
>>>
>>>
>>>
>>> > Equations which are needed to these calculations,
>>> how can i
>>>
>>> get those
>>>
>>>
>>>
>>> > and more about the project.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> -- Shameera Rathnayaka
>>> Undergraduate
>>> Department of Computer Science and Engineering
>>> University of Moratuwa.
>>> Sri Lanka.
>>> T.P. 0719221454
>>
>>
>>
>>
>> --
>> Shameera Rathnayaka
>> Undergraduate
>> Department of Computer Science and Engineering
>> University of Moratuwa.
>> Sri Lanka.
>> T.P. 0719221454
>
> _______________________________________________
> Biojava-l mailing list - [email protected]
<mailto:[email protected]>
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
--
Shameera Rathnayaka
Undergraduate
Department of Computer Science and Engineering
University of Moratuwa.
Sri Lanka.
T.P. 0719221454
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