[Biojava-l] GSOC 2011 - contributing to 'Amino acids physico-chemical properties calculation project'

Peter Troshin p.v.troshin at dundee.ac.uk
Mon Mar 28 10:37:39 UTC 2011


Hi Shameera,

You need to email the Jar file to me or to gsocexercise at gmail.com

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 <andreas at sdsc.edu 
> <mailto:andreas at sdsc.edu>> 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
>     <p.v.troshin at dundee.ac.uk <mailto:p.v.troshin at dundee.ac.uk>> 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
>     <p.v.troshin at dundee.ac.uk <mailto:p.v.troshin at dundee.ac.uk>
>     >> <mailto:p.v.troshin at dundee.ac.uk
>     <mailto:p.v.troshin at dundee.ac.uk>>> 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
>     >>> <p.v.troshin at dundee.ac.uk <mailto:p.v.troshin at dundee.ac.uk>
>     <mailto:p.v.troshin at dundee.ac.uk
>     <mailto:p.v.troshin at dundee.ac.uk>>> 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  - Biojava-l at lists.open-bio.org
>     <mailto:Biojava-l at lists.open-bio.org>
>     > 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




More information about the Biojava-l mailing list