[Biojava-l] GSOC 2011 - contributing to 'Amino acids physico-chemical properties calculation project'
Shameera Rathnayaka
shameerainfo at gmail.com
Mon Mar 28 09:56:32 UTC 2011
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> 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>
> 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 due to the following
> > error
> >
> > " A socket operation was attempted to an unreachable host.
> > svn: Can't connect to host '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 04:30, 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>> 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>: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>> 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
> > 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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