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

[Peter Troshin]

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