[Biojava-l] GSOC 2011 - contributing to 'Amino acids physico-chemical properties calculation project'
Peter Troshin
p.v.troshin at dundee.ac.uk
Fri Mar 25 13:40:43 UTC 2011
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
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