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
<[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>: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]>> 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]
http://lists.open-bio.org/mailman/listinfo/biojava-l
