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 <[email protected]> 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 <[email protected]> > 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 < > [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 > > > -- 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
