[BiO BB] Re: Bioinformatics Project
Gary Van Domselaar
gary at www.bioinformatics.org
Wed Jul 30 10:51:55 EDT 2003
You might want to check out 'Librarian'
Librarian is a free tool for self-creation of virtual annotated library of
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On Wed, 30 Jul 2003, Dan Bolser wrote:
> Srivatsan Pallavaram wrote:
> > Hi all,
> > This open source projects, forum like environment, links, papers, etc sounds
> > like a great idea to me. I am game!
> > Srivatsan Pallavaram
> > ---
> I started working on a 'journal magement system' in PHP,
> maby this would be a good inital project to start to help
> The implemented system uploads a journal in pdf / ps
> format and then converts the document to text.
> The text of the document is then displayed alongside
> a form, to help the user fill in the various fields
> i.e. author, title, date, journal, etc.
> Then there is another form to handle
> multiple authors ....
> Thinking about this it is really clunky - we could have
> a system to query MEDLINE and parse the reference
> tag into a local database of journals. Can we do this with
> PHP? I.E. PHP - SOAP?
> I started to implement browsing of the database, but
> didn't get very far. I am sure there is plenty of stuff
> we could take from 'on line shopping' modules.
> Searching, reader comments and ratings need to be
> implemented, as well as a system to link various
> journals with various projects / sub sections of
> In this way you could click on a project, and search
> all the associated papers for user comments like
> 'a good introduction'. Later you could use the system
> to search medline and add a paper to the project.
> We could list the 'most popular read' in each project.
> Can we borrow some of the infra from BMC ?
> >Dan Bolser <dmb at mrc-dunn.cam.ac.uk> said:
> >>Great!, and thanks for the responses!
> >>I hope you don't mind, but I have opened
> >>this up to the BB for discussion.
> >>I have worked on and with MS bioinfo projects
> >>before, so I have some idea of what is required /
> >>what can be reasonably acheived. In this case I
> >>doubt the same kind of close collaboration will
> >>be possible, where our unit was able to fund students.
> >>I know what you meen about getting 'outside ideas',
> >>the broader your input the better in all fields
> >>I guess. I think it is definatly worth while in
> >>the bioinfo community, as this area of science
> >>more closly resembles the sofware engineering
> >>community than most.
> >>I think the best way to procede is to make the
> >>projects clearly open source, so ideas, progress and
> >>results can be made available to the community.
> >>I guess this would work well within the framework of
> >>bioinformatics.org, but I have no practical experience
> >>of setting up / running open source projects! I.E. I
> >>have no clue what kind of admin this involves / where
> >>responsibility lies etc.
> >>I imagine this should not be too much of a problem if
> >>you and other students are willing to work togeher to
> >>get the projects off the ground within this framework
> >>(maby including university admin where you are?).
> >>I will prepare a list of projects which I think are
> >>reasonable, and then I guess we should initiate
> >>some kind of open discussion on the relevance /
> >>previous work in the area / statement of aims and
> >>objectives / etc.
> >>Is this kind of forum available at bioinfo.org?
> >>I would really like to see an open forum for 'modular'
> >>project discussion, where people can add relevant
> >>papers / link / etc. to form a knowledge base for
> >>further work.
> >>Anyway, I will first have to run the list by the
> >>people in my lab to be sure that they are happy
> >>having these ideas made open (as I have a terrible
> >>habbit of jumping on good ideas which are not my own!).
> >>I will look forward to further comments / suggestions.
> >>P.S. do you have a time frame for project selection, as
> >>I could send one-at-a-time if that would help?
> >>Thanks very much for your idea,
> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
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