[Biophp-dev] Re: [BiO BB] Re: Bioinformatics Project

[Dan Bolser]

Sounds like a great project

On Thu, 31 Jul 2003, Gary Van Domselaar wrote:

> Hey Gang,
> 
> I'm not sure how relevant this is for PHP, but I thought I would mention 
> this kind of cool idea:
> 
> A while back my colleague J.W. Bizzaro suggested a P2P system for
> distribution of scientific articles in PDF (and perhaps other) formats.  
> Users of the system would store their favorite articles locally on their
> server, but make them accessible to others through the P2P system.  The
> system would allow the articles to be restricted to certain authenticated
> groups (eg lab members). Type checking could be enforced so only 'document
> file formats' would be distributed, reducing the potential for abuse.  A 
> system like this combined with the features you describe, like automatic 
> field retrieval and population from PubMed would be a very useful system 
> indeed.
>   
> Like the MPAA and RIAA, most journal publishing companies would feel
> threatened by a distribution system like this, but others such as BMC and
> PLoS would likely embrace it, and might even help out with some funding.
> There is an interesting article by Robert Cringely on how a system like 
> this might possibly be implemented with some protection from litigation:
> 
> http://www.pbs.org/cringely/pulpit/pulpit20030724.html
> 
> 'Soulseek' is a P2P system for music distribution that has some nice 
> features, including 'rooms' for people with similar musical interests.  
> This would be like the 'labs' feature I mentioned above.
> 
> www.slsk.org/
> 
> I think a system like this would be popular and successful.
> 
> Regards,
> 
> g.
> ------------------
> 
> 
> 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
> > admin.
> > 
> > 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
> > projects.
> > 
> > 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 ?
> > 
> > Cheers,
> > Dan.
> > 
> > >Dan Bolser <dmb@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, 
> > >>Dan.
> > >>
> > >>
> > >>    
> > >>
> > 
> > 
> > _______________________________________________
> > BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board@bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> > 
> 
> _______________________________________________
> Biophp-dev mailing list
> Biophp-dev@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biophp-dev
>