[BiO BB] Re: Bioinformatics Project

Gary Van Domselaar gary at www.bioinformatics.org
Thu Jul 31 14:32:11 EDT 2003

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 
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:


'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.


I think a system like this would be popular and successful.



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
> 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 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, 
> >>Dan.
> >>
> >>
> >>    
> >>
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