[BiO BB] Re: Bioinformatics Project

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Wed Jul 30 07:56:47 EDT 2003

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

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, 

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