[BiO BB] Re: Bioinformatics Project

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Tue Jul 29 07:56:52 EDT 2003

J.W. Bizzaro wrote:

> Hi Dan.
> Dan Bolser wrote:
>> 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?
> If the project requires software development, the Biodevelopers forum 
> would be a good place to go:
>   biodevelopers at bioinformatics.org
>   http://bioinformatics.org/lists/biodevelopers

Cheers, I am sure that development will be involved, but I don't see the 
of 'one off' applications as the main aim.

One unifying principal of the work I have in mind is knowledge modelling
(through data modelling). I see this as a kind of ontology of 
bioinformatics, but of
course this isn't an implicitly correct or static model of the domain. 
It makes sense
for this mode to be openly developed (along the lines of an integrated 

Various projects could 'plug in' to the main system in the form of 
specific databases
and analysis pipelines, but there is a unified (but as yet unknown) whole.

I was thinking that we should start a new project with this aim 
(building towards
and defining the 'whole').

>> 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.
> I'd been thinking along these lines too.  I often get e-mail messages 
> from students looking for ideas to pursue, and I have to tell them 
> that most scientists have very few leads and thus covet them (i.e., 
> good luck getting anyone to give them away).

Sadly I have discovered that the ideas in my head are not my property.
However, I am confident that my mind reading alter ego is a free man,
and he should be able to get my ideas across.

> I also know of many knowledgebase projects to archive things that we 
> know.  But, how about things that we **DON'T KNOW**?  How about 
> developing a "lack-of-knowledge-base" or "questionbase", where the 
> literature is mined for unanswered questions (perhaps from the "future 
> directions" sections in published articles)?

I always get the impression that this knowledge is only available to 
experts in the field.
It takes knowledge of the domain to know which 'next step' out of the 
many is the most
relevant for the field. This relates to the idea of getting people to 
post up projects that
they would like to see done, an expert wish list. This inherently comes 
with background
information to motivate why the project should be taken on, what can be 
gained, and what
related work exists etc.

> Does anyone know if anything like that exists (specifcally one where 
> the questions have **NEVER** been answered)?  If not, maybe it should 
> be made (and then, for everyone out there who has asked me for ideas, 
> there you go ;-))

Great! phrased like this I am sure people would be happy to contribute...

'What do you think are the biggest open questions in bioinf?'
'What question would you ask God about Bioinformatics?'

> Cheers.
> Jeff


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