[BiO BB] prototyping

Sameer_Mohta Sameer_Mohta at satyam.com
Mon Sep 17 03:48:27 EDT 2001

hi all,

i have one question. if a IT person wants to do a quick and dirty
prototyping in a weeks time or two weeks time, where can he put effort. I
have seen alignment tools, structure prediction and so on. But what can be
the new area in Bioinformatics where this prototyping can be done in this
short span of time, considering the limitation of in depth scientific
knowledge of a IT person.


-----Original Message-----
From: Val Bykoski [mailto:valb at vtek.com]
Sent: Sunday, September 16, 2001 7:12 AM
To: bio_bulletin_board at bioinformatics.org
Cc: Val Bykoski - valb
Subject: Re: [BiO BB] (no subject)

Hi Indraneel,
    Thanx for your comments.
    I refer to the cell as a biological cell, and my point,
    to put it a little differently, was that data has to work
    inside a (realistic) cell model, not to sit passively in databases.
    Data grouping, visualization, etc. is better than nothing,
    but still there is a huge gap between data (nicely grouped, 
    visualized, etc) and their biological significance or context.
    I guess my point is that if you integrate data into a realistic 
    cell model, the model is both a predictive framework and 
    a (bio)context-sensitive database for the data.  Then,
    data is hidden and work inside the model for predictions,
    and does not require grouping, visualization, etc.
    Sure, the "realistic cell model" is a hard nut...but may be
    worth of efforts, in particular, for a data-driven model.
cheers, val
val at vtek.com

----- Original Message ----- 
From: "Indraneel Majumdar" <indraneel at indialine.org>
To: <bio_bulletin_board at bioinformatics.org>
Sent: Saturday, September 15, 2001 6:35 PM
Subject: Re: [BiO BB] (no subject)

> Hi,
> I'm sorry I didn't understand properly. Do you refer to the cell as a
> biological cell, or as a unit of useful data?
> In case of the former probably that's what we are trying to find out,
> together with the broader perspective of all cells working together.
> In case of the latter, we probably already have the units of data,
> sometimes related and sometimes not. Now is the time to seggregate them
> to it's smallest units and link them up using relations (yes, I'm
> implying relational database systems). We do however need to know what
> to expect out of this database, and also account for the fact that we
> can never know how to scale it when new types of data come along (but
> then this applies to every field). From my personal work, I have found
> that simply being able to group and ungroup data shows up hidden facts,
> and also generates ideas for new studies. (If you're curious, I use
> PostgreSQL :)
> \Indraneel
> On Thu, Sep 13, 2001 at 10:34:18PM -0400, Val Bykoski wrote:
> > Mike,
> > To me, data integration is part of more serious problem 
> > how to build a realistic cell model.  Without cell model,
> > there is no (computational) framework to integrate the
> > data around.  Data needs to be integrated into smth biologically
> > significant - otherwise the data is very much useless...
> > my best, val
> -- 
> http://www.indialine.org/indraneel/
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