[alife] TODAY "Little B, a language for building modular models of biology" given by Aneil Mallavarapu (seminar 4pm every wednesday)

[Alexander (Sasha) Wait]

Hi all -

I am organizing a weekly ALife seminar in Boston this summer.  Today's
talk will be given by Aneil Mallavarapu on "Little b, a language for
building modular models of biology" at 4pm Wednesday  June 15th,
Biolabs 1058 in Harvard square, Cambridge, MA, USA.

After the talk we will meet for an informal meal at 5pm at Pho Pasteur
in Harvard square.  For those that cannot make the talk but can make
dinner it is a good idea to RSVP.

*** Abstract ***

The current pace of discovery in the biological sciences demands
increasingly sophisticated mathematical tools for cataloging, sharing,
modeling, and ultimately---understanding biological systems. However,
construction of mathematical models can be tedious, error prone and
require a broad range of expertise. As a result it is still a practice
largely limited to experts, and most biological models are currently
written in a monolithic, unsharable form. For modeling to become a
part of mainstream biology, it is important to develop tools that
allow models to be shared and reused.

Little b (b) is a programming language that enables the construction
of models from reusable fragments of knowledge. This approach is
inspired by pioneer work in the field of qualitative physics (QP), a
branch of artificial intelligence. Whereas the goal of QP was to
provide human-like qualitative reasoning about physical situations, b
is intended for construction of precise mathematical models which may
be used to discover potentially non-obvious properties of systems.

In b, a mathematical model is formulated by describing a physical
situation in terms of shared objects, relations, quantitative data, as
well as choices of theoretical approaches. The language reasons about
an initial description of a situation, inferring the presence of new
objects and relations (e.g., complexes, species, reactions,
equations). The inference procedure together with type checking and
symbolic mathematics make it easier to write concise and correct
models based on shared knowledge. The resulting mathematics might be
translated to a form suitable for analysis, such as simulation,
null-cline analysis, flux balance, metabolic control analysis, etc.
I'll talk about the current state of the work with b, and show how to
make an ODE (ordinary differential equation) model suitable for
simulation.

*** Abstract ***

The schedule and ideas for new talks can be found (and edited) at:

* http://karma.med.harvard.edu/wiki/ALife_Boston

There should be a seminar every Wednesday June/July/August at
4pm in Harvard square, Biolabs 1058. Map:

* http://www.mcb.harvard.edu/Overview/BigMap.html

If you are in town any Wed afternoon this summer, please, come by! 

Sasha
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