In Vivo In Silico:
A Grand Challenge for Computer Science

Ronan Sleep, University of East Anglia

The talk introduces one of several proposed Grand Challenges[1] for Computing Science arising from the recent workshop Sponsored by the UK Computing Research Committee (supported by EPSRC and NeSC). The challenge discussed arises from potential synergy from combining the knowledge of Biologists and Computing Sciences about complex systems architecture.

There is a growing mass of computer accessible biological data, and theories are beginning to emerge that give causative explanations of this data and predictions of future observations. Many of these theories can be expressed directly as computer simulation programs - active models with both discrete and continuous abstractions or approximations.

The state of the art in Computing Science for specifying, modelling and realising complex systems has advanced sufficiently to attempt constructing fully detailed, accurate and predictive models of some of the most studied life forms used as models in biology e.g. the Nematode worm (C. elegans).

The Computing Science needed is emerging at the right time time to offer the Biologist sophisticated frameworks for representing knowledge about developmental and other life. Conversely the Biologists are beginning to provide very detailed pictures of how living systems organise and manage complex developmental and maintenance processes. These are a potential source of inspiration to Computing Science in its attempt to manage the complexities of the Internet and Ambient Intelligence.

Based on the above, it is argued that the time is right to build a concerted multidisciplinary team to construct a high-fidelity model of a life form such as C. elegans. Such an effort would build on partial computer models that are already under development many laboratories, to create a complete, consistent, integrated representation of all that is known about a particular plant or animal. This representation should be accessible to humans via extensible view selection mechanisms that include the interaction modes possible between an experimenter and the real life form, and also between the life forms themselves.

The coping stone of a successful challenge would be a generic approach to modelling of complex systems which becomes the standard medium for expressing and reasoning in the life sciences and which also has major applications in the design of man made complex distributed reactive adaptive systems.

Ronan Sleep, UEA, Feb 7th 2003

 



[1] http://umbriel.dcs.gla.ac.uk/NeSC/general/esi/events/Grand_Challenges/proposals/index.html