Wolfram Library Archive

Courseware Demos MathSource Technical Notes
All Collections Articles Books Conference Proceedings
Title Downloads

Progress in Computer Algebra-Based Biological Modeling Languages

Eric Mjolsness
Organization: University of California, Irvine
Department: Department of Information and Computer Science

Wolfram Technology Conference 2013
Conference location

Champaign, Illinois, USA

Collaborative projects have resulted in several Mathematica-implemented modeling languages aimed at general-purpose biological modeling, which is a useful and topical but indefinitely expandable goal. We update previous work on reaction arrow translation (Cellerator) and on 'dynamical grammars' (Plenum). Automatic learning of parameters has been developed for (a) stochastic reaction networks and for (b) model reduction of such networks for molecular complexes, using 'dependency diagrams'. Spatial modeling methods have developed in the form of adding some Plenum-like cell-level rules to Cellzilla (a Cellerator add-on package), parallelizable exact stochastic simulation algorithms not yet included in computer algebra software, and a current theoretical project on deriving partial differential equation methods that can be integrated with existing hybrid numerical techniques.

Joint work with Bruce Shapiro, Todd Johnson, and David Orendorff

*Wolfram Technology


MjolsnessWolframTech2013small.pdf (8 MB) - PDF Document