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Progress in Computer Algebra-Based Biological Modeling Languages
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| Organization: | University of California, Irvine |
| Department: | Department of Information and Computer Science |
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Wolfram Technology Conference 2013
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Champaign, Illinois, USA
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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
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http://www.wolfram.com/events/technology-conference/2013
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| MjolsnessWolframTech2013small.pdf (8 MB) - PDF Document |
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