User Evaluation of Biospice
Final technical rept. Jun 2004-Feb 2006
TEXAS UNIV MEDICAL SCHOOL AT HOUSTON DEPT OF NEUROBIOLOGY AND ANATOMY
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The BioComp project was established to provide the system biology community with a tool, a computing environment called Bio- SPICE, to carry out data collection, model development and computer simulation. Usability studies of the Bio-SPICE Dashboard and seven simulatorseditors BioSketchPadCharon, BioSpreadSheetESS, JarnacJDesigner, JigCell, Simpathica, BioNets and Pathway Builder were performed. The usability of each simulator was examined and the interoperability of the various tools using System Biology Markup Language SBML as a language of exchange between the different applications. Each tool provides a model builder component and a simulator component. The model builder components varied from providing a scripting-like language, a tabular editor to a graphical user interface. The simulator components use either deterministic solver algorithms e.g., CVODE, Backward Euler or a stochastic solver using the Gillespie algorithm. Seven simulatorseditors were examined with four models that produce oscillatory behavior or time course of a long duration. A tutorial manual and a use case document were written.
- Medicine and Medical Research
- Computer Programming and Software