User Evaluation of Biospice

Abstract

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 simulators/editors: BioSketchPad/Charon, BioSpreadSheet/ESS, Jarnac/JDesigner, 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 simulators/editors 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.

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Document Details

Document Type
Technical Report
Publication Date
Oct 01, 2006
Accession Number
ADA459405

Entities

People

  • Evyatar Av-ron
  • John H. Byrne

Organizations

  • McGovern Medical School

Tags

Communities of Interest

  • Biomedical

DTIC Thesaurus Topics

  • Air Force Research Laboratories
  • Algorithms
  • Computational Biology
  • Computer Simulations
  • Computers
  • Differential Equations
  • Graphical User Interface
  • Language
  • Markup Languages
  • Mathematical Models
  • Operating Systems
  • Simulations
  • Simulators
  • Systems Biology
  • Test And Evaluation
  • Time Intervals
  • User Interface

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