ssapredict

Stochastic simulation algorithms (SSAs) are used to study biochemical models. Given a set of possible reactions and initial substrate concentrations the SSAs simulate the sequence of reactions happening over time in the modelled system.

As the complexity of modelled systems increases, it is important to select the best performing SSA to obtain the results fast. ssapredict determines which algorithm is best suited to simulate a particular model. It works with models in SBML format and analyses the topology of their reaction and dependency graphs. ssapredict gives a user the option to download ngss, our high performance multi-platform simulator, already configured to simulate the model with the predicted fastests SSA.

ssapredict is a free software and its source code is distributed under the terms of the GNU Affero General Public Licence.

Publications

• DOI eprint code BibTeX
  D. Sanassy, P. Widera, N. Krasnogor
  Meta-Stochastic Simulation of Biochemical Models for Systems and Synthetic Biology
  in ACS Synthetic Biology, 4(1):39-47, January 2015

  @ARTICLE{Sanassy2014,
    title = {Meta-Stochastic Simulation of Biochemical Models for Systems and Synthetic Biology},
    author = {Sanassy, Daven and Widera, Paweł and Krasnogor, Natalio},
    year = 2015,
    doi = {10.1021/sb5001406},
    month = jan,
    journal = {ACS Synthetic Biology},
    volume = {4},
    number = {1},
    pages = {39--47}
  }