title: SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology.
abstract: CONCLUSIONS
  Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI's use of standard data formats.
  
  
  METHODS
  All SBSI binaries and source-code are freely available from http://sourceforge.net/projects/sbsi under an Apache 2 open-source license. The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. The SBSI project website at http://www.sbsi.ed.ac.uk provides documentation and tutorials.
authors: SynthSys Edinburgh, King's Buildings, University of Edinburgh, Edinburgh, UK.
authors: Richard
authors: R
authors: Adams
authors: Allan
authors: A
authors: Clark
authors: Azusa
authors: A
authors: Yamaguchi
authors: Neil
authors: N
authors: Hanlon
authors: Nikos
authors: N
authors: Tsorman
authors: Shakir
authors: S
authors: Ali
authors: Galina
authors: G
authors: Lebedeva
authors: Alexey
authors: A
authors: Goltsov
authors: Anatoly
authors: A
authors: Sorokin
authors: Ozgur E
authors: OE
authors: Akman
authors: Carl
authors: C
authors: Troein
authors: Andrew J
authors: AJ
authors: Millar
authors: Igor
authors: I
authors: Goryanin
authors: Stephen
authors: S
authors: Gilmore
mesh_terms: D000465:Algorithms; D012984:Software; D049490:Systems Biology / Q000379:methods*