Abstract
| Original language | English |
|---|---|
| Pages (from-to) | 664-665 |
| Number of pages | 2 |
| Journal | Bioinformatics |
| Volume | 29 |
| Issue number | 5 |
| Early online date | 17 Jan 2013 |
| DOIs | |
| Publication status | Published - 1 Mar 2013 |
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SBSI : an extensible distributed software infrastructure for parameter estimation in systems biology. / Adams, Richard; Clark, Allan; Yamaguchi, Azusa; Hanlon, Neil; Tsorman, Nikos; Ali, Shakir; Lebedeva, Galina; Goltsov, Alexey; Sorokin, Anatoly; Akman, Ozgur E.; Troein, Carl; Millar, Andrew J.; Goryanin, Igor; Gilmore, Stephen.
In: Bioinformatics, Vol. 29, No. 5, 01.03.2013, p. 664-665.Research output: Contribution to journal › Article
TY - JOUR
T1 - SBSI
T2 - an extensible distributed software infrastructure for parameter estimation in systems biology
AU - Adams, Richard
AU - Clark, Allan
AU - Yamaguchi, Azusa
AU - Hanlon, Neil
AU - Tsorman, Nikos
AU - Ali, Shakir
AU - Lebedeva, Galina
AU - Goltsov, Alexey
AU - Sorokin, Anatoly
AU - Akman, Ozgur E.
AU - Troein, Carl
AU - Millar, Andrew J.
AU - Goryanin, Igor
AU - Gilmore, Stephen
PY - 2013/3/1
Y1 - 2013/3/1
N2 - 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.
AB - 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.
U2 - 10.1093/bioinformatics/btt023
DO - 10.1093/bioinformatics/btt023
M3 - Article
VL - 29
SP - 664
EP - 665
JO - Bioinformatics
JF - Bioinformatics
SN - 1460-2059
IS - 5
ER -