{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T00:51:11Z","timestamp":1772499071255,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1354,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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\u2019s use of standard data formats.<\/jats:p>\n               <jats:p>Availability and implementation: 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.<\/jats:p>\n               <jats:p>Contact: stg@inf.ed.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt023","type":"journal-article","created":{"date-parts":[[2013,1,18]],"date-time":"2013-01-18T01:18:02Z","timestamp":1358471882000},"page":"664-665","source":"Crossref","is-referenced-by-count":21,"title":["SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology"],"prefix":"10.1093","volume":"29","author":[{"given":"Richard","family":"Adams","sequence":"first","affiliation":[{"name":"1 SynthSys Edinburgh, King's Buildings, University of Edinburgh, Edinburgh, UK, 2School of Informatics, Informatics Forum, University of Edinburgh, Edinburgh, UK, 3BSkyB, Watermark House, Livingston, Scotland, 4The Systems Biology Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Tokyo 108-0071, Japan, 5Horizon Digital Economy Research, University of Nottingham, Nottingham, UK, 6University of Abertay Dundee, Dundee, UK, 7Institute of Cell Biophysics RAS, Institutskaya st., 3, Pushchino, Russia, 8Centre for Systems, Dynamics and Control, University of Exeter, UK and 9Computational Biology and Biological Physics, Lund University, S\u00f6lvegatan 14A, Lund, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Allan","family":"Clark","sequence":"additional","affiliation":[{"name":"1 SynthSys Edinburgh, King's Buildings, University of Edinburgh, Edinburgh, UK, 2School of Informatics, Informatics Forum, University of Edinburgh, Edinburgh, UK, 3BSkyB, Watermark House, Livingston, Scotland, 4The Systems Biology Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Tokyo 108-0071, Japan, 5Horizon Digital Economy Research, University of Nottingham, Nottingham, UK, 6University of Abertay Dundee, Dundee, UK, 7Institute of Cell Biophysics RAS, Institutskaya st., 3, Pushchino, Russia, 8Centre for Systems, Dynamics and Control, University of Exeter, UK and 9Computational Biology and Biological Physics, Lund University, S\u00f6lvegatan 14A, Lund, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Azusa","family":"Yamaguchi","sequence":"additional","affiliation":[{"name":"1 SynthSys Edinburgh, King's Buildings, University of Edinburgh, Edinburgh, UK, 2School of Informatics, Informatics Forum, University of Edinburgh, Edinburgh, UK, 3BSkyB, Watermark House, Livingston, Scotland, 4The Systems Biology Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Tokyo 108-0071, Japan, 5Horizon Digital Economy Research, University of Nottingham, Nottingham, UK, 6University of Abertay Dundee, Dundee, UK, 7Institute of Cell Biophysics RAS, Institutskaya st., 3, Pushchino, Russia, 8Centre for Systems, Dynamics and Control, University of Exeter, UK and 9Computational Biology and Biological Physics, Lund University, S\u00f6lvegatan 14A, Lund, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Neil","family":"Hanlon","sequence":"additional","affiliation":[{"name":"1 SynthSys Edinburgh, King's Buildings, University of Edinburgh, Edinburgh, UK, 2School of Informatics, Informatics Forum, University of Edinburgh, Edinburgh, UK, 3BSkyB, Watermark House, Livingston, Scotland, 4The Systems Biology Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Tokyo 108-0071, Japan, 5Horizon Digital Economy Research, University of Nottingham, Nottingham, UK, 6University of Abertay Dundee, Dundee, UK, 7Institute of Cell Biophysics RAS, Institutskaya st., 3, Pushchino, Russia, 8Centre for Systems, Dynamics and Control, University of Exeter, UK and 9Computational Biology and Biological Physics, Lund University, S\u00f6lvegatan 14A, Lund, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikos","family":"Tsorman","sequence":"additional","affiliation":[{"name":"1 SynthSys Edinburgh, King's Buildings, University of Edinburgh, Edinburgh, UK, 2School of Informatics, Informatics Forum, University of Edinburgh, Edinburgh, UK, 3BSkyB, Watermark House, Livingston, Scotland, 4The Systems Biology Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Tokyo 108-0071, Japan, 5Horizon Digital Economy Research, University of Nottingham, Nottingham, UK, 6University of Abertay Dundee, Dundee, UK, 7Institute of Cell Biophysics RAS, Institutskaya st., 3, Pushchino, Russia, 8Centre for Systems, Dynamics and Control, University of Exeter, UK and 9Computational Biology and Biological Physics, Lund University, S\u00f6lvegatan 14A, Lund, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shakir","family":"Ali","sequence":"additional","affiliation":[{"name":"1 SynthSys Edinburgh, King's Buildings, University of Edinburgh, Edinburgh, UK, 2School of Informatics, Informatics Forum, University of Edinburgh, Edinburgh, UK, 3BSkyB, Watermark House, Livingston, Scotland, 4The Systems Biology Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Tokyo 108-0071, Japan, 5Horizon Digital Economy Research, University of Nottingham, Nottingham, UK, 6University of Abertay Dundee, Dundee, UK, 7Institute of Cell Biophysics RAS, Institutskaya st., 3, Pushchino, Russia, 8Centre for Systems, Dynamics and Control, University of Exeter, UK and 9Computational Biology and Biological Physics, Lund University, S\u00f6lvegatan 14A, Lund, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Galina","family":"Lebedeva","sequence":"additional","affiliation":[{"name":"1 SynthSys Edinburgh, King's Buildings, University of Edinburgh, Edinburgh, UK, 2School of Informatics, Informatics Forum, University of Edinburgh, Edinburgh, UK, 3BSkyB, Watermark House, Livingston, Scotland, 4The Systems Biology Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Tokyo 108-0071, Japan, 5Horizon Digital Economy Research, University of Nottingham, 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5Horizon Digital Economy Research, University of Nottingham, Nottingham, UK, 6University of Abertay Dundee, Dundee, UK, 7Institute of Cell Biophysics RAS, Institutskaya st., 3, Pushchino, Russia, 8Centre for Systems, Dynamics and Control, University of Exeter, UK and 9Computational Biology and Biological Physics, Lund University, S\u00f6lvegatan 14A, Lund, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Igor","family":"Goryanin","sequence":"additional","affiliation":[{"name":"1 SynthSys Edinburgh, King's Buildings, University of Edinburgh, Edinburgh, UK, 2School of Informatics, Informatics Forum, University of Edinburgh, Edinburgh, UK, 3BSkyB, Watermark House, Livingston, Scotland, 4The Systems Biology Institute, Falcon Building 5F, 5-6-9 Shirokanedai, Tokyo 108-0071, Japan, 5Horizon Digital Economy Research, University of Nottingham, Nottingham, UK, 6University of Abertay Dundee, Dundee, UK, 7Institute of Cell Biophysics RAS, Institutskaya st., 3, Pushchino, 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