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COPASI and its applications in biotechnology

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dc.contributor.authorBergmann, Frank T.en
dc.contributor.authorHoops, Stefanen
dc.contributor.authorKlahn, Brianen
dc.contributor.authorKummer, Ursulaen
dc.contributor.authorMendes, Pedroen
dc.contributor.authorPahle, Juergenen
dc.contributor.authorSahle, Svenen
dc.date.accessioned2019-09-18T13:57:54Zen
dc.date.available2019-09-18T13:57:54Zen
dc.date.issued2017-11-10en
dc.description.abstractCOPASI is software used for the creation, modification, simulation and computational analysis of kinetic models in various fields. It is open-source, available for all major platforms and provides a user-friendly graphical user interface, but is also controllable via the command line and scripting languages. These are likely reasons for its wide acceptance. We begin this review with a short introduction describing the general approaches and techniques used in computational modeling in the biosciences. Next we introduce the COPASI package, and its capabilities, before looking at typical applications of COPASI in biotechnology.en
dc.description.notesOver the years, COPASI has received funding from the following funding agencies and programmes: the BMBF funded de.NBI initiative (031L0104A) and Virtual Liver Project, National Institutes of Health (NIGMS Grant: GM080219), the BBSRC (grant BB/J019259/1), BBSRC and EPSRC (grant BB/C008219/1) as well as the Klaus Tschira Foundation and the Virginia Bioinformatics Institute. We would like to thank Norman Paton and Yang Cao for their collaboration. We would also like to thank all the programmers and student helpers that worked on COPASI over the years, particularly, Ralph Gauges, Joseph Dada, Ettore Murabito, Peyman Zarrineh, Natalia Simus and Irina Surovtsova. Marina Kaiser is acknowledged for literature digging. Finally, we would like to acknowledge the members of the COPASI user forum for their active support.en
dc.description.sponsorshipBMBF [031L0104A]; Virtual Liver Project, National Institutes of Health (NIGMS) [GM080219]; BBSRC [BB/J019259/1]; BBSRC; EPSRC [BB/C008219/1]; Klaus Tschira Foundation; Virginia Bioinformatics Instituteen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1016/j.jbiotec.2017.06.1200en
dc.identifier.eissn1873-4863en
dc.identifier.issn0168-1656en
dc.identifier.pmid28655634en
dc.identifier.urihttp://hdl.handle.net/10919/93752en
dc.identifier.volume261en
dc.language.isoenen
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivatives 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjectCOPASIen
dc.subjectBiotechnologyen
dc.subjectSystems biologyen
dc.titleCOPASI and its applications in biotechnologyen
dc.title.serialJournal of Biotechnologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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