Cargando…

Software that goes with the flow in systems biology

ABSTRACT: A recent article in BMC Bioinformatics describes new advances in workflow systems for computational modeling in systems biology. Such systems can accelerate, and improve the consistency of, modeling through automation not only at the simulation and results-production stages, but also at th...

Descripción completa

Detalles Bibliográficos
Autores principales: Hucka, Michael, Le Novère, Nicolas
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2993668/
https://www.ncbi.nlm.nih.gov/pubmed/21114874
http://dx.doi.org/10.1186/1741-7007-8-140
_version_ 1782192826094714880
author Hucka, Michael
Le Novère, Nicolas
author_facet Hucka, Michael
Le Novère, Nicolas
author_sort Hucka, Michael
collection PubMed
description ABSTRACT: A recent article in BMC Bioinformatics describes new advances in workflow systems for computational modeling in systems biology. Such systems can accelerate, and improve the consistency of, modeling through automation not only at the simulation and results-production stages, but also at the model-generation stage. Their work is a harbinger of the next generation of more powerful software for systems biologists. See research article: http://www.biomedcentral.com/1471-2105/11/582/abstract/ Ever since the rise of systems biology at the end of the last century, mathematical representations of biological systems and their activities have flourished. They are being used to describe everything from biomolecular networks, such as gene regulation, metabolic processes and signaling pathways, at the lowest biological scales, to tissue growth and differentiation, drug effects, environmental interactions, and more. A very active area in the field has been the development of techniques that facilitate the construction, analysis and dissemination of computational models. The heterogeneous, distributed nature of most data resources today has increased not only the opportunities for, but also the difficulties of, developing software systems to support these tasks. The work by Li et al. [1] published in BMC Bioinformatics represents a promising evolutionary step forward in this area. They describe a workflow system - a visual software environment enabling a user to create a connected set of operations to be performed sequentially using seperate tools and resources. Their system uses third-party data resources accessible over the Internet to elaborate and parametrize (that is, assign parameter values to) computational models in a semi-automated manner. In Li et al.'s work, the authors point towards a promising future for computational modeling and simultaneously highlight some of the difficulties that need to be overcome before we get there.
format Text
id pubmed-2993668
institution National Center for Biotechnology Information
language English
publishDate 2010
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-29936682010-11-30 Software that goes with the flow in systems biology Hucka, Michael Le Novère, Nicolas BMC Biol Commentary ABSTRACT: A recent article in BMC Bioinformatics describes new advances in workflow systems for computational modeling in systems biology. Such systems can accelerate, and improve the consistency of, modeling through automation not only at the simulation and results-production stages, but also at the model-generation stage. Their work is a harbinger of the next generation of more powerful software for systems biologists. See research article: http://www.biomedcentral.com/1471-2105/11/582/abstract/ Ever since the rise of systems biology at the end of the last century, mathematical representations of biological systems and their activities have flourished. They are being used to describe everything from biomolecular networks, such as gene regulation, metabolic processes and signaling pathways, at the lowest biological scales, to tissue growth and differentiation, drug effects, environmental interactions, and more. A very active area in the field has been the development of techniques that facilitate the construction, analysis and dissemination of computational models. The heterogeneous, distributed nature of most data resources today has increased not only the opportunities for, but also the difficulties of, developing software systems to support these tasks. The work by Li et al. [1] published in BMC Bioinformatics represents a promising evolutionary step forward in this area. They describe a workflow system - a visual software environment enabling a user to create a connected set of operations to be performed sequentially using seperate tools and resources. Their system uses third-party data resources accessible over the Internet to elaborate and parametrize (that is, assign parameter values to) computational models in a semi-automated manner. In Li et al.'s work, the authors point towards a promising future for computational modeling and simultaneously highlight some of the difficulties that need to be overcome before we get there. BioMed Central 2010-11-29 /pmc/articles/PMC2993668/ /pubmed/21114874 http://dx.doi.org/10.1186/1741-7007-8-140 Text en Copyright ©2010 Hucka and Le Novère; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Commentary
Hucka, Michael
Le Novère, Nicolas
Software that goes with the flow in systems biology
title Software that goes with the flow in systems biology
title_full Software that goes with the flow in systems biology
title_fullStr Software that goes with the flow in systems biology
title_full_unstemmed Software that goes with the flow in systems biology
title_short Software that goes with the flow in systems biology
title_sort software that goes with the flow in systems biology
topic Commentary
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2993668/
https://www.ncbi.nlm.nih.gov/pubmed/21114874
http://dx.doi.org/10.1186/1741-7007-8-140
work_keys_str_mv AT huckamichael softwarethatgoeswiththeflowinsystemsbiology
AT lenoverenicolas softwarethatgoeswiththeflowinsystemsbiology