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Literature DB >> 18793134

Standards and ontologies in computational systems biology.

Abstract

With the growing importance of computational models in systems biology there has been much interest in recent years to develop standard model interchange languages that permit biologists to easily exchange models between different software tools. In the present chapter two chief model exchange standards, SBML (Systems Biology Markup Language) and CellML are described. In addition, other related features including visual layout initiatives, ontologies and best practices for model annotation are discussed. Software tools such as developer libraries and basic editing tools are also introduced, together with a discussion on the future of modelling languages and visualization tools in systems biology.

Mesh：

Year: 2008 PMID： 18793134 PMCID： PMC2728449 DOI： 10.1042/BSE0450211

Source DB: PubMed Journal: Essays Biochem ISSN： 0071-1365 Impact factor: 8.000

19 in total

Review 1. Molecular interaction map of the mammalian cell cycle control and DNA repair systems.

Authors: K W Kohn
Journal: Mol Biol Cell Date: 1999-08 Impact factor: 4.138

2. E-CELL: software environment for whole-cell simulation.

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Journal: Bioinformatics Date: 1999-01 Impact factor: 6.937

3. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors: M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal: Bioinformatics Date: 2003-03-01 Impact factor: 6.937

4. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.

Authors: Herbert M Sauro; Michael Hucka; Andrew Finney; Cameron Wellock; Hamid Bolouri; John Doyle; Hiroaki Kitano
Journal: OMICS Date: 2003

Review 5. CellML: its future, present and past.

Authors: Catherine M Lloyd; Matt D B Halstead; Poul F Nielsen
Journal: Prog Biophys Mol Biol Date: 2004 Jun-Jul Impact factor: 3.667

6. Automatic generation of cellular reaction networks with Moleculizer 1.0.

Authors: Larry Lok; Roger Brent
Journal: Nat Biotechnol Date: 2005-01 Impact factor: 54.908

7. Predicting temporal fluctuations in an intracellular signalling pathway.

Authors: C J Morton-Firth; D Bray
Journal: J Theor Biol Date: 1998-05-07 Impact factor: 2.691

8. A machine-independent language for the simulation of complex chemical and biochemical systems.

Authors: D Garfinkel
Journal: Comput Biomed Res Date: 1968-08

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Authors: P Mendes
Journal: Comput Appl Biosci Date: 1993-10

10. Model storage, exchange and integration.

Authors: Nicolas Le Novère
Journal: BMC Neurosci Date: 2006-10-30 Impact factor: 3.288

12 in total

1. On the formalization of multi-scale and multi-science processes for integrative biology.

Authors: Vanessa Díaz-Zuccarini; César Pichardo-Almarza
Journal: Interface Focus Date: 2011-03-30 Impact factor: 3.906

Review 2. Computational tools for metabolic engineering.

Authors: Wilbert B Copeland; Bryan A Bartley; Deepak Chandran; Michal Galdzicki; Kyung H Kim; Sean C Sleight; Costas D Maranas; Herbert M Sauro
Journal: Metab Eng Date: 2012-05 Impact factor: 9.783

3. A C library for retrieving specific reactions from the BioModels database.

Authors: M L Neal; M Galdzicki; J T Gallimore; H M Sauro
Journal: Bioinformatics Date: 2013-09-29 Impact factor: 6.937

Review 4. A case for the reuse and adaptation of mechanistic computational models to study transplant immunology.

Authors: Miguel Fribourg
Journal: Am J Transplant Date: 2019-10-23 Impact factor: 8.086

Review 5. Simulation of cellular biochemical system kinetics.

Authors: Daniel A Beard
Journal: Wiley Interdiscip Rev Syst Biol Med Date: 2010-12-17

Review 6. Systems pathology--taking molecular pathology into a new dimension.

Authors: Dana Faratian; Robert G Clyde; John W Crawford; David J Harrison
Journal: Nat Rev Clin Oncol Date: 2009-07-07 Impact factor: 66.675

7. libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.

Authors: Michael Vella; Robert C Cannon; Sharon Crook; Andrew P Davison; Gautham Ganapathy; Hugh P C Robinson; R Angus Silver; Padraig Gleeson
Journal: Front Neuroinform Date: 2014-04-23 Impact factor: 4.081

8. Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.

Authors: M J Swat; S Moodie; S M Wimalaratne; N R Kristensen; M Lavielle; A Mari; P Magni; M K Smith; R Bizzotto; L Pasotti; E Mezzalana; E Comets; C Sarr; N Terranova; E Blaudez; P Chan; J Chard; K Chatel; M Chenel; D Edwards; C Franklin; T Giorgino; M Glont; P Girard; P Grenon; K Harling; A C Hooker; R Kaye; R Keizer; C Kloft; J N Kok; N Kokash; C Laibe; C Laveille; G Lestini; F Mentré; A Munafo; R Nordgren; H B Nyberg; Z P Parra-Guillen; E Plan; B Ribba; G Smith; I F Trocóniz; F Yvon; P A Milligan; L Harnisch; M Karlsson; H Hermjakob; N Le Novère
Journal: CPT Pharmacometrics Syst Pharmacol Date: 2015-06-15

Review 9. Computationally Modeling Lipid Metabolism and Aging: A Mini-review.

Authors: Mark T Mc Auley; Kathleen M Mooney
Journal: Comput Struct Biotechnol J Date: 2014-11-15 Impact factor: 7.271

10. Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases.

Authors: Mufassra Naz; Alpha Tom Kodamullil; Martin Hofmann-Apitius
Journal: Brief Bioinform Date: 2015-08-05 Impact factor: 11.622