Literature DB >> 32759406

CellML 2.0.

Michael Clerx1, Michael T Cooling2, Jonathan Cooper3, Alan Garny2, Keri Moyle2, David P Nickerson2, Poul M F Nielsen2, Hugh Sorby2.   

Abstract

We present here CellML 2.0, an XML-based language for describing and exchanging mathematical models of physiological systems. MathML embedded in CellML documents is used to define the underlying mathematics of models. Models consist of a network of reusable components, each with variables and equations giving relationships between those variables. Models may import other models to create systems of increasing complexity. CellML 2.0 is defined by the normative specification presented here, prescribing the CellML syntax and the rules by which it should be used. The normative specification is intended primarily for the developers of software tools which directly consume CellML syntax. Users of CellML models may prefer to browse the informative rendering of the specification (https://cellml.org/specifications/cellml_2.0/) which extends the normative specification with explanations of the rules combined with examples of their usage.

Keywords:  computational physiology; modularity; physiome project; reproducibility; reusability

Mesh:

Year:  2020        PMID: 32759406      PMCID: PMC7756617          DOI: 10.1515/jib-2020-0021

Source DB:  PubMed          Journal:  J Integr Bioinform        ISSN: 1613-4516


  9 in total

1.  Programmatic modeling for biological systems.

Authors:  Alexander L R Lubbock; Carlos F Lopez
Journal:  Curr Opin Syst Biol       Date:  2021-05-24

2.  A semantics, energy-based approach to automate biomodel composition.

Authors:  Niloofar Shahidi; Michael Pan; Kenneth Tran; Edmund J Crampin; David P Nickerson
Journal:  PLoS One       Date:  2022-06-03       Impact factor: 3.752

3.  Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

Authors:  Anna Niarakis; Dagmar Waltemath; James Glazier; Falk Schreiber; Sarah M Keating; David Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomáš Helikar; Sylvain Soliman; Laurence Calzone
Journal:  Brief Bioinform       Date:  2022-07-18       Impact factor: 13.994

Review 4.  Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges.

Authors:  Xinyu Bi; Yanfeng Liu; Jianghua Li; Guocheng Du; Xueqin Lv; Long Liu
Journal:  Biomolecules       Date:  2022-05-19

5.  RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.

Authors:  Bilal Shaikh; Gnaneswara Marupilla; Mike Wilson; Michael L Blinov; Ion I Moraru; Jonathan R Karr
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

6.  BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Authors:  Bilal Shaikh; Lucian P Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S Andrews; Azraf Anwar; Moritz E Beber; Frank T Bergmann; David Brooks; Lutz Brusch; Laurence Calzone; Kiri Choi; Joshua Cooper; John Detloff; Brian Drawert; Michel Dumontier; G Bard Ermentrout; James R Faeder; Andrew P Freiburger; Fabian Fröhlich; Akira Funahashi; Alan Garny; John H Gennari; Padraig Gleeson; Anne Goelzer; Zachary Haiman; Jan Hasenauer; Joseph L Hellerstein; Henning Hermjakob; Stefan Hoops; Jon C Ison; Diego Jahn; Henry V Jakubowski; Ryann Jordan; Matúš Kalaš; Matthias König; Wolfram Liebermeister; Rahuman S Malik Sheriff; Synchon Mandal; Robert McDougal; J Kyle Medley; Pedro Mendes; Robert Müller; Chris J Myers; Aurelien Naldi; Tung V N Nguyen; David P Nickerson; Brett G Olivier; Drashti Patoliya; Loïc Paulevé; Linda R Petzold; Ankita Priya; Anand K Rampadarath; Johann M Rohwer; Ali S Saglam; Dilawar Singh; Ankur Sinha; Jacky Snoep; Hugh Sorby; Ryan Spangler; Jörn Starruß; Payton J Thomas; David van Niekerk; Daniel Weindl; Fengkai Zhang; Anna Zhukova; Arthur P Goldberg; James C Schaff; Michael L Blinov; Herbert M Sauro; Ion I Moraru; Jonathan R Karr
Journal:  Nucleic Acids Res       Date:  2022-05-07       Impact factor: 19.160

Review 7.  Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation.

Authors:  Catherine Bjerre Collin; Tom Gebhardt; Martin Golebiewski; Tugce Karaderi; Maximilian Hillemanns; Faiz Muhammad Khan; Ali Salehzadeh-Yazdi; Marc Kirschner; Sylvia Krobitsch; Lars Kuepfer
Journal:  J Pers Med       Date:  2022-01-26

8.  Specifications of standards in systems and synthetic biology: status and developments in 2021.

Authors:  Falk Schreiber; Padraig Gleeson; Martin Golebiewski; Thomas E Gorochowski; Michael Hucka; Sarah M Keating; Matthias König; Chris J Myers; David P Nickerson; Björn Sommer; Dagmar Waltemath
Journal:  J Integr Bioinform       Date:  2021-10-22

9.  Compositional modelling of immune response and virus transmission dynamics.

Authors:  W Waites; M Cavaliere; V Danos; R Datta; R M Eggo; T B Hallett; D Manheim; J Panovska-Griffiths; T W Russell; V I Zarnitsyna
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2022-08-15       Impact factor: 4.019

  9 in total

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