M. Hucka

Publications
Influence

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

M. Hucka, A. Finney, +40 authors J. Wang
Computer Science, Medicine
Bioinform.
1 March 2003

We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. Expand

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BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

C. Li, M. Donizelli, +11 authors C. Laibe
Computer Science, Medicine
BMC Systems Biology
29 June 2010

BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. Expand

A community-driven global reconstruction of human metabolism

I. Thiele, Neil Swainston, +43 authors B. Palsson
Biology, Medicine
Nature Biotechnology
1 May 2013

Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction',… Expand

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

N. L. Novère, B. Bornstein, +9 authors M. Hucka
Biology, Computer Science
Nucleic Acids Res.
28 December 2005

BioModels Database (), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Expand

The Systems Biology Graphical Notation

N. L. Novère, M. Hucka, +36 authors H. Kitano
Medicine
Nature Biotechnology
1 August 2009

Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software… Expand

Minimum information requested in the annotation of biochemical models (MIRIAM)

N. L. Novère, A. Finney, +13 authors B. Wanner
Biology, Medicine
Nature Biotechnology
6 December 2005

Most of the published quantitative models in biology are lost for the community because they are either not made available or they are insufficiently characterized to allow them to be reused. The… Expand

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

M. Hucka, A. Finney, +8 authors H. Kitano
Medicine, Computer Science
Systems biology
20 September 2004

We developed the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. Expand

Systems biology markup language: Level 2 and beyond.

A. Finney, M. Hucka
Computer Science, Medicine
Biochemical Society transactions
1 December 2003

We developed an exchange language, the SBML (systems biology markup language) [1], with the help of a community of software developers. Expand

BioModels: ten-year anniversary

V. Chelliah, N. S. Juty, +17 authors C. Laibe
Biology, Computer Science
Nucleic Acids Res.
20 November 2014

BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models of biological processes. Expand

Erratum: Profiling PARP inhibitors

E. Demir, M. P. Cary, +86 authors Gary D. Bader
Biology
Nature Biotechnology
9 September 2010

BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data… Expand

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