CellML: its future, present and past.

By C. Lloyd, Matt D. B. Halstead, P. Nielsen. Progress in Biophysics and Molecular Biology, 2004

540 citations recorded by the source corpus.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/629d5ca618d7528790cf0c8325dce00aba42808d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Biophysics

In Molecular Biology

Citations in the corpus

NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail (2010, methodology): “SBML [30], CellML [31], BrainML [41] and MathML [42].”
Visualization of omics data for systems biology (2010, methodology): “for models of biochemical reactions and gene regulation and CellM”
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems (2005, background): “At present, BioModels Database aims to store and annotate models that can be encoded with SBML. CellML models are also accepted.”
Controlled vocabularies and semantics in systems biology (2011, methodology): “Computational models, expressed in representation formats such as the Systems Biology Markup Language (SBML; Hucka et al , 2003), CellML (Lloyd et al , 2004) and NeuroML (Gleeson et al , 2010), still require much human interpretation.”
BioModels—15 years of sharing computational models in life science (2019, methodology): “Historically, only SBML and CellML (7) models were accepted for submission in the old BioModels platform.”
Systems medicine: the future of medical genomics and healthcare (2009, background): “ing language [124,125], and initial models of the beating heart, the contracting muscle and the breathing lung are already available [126,127].”
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models (2010, methodology): “Models submitted in CellML are converted to the latest SBML level and version since the BioModels Data-base software (annotation interface, simulation tool, etc.) is built around the SBML standard.”
Pathguide: a Pathway Resource List (2005, unknown): “To encourage this, databases are highlighted if they are ‘Free to all users’ and can be downloaded in a standard format, such as the Proteomics Standards Initiative Molecular Interaction (2) and BioPAX (www.biopax.org) pathway data exchange standards and the Systems Biology Markup Language (SBML) (3”
BioPAX – A community standard for pathway data sharing (2010, unknown): “However, BioPAX addresses this need by coor-dinating work (as described below) with the SBML and CellML mathematical modeling language communities 55,56 and a growing software tool set supporting biological process simulation 57 .”
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, background): “Consequently, considerable information is needed to describe the various aspects of a given protein–protein association and a number of standards have been developed for this purpose with distinct levels of expressivity and specialization (9–13).”