SBML Level 3: an extensible format for the exchange and reuse of biological models
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BiBTeXSystems biology has experienced dramatic growth in the number, size and complexity of computational models describing biology. To reproduce simulation results and reuse models, researchers need to exchange precise and unambiguous descriptions of model structure and meaning. SBML (the Systems Biology Markup Language) is a community-developed format for this purpose. The latest edition, called SBML Level 3, has a modular structure, with a core suited to representing reaction-based models, and packages that extend the core with features suited for a variety of model types. Examples include constraint-based models, reaction-diffusion models, logical network models, and rule-based models. SBML and its rich software ecosystem have transformed the way systems biologists build and interact with models, and has played an important role in increasing model interoperability and reuse over the past two decades. More recently, a rise of multiscale models of whole cells and organs, and new data sources such as single cells measurements and live imaging, have precipitated new ways of integrating data and models. SBML Level 3 provides the foundation needed to support this evolution.
SEEK ID: https://seek.lisym.org/publications/261
Projects: LiSyM network, Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)
Publication type: Journal
Journal: Mol Syst Biol.
Citation: Mol Syst Biol.
Date Published: 1st Jul 2020
URL: https://livermetabolism.com/paper/SBML_Keating2019.pdf
Registered Mode: imported from a bibtex file
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Created: 27th Jul 2020 at 14:47
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Projects: LiSyM PALs, Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), LiSyM Pillar IV: Liver Function Diagnostics (LiSyM-LiFuDi), LiSyM network, LiSyM-Krebs Partnering
Institutions: Humboldt-Universität zu Berlin - Institute for Theoretical Biology (ITB)
https://orcid.org/0000-0003-1725-179X
We are investigating liver metabolism and function with the help of computational models and methods.
Group Leader Dr. Matthias König
Institute for Theoretical Biology Humboldt-University Berlin Philippstraße 13, 10115 Berlin, Germany phone +49 30 2093-98435 koenigmx@hu-berlin.de https://www.livermetabolism.com
The König group works on computational modeling, data science, data management, bioinformatics methods and machine learning on ...
Liver Systems Medicine : striving to develop non-invasive methods for diagnosing and treating NAFLD by combining mathematical modeling and biological research. LiSyM, is a multidisciplinary research network, in which molecular and cell biologists, clinical researchers, pharmacologists and experts in mathematical modeling examine the liver in its entirety. LiSyM research focuses on the metabolic liver disease non-alcoholic fatty liver disease (NAFLD), which includes non-alcoholic steatohepatitis ...
Projects: LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI), LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP), LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF), LiSyM Pillar IV: Liver Function Diagnostics (LiSyM-LiFuDi), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), LiSyM PALs, Project Management PTJ, LiSyM network, LiSyM Scientific Leadership Team (LiSyM-LT)
Web page: https://www.lisym.org/
This comprises the whole LiSyM network
Programme: LiSyM: Liver Systems Medicine
Public web page: http://www.lisym.org
Start date: 1st Jan 2016
Dr. Matthias König (Humboldt University, Berlin) models the human liver on the computer. His simulations show the extent of individual differences in liver function and the external factors influencing it. König has shown that smoking falsifies the result of an important liver test (LiMAx). With his models, drug doses can be calculated so that they can be administered in doses that do not harm the liver.
Programme: LiSyM: Liver Systems Medicine
Public web page: https://livermetabolism.com
Start date: 1st Jan 2016
We face a crisis in reproducibility, where it is impossible to believe most of the computational results shown in conferences and papers. Recent replication efforts and theoretical considerations indicate that most published research findings in biomedical research are wrong. This is especially problematic for the translation of computational models into the clinics. Modelling standards, software, and community initiatives are fundamental for reproducibility in systems biology and systems medicine. ...
