Toward Community Standards and Software for Whole-Cell Modeling.
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BiBTeXOBJECTIVE: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells. METHODS: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in the Systems Biology Markup Language. RESULTS: Our analysis revealed several challenges to representing WC models using the current standards. CONCLUSION: We, therefore, propose several new WC modeling standards, software, and databases. SIGNIFICANCE: We anticipate that these new standards and software will enable more comprehensive models.
SEEK ID: https://seek.lisym.org/publications/95
PubMed ID: 27305665
Projects: Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)
Publication type: Not specified
Journal: IEEE Trans Biomed Eng
Citation: IEEE Trans Biomed Eng. 2016 Oct;63(10):2007-14. doi: 10.1109/TBME.2016.2560762. Epub 2016 Jun 10.
Date Published: 10th Jun 2016
Registered Mode: Not specified
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Created: 14th Feb 2018 at 08:44
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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/
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
