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Journal of Integrative Bioinformatics, ISSN 1613-4516, 04/2018, Volume 15, Issue 1
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup... 
standards | SBML | modeling
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 01/2015, Volume 43, Issue 1, pp. D542 - D548
BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models of biological processes. A large set of models is curated to verify both... 
RESOURCES | DATABASE | MAPS | INFORMATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOLOGY | SBML | SYSTEMS | QUANTITATIVE KINETIC-MODELS | SOFTWARE | MIRIAM | Internet | Models, Biological | Computer Simulation | Databases, Factual | Database Issue
Journal Article
Briefings in Bioinformatics, ISSN 1467-5463, 01/2018, Volume 19, Issue 1, pp. 77 - 88
Journal Article
ACS Synthetic Biology, ISSN 2161-5063, 06/2016, Volume 5, Issue 6, pp. 479 - 486
Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for... 
standards | SBML | SBOL | modeling | genetic design automation | VERSION 1 CORE | MODELS | SBML LEVEL 3 | BIOCHEMICAL RESEARCH METHODS | STANDARD | Programming Languages | Synthetic Biology - standards | Models, Biological | Systems Biology - standards
Journal Article
Methods in Molecular Biology, ISSN 1064-3745, 2013, Volume 1021, pp. 189 - 199
Conference Proceeding
BMC Systems Biology, ISSN 1752-0509, 2010, Volume 4, Issue 1, pp. 92 - 92
Background: Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of... 
SBML | LIBRARY | API | EXCHANGE | JWS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Systems Biology - methods | Internet | Kinetics | Models, Biological | Biochemical Phenomena - physiology | Databases, Factual | Genealogical libraries | Biotechnology industry | Information management
Journal Article
Journal of Biomedical Semantics, ISSN 2041-1480, 07/2016, Volume 7, Issue 1, p. 46
Background: Open model repositories provide ready-to-reuse computational models of biological systems. Models within those repositories evolve over time,... 
SBML | Difference detection | Modelling | Version control | Ontology | CellML | MARKUP LANGUAGE SBML | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Models, Biological | Biological Ontologies | Internet
Journal Article
Proceedings of the IEEE, ISSN 0018-9219, 08/2008, Volume 96, Issue 8, pp. 1254 - 1265
Understanding of the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic,... 
Solid modeling | Visualization | Biological system modeling | SBML | kinetic modeling | SBGN | Analytical models | Biochemical simulation | Software packages | Markup languages | Systems biology | Logic | Usability | Graphical user interfaces | Kinetic modeling | systems biology | GENE | INFORMATION | REPRESENTATION | biochemical simulation | ENGINEERING, ELECTRICAL & ELECTRONIC
Journal Article
Bioinformatics, ISSN 1367-4803, 03/2011, Volume 27, Issue 5, pp. 743 - 744
Motivation: The PhysiomeModel Repository 2 (PMR2) software was created as part of the IUPS Physiome Project (Hunter and Borg, 2003), and today it serves as the... 
LANGUAGE | SBML | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Computational Biology - methods | Software | Internet | Models, Biological | Databases, Factual
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 03/2015, Volume 43, Issue 8, pp. 3899 - 3910
The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) tool is a user-friendly Java application that aids the reconstruction of... 
PLATFORM | DATABASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | SEQUENCE | SBML | KEGG | NETWORKS | RE-ANNOTATION | Metabolic Networks and Pathways - genetics | Software | Models, Biological | Genomics | Enzymes - metabolism | Computational Biology
Journal Article
Natural Product Reports, ISSN 0265-0568, 7/2016, Volume 33, Issue 8, pp. 925 - 932
Covering: 2000 to 2016 Progress in synthetic biology is enabled by powerful bioinformatics tools allowing the integration of the design, build and test stages... 
RANDOM MUTAGENESIS | METABOLIC NETWORK | CHEMISTRY, MEDICINAL | MASS-SPECTROMETRY DATA | MARKUP LANGUAGE SBML | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | ALGORITHM | CHEMISTRY, ORGANIC | LIBRARIES | PATHWAY | GENERATION | SYSTEMS BIOLOGY | Biological Products | Synthetic Biology | Molecular Structure | Computational Biology | Chemistry
Journal Article
Bioinformatics, ISSN 1367-4803, 01/2017, Volume 33, Issue 2, pp. 297 - 299
Simulation and behavioral analysis of genetic circuits is a standard approach of functional verification prior to their physical implementation. Many software... 
SBML | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | TOOL | Models, Genetic | Software | Gene Regulatory Networks | Computer Simulation
Journal Article
ACS Synthetic Biology, ISSN 2161-5063, 12/2017, Volume 8, Issue 7, pp. 1548 - 1559
Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modeling often... 
data standards | modeling | genetic design automation | BIOLOGY MARKUP LANGUAGE | BIOCHEMICAL RESEARCH METHODS | SBML | SBOL | SYNTHETIC BIOLOGY | VPR API | STANDARD | TOOL
Journal Article
ACS Synthetic Biology, ISSN 2161-5063, 02/2018, Volume 8, Issue 7, pp. 1560 - 1563
The iBioSim tool has been developed to facilitate the design of genetic circuits via a model-based design strategy. This paper illustrates the new features... 
standards | SED-ML | genetic design automation | BIOLOGY MARKUP LANGUAGE | BIOCHEMICAL RESEARCH METHODS | SBML | SBOL | COMBINE archive | SYNTHETIC BIOLOGY | CELLULAR-POPULATIONS
Journal Article
FRONTIERS IN PHYSIOLOGY, ISSN 1664-042X, 06/2018, Volume 9
Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many... 
PHYSIOLOGY | computational systems biology | model analysis | reproducibility | REPRESENTATION | STANDARDS | SBML | Python programming language | Boolean networks | MODELS | REGULATORY NETWORKS | PACKAGE | GENERATION
Journal Article
BioSystems, ISSN 0303-2647, 09/2018, Volume 171, pp. 74 - 79
Here we present Tellurium, a Python-based environment for model building, simulation, and analysis that facilitates reproducibility of models in systems and... 
SBML | Software | Simulation | Systems biology | BIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | BIOCHEMICAL NETWORKS | ANALYSIS LIBRARY | SBMI | Reproducibility of Results | Synthetic Biology | Tellurium - chemistry | Models, Biological | Systems Biology | Algorithms | Pythons
Journal Article
BMC Systems Biology, ISSN 1752-0509, 12/2011, Volume 5, Issue 200, pp. 198 - 198
Background: The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share... 
NETWORK | MODELS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SBML | API | SYSTEMS BIOLOGY | TOOLS | Programming Languages | Computational Biology - methods | Reproducibility of Results | Software | Computer Simulation | Usage | Reproduction | Computer-generated environments | Research | Computer simulation | Computational biology
Journal Article
Molecular Systems Biology, ISSN 1744-4292, 2011, Volume 7, Issue 1, pp. 543 - n/a
The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and... 
dynamics | model | kinetics | simulation | ontology | BIOCHEMISTRY & MOLECULAR BIOLOGY | MINIMUM INFORMATION | BIOMODELS DATABASE |