Tag: mathematical model


Found 34 sources
Source Match ReputationScore*

SWISS-MODEL Repository of 3D protein structure models


The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for protein sequences of selected model organisms.
100%

Systems Biology Markup Language


The Systems Biology Markup Language (SBML) is a machine-readable exchange format for computational models of biological processes. Its strength is in representating phenomena at the scale of biochemical reactions, but it is not limited to that. By su ...
93%

WikiPathways


WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.
92%

NeuroML


NeuroML is a model description language developed in XML (extensible Markup Language) that was created to facilitate data archiving, data and model exchange, database creation, and model publication in the neurosciences. One of the goals of the Neuro ...
80%

Minimal Information Required In the Annotation of Models


The Minimal Information Required In the Annotation of Models (MIRIAM), initiated by the BioModels.net effort, is a set of guidelines for the consistent annotation and curation of computational models in biology. It is suitable for use with any struct ...
80%

BioModels


BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-link ...
78%

CellML


CellML language is an open standard based on the XML markup language. CellML is being developed by the Auckland Bioengineering Institute at the University of Auckland and affiliated research groups. The purpose of CellML is to store and exchange comp ...
78%

Systems Biology Graphical Notation


The Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in maps of biological processes. The mission of SBGN project is to develop high quality, standard graphical languages for representing biolo ...
78%

Simulation Experiment Description Markup Language


SED-ML is an XML-based format for encoding simulation setups, to ensure exchangeability and reproducibility of simulation experiments. It follows the requirements defined in the MIASE guidelines. SED-ML encodes in a computer-readable exchange format ...
73%

Systems Biology Ontology


The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modelling. It consists of seven orthogonal vocabularies defining: reaction participants roles ( ...
68%

Minimum Information About a Simulation Experiment


The MIASE Guidelines, initiated by the BioModels.net effort, are a community effort to identify the Minimal Information About a Simulation Experiment, necessary to enable the reproducible simulation experiments. Consequently, the MIASE Guidelines lis ...
65%

ModelDB


ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. A ModelDB entry contains a model's source code, concise description, and a citation of the article that published it. Models can be code ...
60%

Model Archive


The Model Archive provides a stable archive for computational macro-molecular models published in the scientific literature. The model archive provides a unique stable accession code (DOI) for each deposited model, which can be directly referenced in ...
59%

Physiome Model Repository


The Physiome Model Repository (PMR) is the main online repository for the IUPS Physiome Project, providing version and access controlled repositories, called workspaces, for users to store their data. PMR also provides a mechanism to create persisten ...
59%

Continuously Automated Model Evaluation


Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. Benchmarking results are made ...
57%

Ontology of Physics for Biology


The Ontology of Physics for Biology is a reference of classical physics as applied to the dynamics of biological systems. This resource provides a reference ontology of physical properties (e.g., pressure, chemical concentration) and principles (e.g. ...
57%

Open Modeling EXchange format


Open Modeling EXchange format (OMEX), together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), is the basis of the COMBINE Archive, a single file that supports the exchange of all the information n ...
56%

JWS Online


JWS Online is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models.
55%

Cell Behavior Ontology


The Cell Behavior Ontology (CBO) describes multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors.
52%

Pathway Ontology


The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes o ...
51%

KEGG Mark-up Language


The KEGG Markup Language (KGML) is an exchange format of the KEGG pathway maps, which is converted from internally used KGML+ (KGML+SVG) format. KGML enables automatic drawing of KEGG pathways and provides facilities for computational analysis and mo ...
50%

Chemical Markup Language


CML (Chemical Markup Language) is an XML language designed to hold most of the central concepts in chemistry. It was the first language to be developed and plays the same role for chemistry as MathML for mathematics and GML for geographical systems. ...
50%

BioModels Ontology


OWL Representation of the models in the BioModels repository.
49%

Tumor model repositories Markup Language


Originally developed as part of the FP7 Transatlantic Tumor Model Repositories project, TumorML has been developed as an XML-based domain-specific vocabulary that includes elements from existing vocabularies, to deal with storing and transmitting exi ...
45%

Enzyme Mechanism Ontology


The "Enzyme Mechanism Ontology " describes the components of an enzyme and its reaction mechanism including the roles that the components play in the reaction mechanism.
45%

Ontology and Knowledge Base of Probability Distributions


ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than 150 uni- and multivariate distributions with their defining functions, characteristics, relationships and re-parameterization formulas. It can be used for ...
43%

Numerical Markup Language


The Numerical Markup Language (NuML) (pronounce "neumeul" and not "new em el", that sounds like NewML) is a simple XML format to exchange multidimensional arrays of numbers to be used with model and simulation descriptions. NuML was initially develop ...
42%

ModelSEED Biochemistry Database


For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. The ModelSEED biochemistry database is the foundation of the biochemical data underlyi ...
40%

General Formal Ontology


The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functi ...
40%

BioSimulators


BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (support ...
38%

BioSimulations


BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model ...
35%

MDL reaction Format


MDL reaction Format is used to describe the kinetics of chemical reactions and the chemical structure of the reactants and products.
33%

eXtensible Graph Markup and Modeling Language


XGMML (eXtensible Graph Markup and Modeling Language) is an XML application based on GML which is used for graph description. XGMML uses tags to describe nodes and edges of a graph. The purpose of XGMML is to make possible the exchange of graphs betw ...
33%

BioSimulators formats for the inputs, outputs, and capabilities of biosimulation software tools


The BioSimulators conventions encompass several conventions for biosimulation tools (see below). In combination with modeling languages such as Cell-ML and SBML, SED-ML, KISAO, and COMBINE/OMEX, the BioSimulators standards enable investigators to use ...
33%

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