Tag: modeling and simulation

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 ...

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 ...

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 ...

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 ...

BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange bet ...

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 ...

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 ...

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 ( ...

The Kinetic Simulation Algorithm Ontology aims at providing support in unambiguously referring to simulation algorithms when describing a simulation experiment. It describes and classifies existing algorithms and their inter-relationships through the ...

PharmML is an exchange format for non-linear mixed effect models used in pharmacometrics and provides means to encode models, trial designs, and modelling steps. This standard allows for a smooth exchange of models between different software tools us ...

The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.

The Synthetic Biology Open Language (SBOL) is a standard used for the in silico representation of genetic designs. SBOL is designed to allow synthetic biologists and genetic engineers to electronically exchange designs, send and receive genetic desig ...

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 ...

The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more.

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 ...

FieldML is a declarative language for building hierarchical models represented by generalized mathematical fields. FieldML is developed as a data model and accompanying API. FieldML can be used to represent the dynamic 3D geometry and solution fields ...

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 ...

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 ...

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

Database of all known neuronal connections of the rat brainstem. Connections are directed, weighted and bilateral. It is built using the neuroVIISAS platform. The Brainstem Connectome is a highly structured neuroontology composed of datasets from ove ...

Systems Biology Results markup language (SBRML) specifies models composed of molecular species, and their interactions (including reactions). The markup language is intended to specify results from operations carried out on models Ñ SBRML. This resou ...

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. ...

The BioModels Ontology is an OWL Representation of the models in the BioModels repository. This resource has not been updated recently within BioPortal, and no official homepage can be found, therefore we have marked its status as Uncertain. Please g ...

Classification of the types of mathematical models used mostly in the life sciences, the types of variables, the types of readout and other relevant features.

The CardioVascular Research Grid (CVRG) project is creating an infrastructure for sharing cardiovascular data and data analysis tools. CVRG tools are developed using the Software as a Service model, allowing users to access tools through their browse ...

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 ...

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator cu ...

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 ...

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 ...

Atomistic Molecular Dynamics Simulation Trajectories and Analyses of Nucleic Acid Structures. BIGNASim is a complete platform to hold and analyse nucleic acids simulation data, based on two noSQL database engines: Cassandra to hold trajectory data an ...

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 ...

The anaeeThes thesaurus aims at providing a controlled vocabulary for the semantic description of the study of continental ecosystems and their biodiversity. The thesaurus consists of concepts handled in different main thematic areas: abiotic (e.g. a ...

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 ...

CNO is a controlled vocabulary of terms used in Computational Neurosciences to describe models of the nervous system. This first release of CNO is an alpha version and should be further aligned with other ontologies accessible on Bioportal and should ...

EngMeta is a metadata model for data from computational engineering based on existing standards and developed to enable a structured documentation of the research process and the simulation environment all together with discipline specific informatio ...

The Virtual Parts Repository (VPR) is a repository of reusable, modular and composable models of biological parts.

The Ocean Data Explorer allows scientists, managers, and the general public to discover and access information including real-time conditions, operational and research forecasts, satellite observations, and other spatially referenced datasets that de ...

The international Network for the Detection of Atmospheric Composition Change (NDACC) is composed of more than 70 globally distributed, ground-based, remote-sensing research stations with more than 160 currently active instruments. The repository is ...