With the growing complexity and quantity of biosimulation models, annotation tools that can accommodate a variety of modeling languages and simulation environments were needed to encourage models which could be easily understood and uniquely identified. The COMBINE community developed a consensus on the utilities required for this open-source, cross-platform software library for model annotation. [...]
As a common language to represent annotations for models, we have developed, in close collaboration with the COMBINE community, the OMEX metadata specification. This standard provides not only the specification of sharable, RDF formatted annotations, but also detailed examples and a set of recommended biological ontologies to use in those annotations. This standard is [...]
The Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories(NLIMED) was developed by Yuda Munarko to convert natural language queries into the SPARQL syntax which is typically used to search semantic annotations encoded in RDF. The SPARQL syntax is complex and rigid, making it difficult to understand and use for many modeling [...]
The Simulation Experiment Description Markup Language (SED-ML) is a standardized, community-based format that explicitly describes simulation processes for biochemical models, ensuring that researchers who are interested in a published model can efficiently reproduce and build upon that model. Its use is independent of specific operating systems or versions of software. The CRBM and COMBINE [...]
BioSimulations is a free platform for sharing and re-using biomodels, simulations, simulation results, and visualizations of simulation results. BioSimulations supports a wide range of frameworks (e.g., logical, Flux-Balance Analysis (FBA), continuous kinetic, discrete kinetic), simulation algorithms (e.g., FBA, SSA), model formats (e.g., SBML), and tools (e.g., COBRApy, COPASI, tellurium). BioSimulations, developed by Jonathan Karr, [...]
runBioSimulations is a free tool for running a wide range of biological simulations. Through the BioSimulators registry of biosimulation tools, runBioSimulations supports a broad range of modeling frameworks (e.g., logical, kinetic), simulation algorithms (e.g., FBA, SSA), modeling formats (e.g., SBML, SED-ML), and simulation tools (e.g., COBRApy, COPASI). run.biosimulations.org
BioSimulators is a free registry of biosimulation tools. The registry includes tools for a broad range of frameworks (e.g., logical, kinetic), simulation algorithms (e.g., FBA, SSA), and model formats (e.g., BNGL, CellML, NeuroML/LEMS, SBML, Smoldyn). Many of the simulation tools provide Python packages, command-line programs, and Docker images with consistent interfaces. Together, BioSimulators makes it [...]
https://youtu.be/OJmqtJey4zg ObjTables is a community initiative to make supplementary spreadsheets to journal articles - one of the most common methods for sharing scientific data - more reusable. The long-term goal is to create an ecosystem of reusable data for comparative and integrative research. ObjTables combines the ease of use of spreadsheets (XLSX file [...]
Danator is an integrated database of molecular data designed to facilitate integrative analysis of multiple cellular subsystems. To help investigators overcome the lack of complete data about every molecule and reaction in every organism, Datanator includes tools for building "clouds" of data that include data about chemically similar molecules and reactions in phylogenetically similar [...]
SemGen is an experimental software tool for automating the modular composition and decomposition of biosimulation models. SemGen facilitates the construction of complex, integrated models, and the swift extraction of reusable sub-models from larger ones. SemGen relies on the semantically-rich SemSim model description format to help automate these modeling tasks. With SemGen, users can: Visualize [...]
