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. [...]
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 [...]
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 [...]
Kinetic Datanator is a tool for discovering the data needed to build, calibrate, and validate whole-cell models. Kinetic Datanator is composed of an integrated database of experimental data for whole-cell modeling and tools for identifying relevant data for modeling a specific organism and environmental condition. Kinetic Datanator has a web-based graphical interface, a REST [...]
libRoadRunner is a high-performance and portable simulation engine for systems and synthetic biology. It can run on many platforms including Windows, Mac OS, and Linux. libRoadRunner is a major rewrite of the original C# roadRunner developed by Frank Bergmann and Herbert Sauro. The same original functionality however remains, including the original C API, the [...]
The Random Whole-cell model generator is a tool for generating WC models that represent user-specified numbers of genes, RNA, proteins, and reactions of an archetypal bacterium. The models generated by the model generator represent the metabolism, replication, transcription, translation, RNA and protein degradation, and cell division of a typical bacterium. The archetypal bacterium model [...]
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 [...]
Tellurium (te.) is a Python environment based on spyder2 IDE. It combines a number of existing libraries, including libSBML, libRoadRunner (including libStruct), libAntimony, and is extensible via telPlugins. In addition, other tools kits such as matplotlib and NumPy are used to provide additional analysis and plotting support. On Windows, Tellurium comes with pip, so [...]
VCell (Virtual Cell) is a comprehensive platform for modeling cell biological systems that are built on a central database and disseminated as a web application. VCell permits the construction of models, application of numerical solvers to perform simulations, and analysis of simulation results, offering the choice of multiple physical approximations and simulation technologies to [...]
