libOMEXMeta C++ and Python libraries
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 [...]
NLIMED
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 [...]
ObjTables
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 [...]
Datanator
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, [...]
Kinetic Datanator
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 [...]
libRoadRunner
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# [...]
Random WC model generator
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 [...]
SemGen
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. [...]
Tellurium
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 [...]
VCell
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 [...]
WC-KB
Whole-cell KB (WC-KB) is a data model for describing the experimental data needed to build, calibrate, and validate a whole-cell model. WC-KB includes a command line program and a Python API. Whole-cell KB [...]
WC-KB-Gen
WC-KB-Gen is a Python framework for programmatically constructing knowledge bases for whole-cell models. WC-KB-Gen helps modelers retrieve data from external sources, organize this data, and record the provenance of this data. In turn, WC-KB-Gen [...]
WC-Lang
WC-Lang is a data model and a file format for describing composite, multi-algorithmic whole-cell models. WC-Lang includes a command line interface and a Python API. WC-Lang
WC-Model-Gen
WC-Model-Gen is a Python framework for programmatically constructing whole-cell models from large datasets described with WC-KB. WC-Model-Gen helps modelers retrieve data from a WC-KB and use the data to scalably design species and reactions. [...]
WC-Rules
WC-Rules is a formalism for describing composite, mixed-grained, multi-algorithmic WC models. WC-Rules provides modelers a high-level, biologically-intuitive language for describing models in terms of patterns of metabolite, DNA, RNA, and protein species, and rules [...]
WholeCellSimDB
WholeCellSimDB.org is a database of whole-cell model simulations designed to make it easy for researchers to explore and analyze whole-cell model predictions including predicted: Metabolite concentrations, DNA, RNA and protein expression, DNA-bound protein positions, [...]
WholeCellViz
WholeCellViz.org is a web-based software program for visually analyzing whole-cell simulations. WholeCellViz enables users to interactively analyze many aspects of cell physiology including: Cell mass, volume, and shape, Metabolite, RNA, and protein copy numbers, [...]