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 [...]
As part of the CRBM’s annotation and simulation service, we have selected the following models which abide by the agreed standards and annotation practices as defined in Annotation Protocol. These models cover a wide range of domains and include semantic annotations of physical processes (including chemical reactions, molar flow rates, rates of changes of [...]
The H1 human embryonic stem cell (hESC) model is the first step toward whole-cell models of human cells. The model will represent the core cellular functions of all human cells including their metabolism, DNA replication, transcription, translation, protein complexation, RNA and protein degradation, and division. The model focuses on H1-hESCs because ESCs behave as individual [...]
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 M. genitalium whole-cell model was the first model that represented each characterized gene function of an organism. The model is composed of 28 submodels of 28 cellular processes. In total, the model represents the functions of 401 genes, 722 compounds, 1,857 reactions, and 1,836 parameters. In addition to demonstrating the feasibility of whole-cell models, [...]
The Mycoplasma pneumoniae whole-cell model will be the most comprehensive, most systematically constructed, and most extensible whole-cell model to date. The model will represent all of the major cellular functions of M. pneumoniae, including the function each characterized gene. The model will be based primarily on M. pneumoniae genomic data. The model will be used [...]
