TR&D 1 – Software

///TR&D 1 - Software

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 identifying relevant data for modeling a specific organism and environmental condition. Kinetic Datanator has a web-based graphical interface, a REST API, [...]

August 24th, 2017|Software, TR&D 1 - Software|

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 the metabolism, replication, transcription, translation, RNA and protein degradation, and cell division of a typical bacterium. The archetypal bacterium model generator [...]

May 2nd, 2018|Model, Software, TR&D 1 - Software|

WC-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.

September 12th, 2016|Software, TR&D 1 - Software|

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 helps modelers scalably, reproducibly, and comprehensibly discover and aggregate data for whole-cell models.

May 2nd, 2018|Software, TR&D 1 - Software|

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.

May 2nd, 2018|Software, TR&D 1 - Software|

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. In turn, WC-Model-Gen helps modelers build models scalably, reproducibly, and comprehensibly.

May 2nd, 2018|Software, TR&D 1 - Software|

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 for their interactions. Together, these species patterns and interaction rules enable modelers to describe the molecular complexity of any biochemical process [...]

May 2nd, 2018|Software, TR&D 1 - Software|