TR&D 1 – Software

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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, [...]

2019-09-17T10:32:18-07:00August 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 [...]

2019-09-17T10:43:29-07:00May 2nd, 2018|Model, Software, TR&D 1 - Software|


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.

2019-09-17T10:16:40-07:00September 12th, 2016|Software, TR&D 1 - Software|


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.

2019-09-17T10:14:59-07:00May 2nd, 2018|Software, TR&D 1 - Software|


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.

2019-09-17T10:13:23-07:00May 2nd, 2018|Software, TR&D 1 - Software|


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 [...]

2019-09-17T09:50:21-07:00May 2nd, 2018|Software, TR&D 1 - Software|