Karr whole-cell modeling lab

de_sim

Python-based object-oriented discrete-event simulation tool for complex, data-driven modeling

datanator

Toolkit for discovering and aggregating data for whole-cell modeling

gdoc_down

Command line programs to save Google documents to text and LaTeX files

conv_opt

Python package for linear and quadratic programming

wc_lang

Language for describing whole-cell models as reaction networks

wc_rules

Rule-based modeling for whole-cell models.

obj_tables

Tools for creating and reusing high-quality spreadsheets

bpforms

Toolkit for concretely describing non-canonical DNA, RNA, and proteins

wc_sim

A multi-algorithmic simulator for whole-cell models

wc_model_gen

Framework for systematically and scalably designing whole-cell models from large datasets

wc_kb

Tools for building databases of experimental data for constructing whole-cell models

datanator_frontend

Graphical web-based interface for the Datanator toolkit for discovering data for modeling cells

rand_wc_model_gen

Generate random whole-cell models

wc_onto

Ontology for whole-cell modeling

wc_sandbox

A public jupyter notebook server for live documentation of karr lab packages

wc_utils

Utilities for whole-cell modeling such as logging, plotting, managing git repos, random number generation and others

datanator_rest_api

A OAS3 compliant REST API for the Datanator integrated database

karr_lab_website

Code for the Karr Lab website

wc_kb_gen

Framework for constructing knowledge bases for whole-cell models

wc_rules_deps

Instructions to build docker image for wc_rules

bcforms

Toolkit for concretely describing macromolecular complexes

Cell_model

FBA Cell Modeling Project

datanator_frontend_feedback_screenshots

datanator_pattern_design

Designing pattern of Datanator data models

datanator_query_python

A package to query and format the data in the integrated Datanator database

karr_lab_aws_manager

Package to manage AWS services run by the Karr Lab

karr_lab_build_utils

Utilities for testing Python code and its downstream dependencies, submitting coverage reports, conducting static analyses, and generating documenation

paper_cell_sys__guidelines_4_repro_models_2020

Data and code used by Porubsk, Goldberg, et al., Best practices for making reproducible biochemical models, to be published in Cell Systems, 2020

wc_env_manager

Tools for managing computing environments for WC modeling

wc_test

Framework for testing whole-cell knowledge bases and models