Karr whole-cell modeling lab

Repositories

• de_sim

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

  python simulation object-oriented-programming discrete-event-simulation computational-modelling data-driven-model
  Python MIT 1 1 14 (2 issues need help) 0 Updated Sep 9, 2020

• wc_sim

  A multi-algorithmic simulator for whole-cell models
  Python MIT 2 4 34 0 Updated Sep 9, 2020

• test_wc_lang_test_io
  0 0 0 0 Updated Sep 8, 2020

• test_wc_kb_test_io
  0 0 0 0 Updated Sep 8, 2020

• obj_tables

  Tools for creating and reusing high-quality spreadsheets

  python tsv schema csv excel data-tables object-mapping
  Python MIT 0 3 23 0 Updated Sep 8, 2020

• wc_utils

  Utilities for whole-cell modeling such as logging, plotting, managing git repos, random number generation and others
  Python MIT 1 1 4 0 Updated Sep 8, 2020

• datanator

  Toolkit for discovering and aggregating data for whole-cell modeling

  systems-biology data-discovery data-integration cells data-aggregation mathematical-modeling
  Python 2 10 11 0 Updated Sep 8, 2020

• wc_lang

  Language for describing whole-cell models as reaction networks

  simulation modeling systems-biology computational-biology cell-biology whole-cell-modeling
  Python MIT 3 5 25 0 Updated Sep 8, 2020

• wc_model_gen

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

  systems-biology computational-biology dynamical-modeling cell-biology whole-cell-modeling
  Python MIT 2 4 10 0 Updated Sep 7, 2020

• datanator_query_python

  A package to query and format the data in the integrated Datanator database
  Python MIT 0 0 1 0 Updated Sep 2, 2020

• datanator_frontend

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

  search-engine database simulation biology modeling systems-biology computational-biology
  JavaScript 1 0 17 0 Updated Aug 19, 2020

• wc_sandbox

  A public jupyter notebook server for live documentation of karr lab packages
  Python MIT 0 0 0 0 Updated Aug 12, 2020

• datanator_rest_api

  A OAS3 compliant REST API for the Datanator integrated database
  Python MIT 0 0 7 0 Updated Aug 11, 2020

• karr_lab_build_utils

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

  python unit-testing documentation coverage circleci continuous-integration sphinx
  Python MIT 0 0 1 0 Updated Jul 25, 2020

• 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
  TeX MIT 1 0 0 0 Updated Jul 21, 2020

• gdoc_down

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

  command-line google-docs google-drive-api
  Python MIT 1 9 0 0 Updated Jul 20, 2020

• wc_rules

  Rule-based modeling for whole-cell models.

  systems-biology cell-biology kinetic-modeling rule-based-modeling whole-cell-modeling
  Python MIT 3 3 5 0 Updated Jul 17, 2020

• bcforms

  Toolkit for concretely describing macromolecular complexes
  Python MIT 0 0 0 0 Updated Jul 9, 2020

• bpforms

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

  dna methylation epigenetics protein rna phosphorylation dna-damage
  Python MIT 1 3 3 0 Updated Jul 9, 2020

• wc_kb

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

  bioinformatics genomics systems-biology data-integration molecular-biology data-aggregation cell-biology
  Python MIT 5 1 12 0 Updated Jul 9, 2020

• datanator_pattern_design

  Designing pattern of Datanator data models
  Python 0 0 1 0 Updated Jul 7, 2020

• datanator_frontend_feedback_screenshots
  0 0 0 0 Updated Jun 30, 2020

• obj_tables_test_migration_repo

  Code for testing obj_tables migration
  Python MIT 0 0 0 0 Updated Jun 27, 2020

• wc_kb_gen

  Framework for constructing knowledge bases for whole-cell models
  Python MIT 0 0 6 0 Updated Jun 27, 2020

• rand_wc_model_gen

  Generate random whole-cell models
  Python MIT 0 0 3 0 Updated Jun 26, 2020

• karr_lab_aws_manager

  Package to manage AWS services run by the Karr Lab
  Python MIT 0 0 1 0 Updated Jun 26, 2020

• wc_test

  Framework for testing whole-cell knowledge bases and models
  Python MIT 0 0 0 0 Updated Jun 26, 2020

• wc_env_manager

  Tools for managing computing environments for WC modeling

  docker installation dependencies whole-cell-modeling
  Python MIT 0 0 7 0 Updated Jun 26, 2020

• unitth

  Python interface for UnitTH unit test history report generator

  html-report unit-test unitth unit-test-result-parser
  Python MIT 0 3 0 0 Updated Jun 26, 2020

• wc_analysis

  Tools for analyzing whole-cell knowledge bases, models, and simulation results

  visualization simulation systems-biology computational-biology whole-cell-modeling
  Python MIT 1 1 0 0 Updated Jun 26, 2020