Projects in Awesome Lists by KarrLab
A curated list of projects in awesome lists by KarrLab .
https://github.com/karrlab/de_sim
Python-based object-oriented discrete-event simulation tool for complex, data-driven modeling
computational-modelling data-driven-model discrete-event-simulation object-oriented-programming python simulation
Last synced: 24 Jul 2025
https://github.com/KarrLab/de_sim
Python-based object-oriented discrete-event simulation tool for complex, data-driven modeling
computational-modelling data-driven-model discrete-event-simulation object-oriented-programming python simulation
Last synced: 22 Apr 2025
https://github.com/karrlab/latex-grant
LaTeX classes for formatting scientific documents, including US federal grant proposals.
Last synced: 25 Jun 2025
https://github.com/karrlab/intro_to_wc_modeling
Whole-cell modeling tutorials
cell-modeling computational-biology dynamical-modeling systems-biology
Last synced: 13 Oct 2025
https://github.com/karrlab/gdoc_down
Command line programs to save Google documents to text and LaTeX files
command-line google-docs google-drive google-drive-api latex
Last synced: 27 Aug 2025
https://github.com/karrlab/datanator
Toolkit for discovering and aggregating data for whole-cell modeling
cells data-aggregation data-discovery data-integration mathematical-modeling systems-biology
Last synced: 02 Sep 2025
https://github.com/karrlab/wc_rules
Rule-based modeling for whole-cell models.
cell-biology kinetic-modeling rule-based-modeling systems-biology whole-cell-modeling
Last synced: 25 Jun 2025
https://github.com/karrlab/conv_opt
Python package for linear and quadratic programming
convex-optimization linear-programming python quadratic-programming
Last synced: 25 Jun 2025
https://github.com/karrlab/wc_lang
Language for describing whole-cell models as reaction networks
cell-biology computational-biology modeling simulation systems-biology whole-cell-modeling
Last synced: 18 Aug 2025
https://github.com/karrlab/obj_tables
Tools for creating and reusing high-quality spreadsheets
complex-datasets csv data-tables excel object-mapping python relational-data schema tsv
Last synced: 01 Aug 2025
https://github.com/karrlab/wc_model_gen
Framework for systematically and scalably designing whole-cell models from large datasets
cell-biology computational-biology dynamical-modeling systems-biology whole-cell-modeling
Last synced: 25 Jun 2025
https://github.com/karrlab/wc_sim
A multi-algorithmic simulator for whole-cell models
Last synced: 25 Jun 2025
https://github.com/karrlab/bpforms
Toolkit for concretely describing non-canonical DNA, RNA, and proteins
crosslinks dna dna-damage epigenetics methylation phosphorylation post-transcriptional-regulation post-translational-modification protein proteoform rna
Last synced: 25 Jun 2025
https://github.com/karrlab/wc_kb
Tools for building databases of experimental data for constructing whole-cell models
bioinformatics cell-biology data-aggregation data-integration genomics molecular-biology systems-biology whole-cell-modeling
Last synced: 03 Sep 2025
https://github.com/karrlab/synnetgen
Software to generate synthetic dynamic transcriptomic and proteomic data
Last synced: 03 Feb 2026
https://github.com/karrlab/unitth
Python interface for UnitTH unit test history report generator
html-report unit-test unit-test-result-parser unitth
Last synced: 25 Jun 2025
https://github.com/karrlab/paper_2018_curr_opin_biotechnol
Code associated with the Karr Lab's 2018 whole-cell modeling review in Current Opinion in Biotechnology
computational-biology dynamical-modeling mathematical-model systems-biology
Last synced: 31 Oct 2025
https://github.com/karrlab/wc_analysis
Tools for analyzing whole-cell knowledge bases, models, and simulation results
computational-biology simulation systems-biology visualization whole-cell-modeling
Last synced: 25 Jun 2025
https://github.com/karrlab/wc_onto
Ontology for whole-cell modeling
bioinformatics computational-biology ontology single-cell systems-biology whole-cell-modeling
Last synced: 16 Oct 2025
https://github.com/karrlab/datanator_frontend
Graphical web-based interface for the Datanator toolkit for discovering data for modeling cells
biology cell computational-biology database modeling molecular-biology search-engine simulation systems-biology
Last synced: 09 Oct 2025
https://github.com/karrlab/rand_wc_model_gen
Generate random whole-cell models
Last synced: 15 Oct 2025
https://github.com/karrlab/wc_sandbox
A public jupyter notebook server for live documentation of karr lab packages
Last synced: 14 Jul 2025
https://github.com/karrlab/wc_utils
Utilities for whole-cell modeling such as logging, plotting, managing git repos, random number generation and others
Last synced: 25 Jun 2025
https://github.com/karrlab/examples_for_presentations
Examples for presentations
Last synced: 09 Oct 2025
https://github.com/karrlab/datanator_rest_api
A OAS3 compliant REST API for the Datanator integrated database
Last synced: 08 Oct 2025
https://github.com/karrlab/obj_tables_revisioning_tutorial_repo
Dummy repository for the ObjTables tutorial on revisioning and migration
Last synced: 31 Jan 2026
https://github.com/karrlab/wc_rules_deps
Instructions to build docker image for wc_rules
Last synced: 02 Feb 2026
https://github.com/karrlab/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
Last synced: 02 Feb 2026
https://github.com/karrlab/wc_school_2019
Examples and exercises for the 2019 whole-cell modeling summer school
Last synced: 10 Jul 2025
https://github.com/karrlab/wc_kb_gen
Framework for constructing knowledge bases for whole-cell models
Last synced: 10 Jul 2025
https://github.com/karrlab/wc_env_manager
Tools for managing computing environments for WC modeling
dependencies docker installation whole-cell-modeling
Last synced: 25 Jun 2025
https://github.com/karrlab/test_history_server
Unit test history report server
Last synced: 25 Jun 2025
https://github.com/karrlab/karr_lab_aws_manager
Package to manage AWS services run by the Karr Lab
Last synced: 25 Jun 2025
https://github.com/karrlab/datanator_query_python
A package to query and format the data in the integrated Datanator database
Last synced: 25 Jun 2025
https://github.com/karrlab/pkg_utils
Utilities for packaging Python code
packaging pip requirements setuptools
Last synced: 25 Jun 2025
https://github.com/karrlab/bcforms
Toolkit for concretely describing macromolecular complexes
Last synced: 25 Jun 2025
https://github.com/karrlab/nose2unitth
Convert nose-style test reports to UnitTH-style test reports
Last synced: 25 Jun 2025
https://github.com/karrlab/karr_lab_build_utils
Utilities for testing Python code and its downstream dependencies, submitting coverage reports, conducting static analyses, and generating documenation
circleci continuous-integration coverage documentation packaging-python python sphinx unit-testing
Last synced: 25 Jun 2025
https://github.com/karrlab/wc_test
Framework for testing whole-cell knowledge bases and models
Last synced: 25 Jun 2025
https://github.com/karrlab/wc_cli
Whole-cell models and whole-cell modeling tools
Last synced: 25 Jun 2025
https://github.com/karrlab/obj_tables_test_schema_repo
Test schema repository for obj_tables migration
Last synced: 25 Jun 2025
https://github.com/karrlab/obj_tables_test_migration_repo
Code for testing obj_tables migration
Last synced: 25 Jun 2025
https://github.com/karrlab/paper_2018_curr_opin_sys_biol
Code associated with our 2018 review in Current Opinion in Systems Biology
biology citations corresponding-author email-address europe-pmc mathematical-modelling simulation
Last synced: 25 Jun 2025
https://github.com/karrlab/karr_lab_data
Code for the Karr Lab data website
Last synced: 25 Jun 2025
https://github.com/karrlab/karr_lab_code
Code for the Karr Lab's code website
Last synced: 25 Jun 2025
https://github.com/karrlab/datanator_pattern_design
Designing pattern of Datanator data models
Last synced: 25 Jun 2025
https://github.com/karrlab/distribution_script
Scripts to generate protein abundance distributions per publication in paxdb
Last synced: 25 Jun 2025
https://github.com/karrlab/karr_lab_docs
Code for the Karr Lab docs website
documentation whole-cell-modeling
Last synced: 29 Oct 2025