Karr whole-cell modeling lab

All

64 repositories

datanator_rest_api
Public
A OAS3 compliant REST API for the Datanator integrated database
Python
•
MIT License
•3•0•7•1•Updated Oct 18, 2022Oct 18, 2022
wc_rules
Public
Rule-based modeling for whole-cell models.
systems-biology cell-biology kinetic-modeling rule-based-modeling whole-cell-modeling
Python
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MIT License
•3•10•1•0•Updated May 20, 2022May 20, 2022
wc_utils
Public
Utilities for whole-cell modeling such as logging, plotting, managing git repos, random number generation and others
Python
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MIT License
•1•1•5•0•Updated Apr 29, 2022Apr 29, 2022
datanator
Public
Toolkit for discovering and aggregating data for whole-cell modeling
systems-biology data-discovery data-integration cells data-aggregation mathematical-modeling
Python
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MIT License
•3•15•7•0•Updated Jan 19, 2022Jan 19, 2022
karr_lab_website
Public
Code for the Karr Lab website
HTML
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MIT License
•0•0•1•1•Updated Nov 24, 2021Nov 24, 2021
Cell_model
Public
FBA Cell Modeling Project
Python
•2•0•0•0•Updated Aug 13, 2021Aug 13, 2021
wc_kb
Public
Tools for building databases of experimental data for constructing whole-cell models
bioinformatics genomics systems-biology data-integration molecular-biology data-aggregation cell-biology whole-cell-modeling
Python
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MIT License
•5•4•12•0•Updated Jul 8, 2021Jul 8, 2021
wc_model_gen
Public
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 License
•2•6•9•0•Updated Jul 6, 2021Jul 6, 2021
obj_tables
Public
Tools for creating and reusing high-quality spreadsheets
tsv csv excel data-tables object-mapping relational-data python schema complex-datasets
Python
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MIT License
•2•8•25•0•Updated Jun 14, 2021Jun 14, 2021
wc_kb_gen
Public
Framework for constructing knowledge bases for whole-cell models
Python
•
MIT License
•0•0•4•0•Updated Jun 13, 2021Jun 13, 2021
wc_env_manager
Public
Tools for managing computing environments for WC modeling
docker installation dependencies whole-cell-modeling
Python
•
MIT License
•0•0•7•0•Updated Jun 13, 2021Jun 13, 2021
wc_sim
Public
A multi-algorithmic simulator for whole-cell models
Jupyter Notebook
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MIT License
•2•6•36•0•Updated Jun 3, 2021Jun 3, 2021
wc_test
Public
Framework for testing whole-cell knowledge bases and models
Python
•
MIT License
•0•0•0•0•Updated May 28, 2021May 28, 2021
rand_wc_model_gen
Public
Generate random whole-cell models
Python
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MIT License
•0•1•3•0•Updated May 28, 2021May 28, 2021
conv_opt
Public
Python package for linear and quadratic programming
python linear-programming quadratic-programming convex-optimization
Python
•
MIT License
•2•9•2•0•Updated May 28, 2021May 28, 2021
wc_lang
Public
Language for describing whole-cell models as reaction networks
simulation modeling systems-biology computational-biology cell-biology whole-cell-modeling
Python
•
MIT License
•3•9•30•0•Updated May 24, 2021May 24, 2021
wc_rules_deps
Public
Instructions to build docker image for wc_rules
Dockerfile
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MIT License
•0•0•0•0•Updated May 20, 2021May 20, 2021
datanator_frontend
Public
Graphical web-based interface for the Datanator toolkit for discovering data for modeling cells
search-engine database simulation biology modeling systems-biology computational-biology cell molecular-biology
JavaScript
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MIT License
•1•1•16•1•Updated Jan 5, 2021Jan 5, 2021
datanator_frontend_feedback_screenshots
Public
0•0•0•0•Updated Dec 18, 2020Dec 18, 2020
de_sim
Public
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
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MIT License
•6•32•15•1•Updated Dec 17, 2020Dec 17, 2020
wc_onto
Public
Ontology for whole-cell modeling
bioinformatics systems-biology computational-biology ontology single-cell whole-cell-modeling
Python
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MIT License
•0•1•0•0•Updated Dec 16, 2020Dec 16, 2020
wc_sandbox
Public
A public jupyter notebook server for live documentation of karr lab packages
Python
•
MIT License
•0•1•0•0•Updated Oct 29, 2020Oct 29, 2020
datanator_query_python
Public
A package to query and format the data in the integrated Datanator database
Python
•
MIT License
•2•0•1•0•Updated Oct 27, 2020Oct 27, 2020
karr_lab_aws_manager
Public
Package to manage AWS services run by the Karr Lab
Python
•
MIT License
•0•0•1•0•Updated Oct 9, 2020Oct 9, 2020
bpforms
Public
Toolkit for concretely describing non-canonical DNA, RNA, and proteins
dna methylation epigenetics protein rna phosphorylation dna-damage proteoform post-transcriptional-regulation post-translational-modification
Python
•
MIT License
•2•6•5•0•Updated Oct 5, 2020Oct 5, 2020
gdoc_down
Public
Command line programs to save Google documents to text and LaTeX files
latex command-line google-drive google-docs google-drive-api
Python
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MIT License
•2•15•2•0•Updated Oct 2, 2020Oct 2, 2020
karr_lab_build_utils
Public
Utilities for testing Python code and its downstream dependencies, submitting coverage reports, conducting static analyses, and generating documenation
python unit-testing documentation coverage continuous-integration circleci sphinx packaging-python
Python
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MIT License
•0•0•1•0•Updated Jul 25, 2020Jul 25, 2020
paper_cell_sys__guidelines_4_repro_models_2020
Public
Data and code used by Porubsk, Goldberg, et al., Best practices for making reproducible biochemical models, to be published in Cell Systems, 2020
TeX
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MIT License
•1•0•0•0•Updated Jul 21, 2020Jul 21, 2020
bcforms
Public
Toolkit for concretely describing macromolecular complexes
Python
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MIT License
•0•0•0•0•Updated Jul 9, 2020Jul 9, 2020
datanator_pattern_design
Public
Designing pattern of Datanator data models
Python
•0•0•1•0•Updated Jul 7, 2020Jul 7, 2020