Karr whole-cell modeling lab (@KarrLab)
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KarrLab

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Top repositories

1

de_sim

Python-based object-oriented discrete-event simulation tool for complex, data-driven modeling
Python
32
star
2

latex-grant

LaTeX classes for formatting scientific documents, including US federal grant proposals.
TeX
23
star
3

intro_to_wc_modeling

Whole-cell modeling tutorials
Python
16
star
4

datanator

Toolkit for discovering and aggregating data for whole-cell modeling
Python
15
star
5

gdoc_down

Command line programs to save Google documents to text and LaTeX files
Python
15
star
6

wc_rules

Rule-based modeling for whole-cell models.
Python
10
star
7

wc_lang

Language for describing whole-cell models as reaction networks
Python
9
star
8

conv_opt

Python package for linear and quadratic programming
Python
9
star
9

obj_tables

Tools for creating and reusing high-quality spreadsheets
Python
8
star
10

wc_model_gen

Framework for systematically and scalably designing whole-cell models from large datasets
Python
6
star
11

bpforms

Toolkit for concretely describing non-canonical DNA, RNA, and proteins
Python
6
star
12

wc_sim

A multi-algorithmic simulator for whole-cell models
Jupyter Notebook
6
star
13

SynNetGen

Software to generate synthetic dynamic transcriptomic and proteomic data
MATLAB
4
star
14

wc_kb

Tools for building databases of experimental data for constructing whole-cell models
Python
4
star
15

WcModelingTutorial

Python
3
star
16

unitth

Python interface for UnitTH unit test history report generator
Python
3
star
17

paper_2018_curr_opin_biotechnol

Code associated with the Karr Lab's 2018 whole-cell modeling review in Current Opinion in Biotechnology
Python
2
star
18

wc_analysis

Tools for analyzing whole-cell knowledge bases, models, and simulation results
Python
1
star
19

rand_wc_model_gen

Generate random whole-cell models
Python
1
star
20

wc_onto

Ontology for whole-cell modeling
Python
1
star
21

datanator_frontend

Graphical web-based interface for the Datanator toolkit for discovering data for modeling cells
JavaScript
1
star
22

examples_for_presentations

Examples for presentations
Python
1
star
23

wc_utils

Utilities for whole-cell modeling such as logging, plotting, managing git repos, random number generation and others
Python
1
star
24

wc_sandbox

A public jupyter notebook server for live documentation of karr lab packages
Python
1
star