KarrLab/bpforms

Stars
6
Rank 2,526,772 (Top 51 %)
Language
Python
License
MIT License
Created over 5 years ago
Updated almost 4 years ago

KarrLab/bpforms

KarrLab

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

de_sim

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

latex-grant

LaTeX classes for formatting scientific documents, including US federal grant proposals.

intro_to_wc_modeling

Whole-cell modeling tutorials

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

wc_lang

Language for describing whole-cell models as reaction networks

conv_opt

Python package for linear and quadratic programming

wc_rules

Rule-based modeling for whole-cell models.

obj_tables

Tools for creating and reusing high-quality spreadsheets

wc_sim

A multi-algorithmic simulator for whole-cell models

Jupyter Notebook

wc_model_gen

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

SynNetGen

Software to generate synthetic dynamic transcriptomic and proteomic data

unitth

Python interface for UnitTH unit test history report generator

WcModelingTutorial

wc_kb

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

paper_2018_curr_opin_biotechnol

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

wc_analysis

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

rand_wc_model_gen

Generate random whole-cell models

wc_onto

Ontology for whole-cell modeling

datanator_frontend

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

examples_for_presentations

Examples for presentations

wc_utils

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

wc_sandbox

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