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pnerf

porter5

Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes

prob

pseudotemporal progression-based Bayesian method for inferring GRNs from cross-sectional clinical transcriptomic data

proteinevolutiontoolbox

proteinnet

Standardized data set for machine learning of protein structure

provis

Official code repository of "BERTology Meets Biology: Interpreting Attention in Protein Language Models."

pyabc

distributed, likelihood-free inference

pybnf

An application for fitting systems biology models using metaheuristic algorithms

pydream

pyfba

A python implementation of flux balance analysis to model microbial metabolism

pyme

Python Solver for The Chemical Master Equation

pypesto

python Parameter EStimation TOolbox

pypiret

Pythonic PiReT

pysb

Python framework for Systems Biology modeling

pysster

pysster: Learning Sequence And Structure Motifs In Biological Sequences Using Convolutional Neural Networks

pythoncyc

pyvipr

Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML

r4kappa

Set of packages designed to bridge kappa language modelling and bioinformatics.

racipe-1.0

Random Circuit Perturbation Method

raven

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

rc_e_coli

MATLAB code for resource competition and growth modelling in E.coli

rctd

rebop

Fast stochastic simulator for chemical reaction networks

recon3d

A 3-Dimensional View of Human Metabolism and Disease

redm

Applications of Empirical Dynamic Modeling from Time Series

reframed

ReFramed: metabolic modeling package

res4flu

Resources for Influenza Research

resourceawarewholecellmodel

Here, we model a two-strain consortium, with one strain expressing an endohydrolase and a second strain expressing an exohydrolase, for cooperative degradation of a complex substrate.

rgn

Recurrent Geometric Networks for end-to-end differentiable learning of protein structure

rlmolecule