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2022-sbi-ci-workshop

biomart

Python biomart API

bridge-simple

An faster implementation of the BRIDGE keyword in Plumed

comet

C++ code for optimising coefficients of individual CVs for PCV MD simulations

folding-gillespie-mc

C++ code for simulating folding and unfolding of protein domains using the Gillespie algorithm

general-path

C++ implementation of the general PCV as a function for Plumed

gervasio-protein-dynamics

A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery

gillespie-mc

C++ code for simulating a system of reactions using the Gillespie algorithm

lioness_sparsity_testing

netzoopy

netZooPy is a network biology package implemented in Python.

phafin2

Software for Phafin2 manuscript

plumed2

Development version of plumed 2

retriever

Generate Robust Disease-Specific Response Signatures from the LINCS-L1000 Data

scorpion

Supplementary information for "Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomic data"

sim-plusplus

C++ code for doing simple molecular dynamics of particles with Lennard-Jones potential

software_quality_seminars

This is a repo for scripts and documents that are related to the NCMM Software quality seminars.

sponge

A Python package to generate prior gene regulatory networks.

stoat

A Python package to generate spatially resolved gene regulatory networks from spatial transcriptomics data.