migp11 Goto Github PK

alephsys.github.io

booleannet

Boolean Network Modeling

chisim

Chicago Social Interaction Model (chiSIM) framework repository

cobra_cbm_tutorial

This a basic tutorial on Constraint-Based Metabolic Modeling based on python-cobra

cobrapy

COBRApy is a package for constraint-based modeling of biological networks

cobrapy-tutorial

A tutorial on cobrapy

consistency-analysis

consistency_analysis

Python implementation of the unconnected modules detection method.

corda

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

csm4cobra

A set of functions and scripts to perform context-specific gene deletions in-silico experiments on genome-scale metabolic models

eccb2020-t05

Material for the tutorial 05 of ECCB (Computational modelling of cellular processes: regulatory vs metabolic systems)

epicommute

Simulate an epidemic metapopulation model with mobility-reducing containment strategies

gim3e

Gene Inactivation Moderated by Metabolism, Metabolomics, and Expression (COBRApy)

isim

Python, R, and Matlab code relating to the iSIM manuscript

mcadre

metabolic Context-specificity Assessed by Deterministic Reaction Evaluation (mCADRE) for generating draft tissue-specific metabolic models

mig-testing

this is just a test to lear how to connect data to zeno

mmcacovid19.jl

Microscopic Markov Chain Approach to model the spreading of COVID-19

pctk

A set of scripts and utilities to analyze PhysiCell/hisyBoSS simulations

physibossv2-emews

EMEWS template for PhysiBoSSa

physibossv2_tnf_model

physicell-povwriter

Simple cutaway POV-Ray

physicelldfba

PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch. Thanks!

practica_fba

pyfastcore

A python implementation of the context-specific model extraction method FastCore by Vlassis et al. (2014).

python-loader

Python data loader for PhysiCell digital snapshots

scikit-mobility

scikit-mobility: mobility analysis in Python

spheroid-tnf-v2-emews

thesis_supp_material