Systems and Synthetic Biology's repositories
carveme
CarveMe: genome-scale metabolic model reconstruction
smetana
SMETANA: a tool to analyse interactions in microbial communities
reframed
ReFramed: metabolic modeling package
rc_e_coli
MATLAB code for resource competition and growth modelling in E.coli
community-simulator
Simulate microbial community batch culture experiments.
PanGEM
Pangenome-scale metabolic network reconstruction, analysis, and strain-model extraction
ncmw
A metabolic modeling workflow for communities of organisms in an nasal medium.
designmc
Designing microbial communities
Cocktail-phage-infection-kinetics
Cocktail is a program for mathematical modelling of bacteriophage (phage) infection kinetics. Cocktail is a Windows 64-bit program and the source code can be developed in the directions that users see fit. This will be updated soon with a link to the scientific publication describing the program.
Baranwal_et_al_2022
PyTorch Implementation of LSTM-based dynamical model for predicting species abundance and metabolite concentrations in a heterogeneous community
d2d
a modeling environment tailored to parameter estimation in dynamical systems
mutualistic-crossfeeding
Kinetic Monte Carlo simulator for cross-feeding species growth
scTOP
A package for identifying cell phenotype from single-cell RNA-sequencing data.
NESS-Topology
This contains notebook associated with paper "Thermodynamic origins of topological protection in nonequilibrium stochastic systems" by Mehta and Rocks.
EcosystemAssembly
Repository for my code attempting to address the problem of the thermodynamics of ecosystem assembly.
marm2-supplement
Supplementary Material for the MARM2.0 model
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.
rebop
Fast stochastic simulator for chemical reaction networks
biobox
a toolbox for the manipulation, modelling and analysis of molecular structures
genCRN
genCRN: Fast enumeration of non-isomorphic chemical reaction networks
HiOrCo
Higher-Order Co-occurrence
ssGSEA2.0
Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)