Roberto Alejandro Calzadilla's starred repositories
OpenFOAM-dev
OpenFOAM Foundation development repository
WholeCellEcoliRelease
Release of the whole cell E. coli model.
CellModeller
GPU-accelerated multicellular modelling framework
torchmd-cg
Example to fit parameters and run CG simulations using TorchMD and Schnet
decombinator
Decombinator v5: fast, error-correcting analysis of TCR repertoires
UC2-Software-GIT
This repository hosts all necessary software for the UC2 project.
PathogenTransmissionOntology
The Pathogen Transmission Ontology describes the transmission methods of human disease pathogens from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.
ProteiNN-Structure-Predictor
A transformer network trained to predict end-to-end single sequence protein structure as a set of angles given amino acid sequences.
Contact-Process
A spatially distributed stochastic simulation of competition for space (a lattice population of replicating particles)
Contact-Process-Ising-Model
The idea is to mix the Ising Model (IM) and the Contact Process (CP).
rdkit_scripts
Code used in Kilgore et al. NCB.
MorphoEngineering
CellModeller model files for publication on morphogenetic engineering of bacterial colonies - in submission.
partitioning_PLSR
Code related to PLSR model for predicting small molecule partitioning in 2023 Kilgore et al.
sarscov2_intrahost
SARS-CoV-2 intrahost pipeline
IDP_structural_bias
Associated data for "Structural biases in disordered proteins are prevalent in the cell"