racalzadilla

LoMRF

LoMRF is an open-source implementation of Markov Logic Networks

crewAI

Framework for orchestrating role-playing, autonomous AI agents. By fostering collaborative intelligence, CrewAI empowers agents to work together seamlessly, tackling complex tasks.

IDP_structural_bias

Associated data for "Structural biases in disordered proteins are prevalent in the cell"

OpenFOAM-dev

OpenFOAM Foundation development repository

torchmd-cg

Example to fit parameters and run CG simulations using TorchMD and Schnet

nomen

A nomenclatural ontology for names (not concepts).

miapa

Minimum Information About a Phylogenetic Analysis (MIAPA) vocabularies and tools

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.

cido

CIDO: Coronavirus Infectious Disease Ontology

ssbio

A Python framework for structural systems biology

SBO

The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling.

ino

INO: Interaction Network Ontology

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.

jaccard

Statistical test of similarity between binary data using the Jaccard/Tanimoto coefficients

flexidot

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

WholeCellEcoliRelease

Release of the whole cell E. coli model.

covid19_oral

sarscov2_intrahost

SARS-CoV-2 intrahost pipeline

Decombinator

Decombinator v4: fast, error-correcting analysis of TCR repertoires

stitchr

Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info

Contact-Process

A spatially distributed stochastic simulation of competition for space (a lattice population of replicating particles)

BIO266E

Acá se encuentra el material para los análisis de resultados y las actividades in silico del curso "Laboratorio de Bioquímica II: Genética Molecular"

Contact-Process-Ising-Model

The idea is to mix the Ising Model (IM) and the Contact Process (CP).

MorphoEngineering

CellModeller model files for publication on morphogenetic engineering of bacterial colonies - in submission.

CellModeller

GPU-accelerated multicellular modelling framework

UC2-Software-GIT

This repository hosts all necessary software for the UC2 project.

UC2-GIT

Respository for Open-Science modular microscope system.

chemprop

Message Passing Neural Networks for Molecule Property Prediction

partitioning_PLSR

Code related to PLSR model for predicting small molecule partitioning in 2023 Kilgore et al.

rdkit_scripts

Code used in Kilgore et al. NCB.