A set of ready to use Agent Skills for research, science, engineering, analysis, finance and writing.

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

A comprehensive library for computational molecular biology

Working with molecular structures in pandas DataFrames

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

Interactive network visualization in Python and Dash, powered by Cytoscape.js

Cell type annotation for single-cell RNA-seq using multi-LLM consensus

COBRApy is a package for constraint-based modeling of metabolic networks.

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

DANCE: a deep learning library and benchmark platform for single-cell analysis

Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

A geometry-complete diffusion generative model (GCDM) for 3D molecule generation and optimization. (Nature CommsChem)

Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Clustering scRNAseq by genotypes

CodonTransformer (2M+ Downloads); The tool for codon optimization, optimizing DNA for protein expression

dna2vec: Consistent vector representations of variable-length k-mers

Mixed continous/categorical flow-matching model for de novo molecule generation.