OpenBioMed is an agent platform and toolkit collection for biomedical research and drug discovery, covering areas such as molecular design, protein analysis, and single-cell data analysis. It is intended for researchers and provides the biomedical skills listed in the catalogue as workflows for Claude Code.
This repository also configures its own agents. See what OpenBioMed tells them →
Skill Claude CodeCodex
Query PubChem database for chemical structures, similar compounds, and bioactivity data. Use this skill when: (1) Converting drug name to molecular structure (SMILES, SDF), (2) Finding similar compounds for lead optimization, (3) Querying bioactivity data against protein targets, (4) Getting compounds active in…
Skill Claude CodeCodex
Expert-in-the-loop retrosynthetic planning workflow. Use when you need to break down complex target molecules into available starting materials, design synthetic routes, or collaborate with a human chemist to refine a proposed synthesis pathway.
Skill Claude CodeCodex
Retrieve proteins with similar structures, sequences, or from the same family. Use this skill when: (1) Finding similar proteins or homologs, (2) Searching for proteins with similar 3D structure, (3) Performing sequence similarity search, (4) Discovering proteins in the same family.
Skill Claude CodeCodex
Call accessible chromatin peaks from ATAC-seq BAM files, annotate peaks to genomic features and genes, and identify differentially accessible regions between experimental conditions.
Skill Claude CodeCodex
Trim adapters, align reads, remove duplicates and mitochondrial contamination, and evaluate chromatin accessibility data quality before calling peaks.
Skill Claude CodeCodex
Use this skill when a task involves Geneformer workflows, especially TranscriptomeTokenizer input preparation, tokenized .dataset generation, cell or gene classification with Classifier, embedding extraction with EmbExtractor, and in silico perturbation analysis with InSilicoPerturber.
Skill Claude CodeCodex
Use this skill when a task involves the LangCell project for single-cell language-cell modeling, especially zero-shot cell type annotation, few-shot annotation, LangCell-CE finetuning, Geneformer-style tokenization, or preparing text descriptions for candidate cell identities and multimodal cell-text matching…
Skill Claude CodeCodex
Use this skill when a task involves the local scGPT project in /DATA/disk0/zhaosy/home/scGPT, especially scGPT preprocessing and binning, checkpoint vocabulary matching, cell embedding extraction, reference mapping, fine-tuning scGPT for integration or annotation, or using scGPT tutorials for GRN, perturbation…
Skill Claude CodeCodex needs its repo
Probabilistic deep learning framework for single-cell multi-omics data analysis. Use this skill when: (1) Analyzing single-cell RNA-seq data with batch correction, (2) Integrating multi-modal data (CITE-seq, ATAC-seq, multi-omics), (3) Performing cell type annotation with scANVI, (4) Spatial transcriptomics…
Skill Claude CodeCodex
Prepare your RNA-seq, proteomics, methylation, and other omics datasets for joint integration by applying per-assay normalization, cross-assay batch correction, feature ID alignment, and missing value handling.
Skill Claude CodeCodex
Load, inspect, centroid, and extract features from raw LC-MS/MS data files. This is Step 1 of the proteomics pipeline — all downstream peptide identification and quantification steps require centroided, quality-checked spectra as input.
Skill Claude CodeCodex
Search MS2 spectra against a protein sequence database to identify peptides and proteins in your sample. Apply target-decoy FDR filtering to control false discovery rate at both PSM and protein levels.
Skill Claude CodeCodex needs its repo
Complete single-cell RNA-seq analysis workflow built on Scanpy and AnnData. Use this skill when: (1) Loading diverse single-cell data formats (10X, h5ad, CSV), (2) Performing quality control and filtering, (3) Normalization, dimensionality reduction, and clustering, (4) Marker gene identification and cell type…
Skill Claude CodeCodex
Use this skill when a task involves the local SToFM project in /DATA/disk0/zhaosy/home/SToFM, especially preprocessing spatial transcriptomics data for SToFM, generating cell embeddings with the cell encoder plus SE(2) Transformer pipeline, handling spatial coordinates, or preparing SToFM embeddings for downstream…
Skill Claude CodeCodex
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Use this skill when: (1) Loading Visium spatial transcriptomics data from Space Ranger output, (2) Loading Xenium single-cell resolution spatial data, (3) Loading MERFISH, CosMx, or other…
Skill Claude CodeCodex
Structure prediction using Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Predicting protein-ligand complexes, (4) Using local GPU resources. For protein complex binding affinity evaluation, use prodigy.
Skill Claude CodeCodex
Generate diverse lead compounds for a specific protein target using structure-based drug design with MolCraft. Use this skill when: (1) Designing drug candidates for a known protein target (PDB ID or disease name), (2) Generating structurally diverse molecules with optimized binding affinity, (3) Filtering candidates…
Skill Claude CodeCodex
A report generator for tracking how a drug target is progressing through research and development. A drug target is a biological molecule or process that medicines are designed to affect.
Skill Claude CodeCodex
Modify molecules based on natural language descriptions using MolT5/BioT5 models. Use this skill when: (1) User wants to modify a molecule to improve specific properties (solubility, potency, etc.), (2) User provides a molecule and asks to "make it more X" or "improve Y", (3) User wants to generate molecule variants…
Skill Claude CodeCodex
Query UniProt database for protein sequences, metadata, and search by criteria. Use this skill when: (1) Looking up protein information by UniProt accession ID, (2) Searching proteins by gene name, organism, function, or disease, (3) Retrieving comprehensive protein metadata including domains, PTMs, and annotations.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: