The open-source AI workbench for scientific research
synthetic-sciences/openscience is an AI workbench that carries out scientific research by reading papers, forming hypotheses, writing and running code, conducting experiments, analyzing results, and preparing reports. Researchers use it for work in machine learning, biology, physics, and chemistry with remote or local models. Catalogue add-ons extend its scientific workflows through skills and instructions.
This repository also configures its own agents. See what openscience tells them →
synthetic-sciences/openscience
Skill Claude CodeCodex
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
synthetic-sciences/openscience
Skill Claude CodeCodex
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
synthetic-sciences/openscience
Skill Claude CodeCodex
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
synthetic-sciences/openscience
Skill Claude CodeCodex
Query FRED (Federal Reserve Economic Data) API for 800,000+ economic time series from 100+ sources. Access GDP, unemployment, inflation, interest rates, exchange rates, housing, and regional data. Use for macroeconomic analysis, financial research, policy studies, economic forecasting, and academic research requiring…
synthetic-sciences/openscience
Skill Claude CodeCodex
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
synthetic-sciences/openscience
Skill Claude CodeCodex
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
synthetic-sciences/openscience
Skill Claude CodeCodex
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
synthetic-sciences/openscience
Skill Claude CodeCodex
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
synthetic-sciences/openscience
Skill Claude CodeCodex needs its repo
Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.
synthetic-sciences/openscience
Skill Claude CodeCodex
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
synthetic-sciences/openscience
Skill Claude CodeCodex
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
synthetic-sciences/openscience
Skill Claude CodeCodex
Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or institutions, tracking citations, discovering open access publications, or conducting bibliometric analysis across 240M+ scholarly…
synthetic-sciences/openscience
Skill Claude CodeCodex
Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
synthetic-sciences/openscience
Skill Claude CodeCodex
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
synthetic-sciences/openscience
Skill Claude CodeCodex
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
synthetic-sciences/openscience
Skill Claude CodeCodex
Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
synthetic-sciences/openscience
Skill Claude CodeCodex
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
synthetic-sciences/openscience
Skill Claude CodeCodex
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
synthetic-sciences/openscience
Skill Claude CodeCodex
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.
synthetic-sciences/openscience
Skill Claude CodeCodex
Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
synthetic-sciences/openscience
Skill Claude CodeCodex
Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.
synthetic-sciences/openscience
Skill Claude CodeCodex
Use this skill when the user asks to parse, perform multi-format document conversion or spatially extract text from an unstructured file (PDF, DOCX, PPTX, XLSX, images, etc.) locally without cloud dependencies.
synthetic-sciences/openscience
Skill Claude CodeCodex
Autonomous AI agent platform for building and deploying continuous agents. Use when creating visual workflow agents, deploying persistent autonomous agents, or building complex multi-step AI automation systems.
synthetic-sciences/openscience
Skill Claude CodeCodex
Vision-language pre-training framework bridging frozen image encoders and LLMs. Use when you need image captioning, visual question answering, image-text retrieval, or multimodal chat with state-of-the-art zero-shot performance.
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: