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
Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics…
synthetic-sciences/openscience
Skill Claude CodeCodex
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.
synthetic-sciences/openscience
Skill Claude CodeCodex
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
synthetic-sciences/openscience
Skill Claude CodeCodex
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard…
synthetic-sciences/openscience
Skill Claude CodeCodex
Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed…
synthetic-sciences/openscience
Skill Claude CodeCodex
Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving…
synthetic-sciences/openscience
Skill Claude CodeCodex
Patterns for loading PDE simulation datasets (PDEBench, PhiFlow, JAX-CFD) from HDF5 files. Handles layout detection (single tensor vs separate variables), spatial/temporal downsampling, multi-variable systems, HuggingFace and DaRUS data sources, and efficient PyTorch DataLoader creation. Use when preparing PDE data…
synthetic-sciences/openscience
Skill Claude CodeCodex
Create and manage datasets on Hugging Face Hub. Supports initializing repos, defining configs/system prompts, streaming row updates, and SQL-based dataset querying/transformation. Designed to work alongside HF MCP server for comprehensive dataset workflows.
synthetic-sciences/openscience
Skill Claude Code needs its repo
Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
synthetic-sciences/openscience
Skill Claude CodeCodex
Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pipelines, faster pandas replacement. For larger-than-RAM data use dask or vaex.
synthetic-sciences/openscience
Skill Claude CodeCodex
Scalable data processing for ML workloads. Streaming execution across CPU/GPU, supports Parquet/CSV/JSON/images. Integrates with Ray Train, PyTorch, TensorFlow. Scales from single machine to 100s of nodes. Use for batch inference, data preprocessing, multi-modal data loading, or distributed ETL pipelines.
synthetic-sciences/openscience
Skill Claude CodeCodex
Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large…
synthetic-sciences/openscience
Skill Claude CodeCodex
Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.
synthetic-sciences/openscience
Skill Claude CodeCodex
Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
synthetic-sciences/openscience
Skill Claude CodeCodex needs its repo
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
synthetic-sciences/openscience
Skill Claude CodeCodex
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
synthetic-sciences/openscience
Skill Claude CodeCodex
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.
synthetic-sciences/openscience
Skill Claude CodeCodex
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
synthetic-sciences/openscience
Skill Claude CodeCodex
Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.
synthetic-sciences/openscience
Skill Claude CodeCodex
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
synthetic-sciences/openscience
Skill Claude CodeCodex
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
synthetic-sciences/openscience
Skill Claude CodeCodex
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
synthetic-sciences/openscience
Skill Claude CodeCodex
Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population…
synthetic-sciences/openscience
Skill Claude CodeCodex
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction…
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