synthetic-sciences

synthetic-sciences/openscience

Skill Claude CodeCodex

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.

synthetic-sciences/openscience

Skill Claude Code

Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships. Use for Biolink-constrained RTX-KG2 lookup, explicit selected-provider ARAX federation, separate entity normalization, qualifier-aware graph traversal, and…

synthetic-sciences/openscience

Skill Claude Code

Query the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or variants in the 1000 Genomes Project cohort: which individuals carry variants matching specific criteria in a gene or region, which individuals…

synthetic-sciences/openscience

Skill Claude Code

Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also look up prefixes in Bioregistry, resolve compact identifiers via Identifiers.org, map lab shorthand with ZOOMA, and build Ontobee term pages. Use whenever an ontology identifier…

synthetic-sciences/openscience

Skill Claude CodeCodex

Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.

synthetic-sciences/openscience

Skill Claude Code

Query the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasury securities auctions, interest rates, foreign exchange rates, savings bonds, or U.S. government revenue and spending…

synthetic-sciences/openscience

Skill Claude CodeCodex needs its repo

Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', '.dotx', or requests to produce professional documents with formatting like tables of contents, headings, page…

synthetic-sciences/openscience

Skill Claude CodeCodex

Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rotating pages, adding watermarks, creating new PDFs, filling PDF forms, encrypting/decrypting PDFs, extracting images, and…

synthetic-sciences/openscience

Skill Claude CodeCodex needs its repo

Use this skill any time a .pptx or .potx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from any .pptx or .potx file (even if the extracted content will be used elsewhere, like in an email or summary)…

synthetic-sciences/openscience

Skill Claude Code

Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary deliverable. Use for formulas, formatting, financial models, multi-sheet workbooks, and tabular cleanup exported to Excel. Also applies to .csv/.tsv when the user wants spreadsheet output. Do NOT use for…

synthetic-sciences/openscience

Skill Claude Code

Handles protein structure files and geometric criteria so that residue counts, contacts, hydrogen bonds and interfaces are reproducible, covering PDB versus mmCIF, author versus label chains and numbering, HETATM, water and ligand policy, alternate locations, insertion codes, biological assemblies versus the…

synthetic-sciences/openscience

Skill Claude Code

Sets up and reports atomistic calculations so they are reproducible and converged, covering ASE Atoms, calculators, optimizers and MD drivers, pymatgen structures, symmetry analysis and the Materials Project API, LAMMPS and GROMACS input basics for molecular dynamics, convergence tests for k-points, plane-wave cutoffs…

synthetic-sciences/openscience

Skill Claude Code

Pins down the RDKit definitions that differ between conventions before computing molecular descriptors, including Lipinski donor and acceptor counts (Lipinski.NumHDonors and NumHAcceptors versus rdMolDescriptors.CalcNumLipinskiHBD and HBA), TPSA with or without sulfur and phosphorus, QED weighting, standard versus…

synthetic-sciences/openscience

Skill Claude Code

Runs computations so they finish, reproduce and fit the machine that will re-execute them, detaching long jobs through computejob instead of blocking or sleeping shells, checkpointing so reruns resume, fixing seeds and capping BLAS and OpenMP threads, streaming large tables with explicit dtypes, writing outputs…

synthetic-sciences/openscience

Skill Claude Code

Run NVIDIA BioNeMo NIMs through the hosted scientificcapability tool with your own NVIDIA API key. Boltz-2 and OpenFold2/OpenFold3 structure prediction, MSA Search alignments, DiffDock docking, ProteinMPNN sequence design, RFdiffusion backbones, GenMol and MolMIM molecule generation, Evo 2 genomic sequence modeling.…

synthetic-sciences/openscience

Skill Claude Code

Creates and audits truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn or Plotly, covering figure design, multi-panel layouts, uncertainty and missing-data displays, colour and contrast review, image metadata validation and journal export planning. Load alongside figures when a plot…

synthetic-sciences/openscience

Skill Claude CodeCodex

Assigns cell-type labels to clusters from a protein marker panel (multiplexed imaging such as MIBI, CODEX, IMC and CyCIF; mass and flow cytometry; CITE-seq protein), where the labels are judged against an expert reference. Within-dataset normalisation of cluster summaries, lineage first by positive defining markers…

synthetic-sciences/openscience

Skill Claude Code

Turns a crystal structure (CIF) of a hydrogen-bonded, coordination or covalent framework into its underlying net and the quantities a topology question asks for: node definition, the periodic quotient graph, connectivity as distinct neighbours rather than bond counts, degree of interpenetration, coordination sequences…

synthetic-sciences/openscience

Skill Claude Code

Turns the acceptance criteria a task states into executable checks and runs them against the finished outputs before delivering, rather than trusting that a correct-looking analysis satisfies them; rehearses the hidden condition when the grader scores unseen instances from a described family; treats a stated formula…

synthetic-sciences/openscience

Skill Claude Code

Writes the trace and report for an analysis whose output a reader will judge, restating the question with its binding clauses, recording data provenance, the method with every parameter that matters, results with raw and adjusted numbers and uncertainty, the checks performed, limitations, a decision log of…

synthetic-sciences/openscience

Skill Claude Code

Chooses and reports statistical tests the way a careful referee expects, deciding paired versus unpaired and parametric versus rank-based from the design, using ordered-trend tests such as Jonckheere-Terpstra and Cochran-Armitage for dose or grade levels, correcting for multiple comparisons with Bonferroni, Holm or…

synthetic-sciences/openscience

Skill Claude Code

Writes code that survives being re-executed by someone else on inputs you never saw, targeting the grader's or collaborator's runtime rather than your own, with one self-contained entry point using only the libraries the specification names, no reliance on packages you installed or files you cached during development…

synthetic-sciences/openscience

Skill Claude CodeCodex

Analyze 1D 1H or 13C NMR data with nmrglue, generate spectrum plots and peak tables, compare against standard NMR libraries such as BMRB, HMDB, SDBS, and nmrshiftdb2, then produce a ranked candidate-compound report with evidence, caveats, and direct links.