Claude Skills by ma-compbio-lab

Use this starter when a task lands in the `Interface analysis` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to fetch a protein family or domain entry from the official InterPro API and summarize its key metadata.

Use this starter when a task lands in the `MS proteomics preprocessing` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to search PRIDE Archive v2 proteomics projects by keyword and return compact dataset-discovery summaries. Do not use it for raw file download orchestration or unsupported PRIDE endpoints.

Use this starter when a task lands in the `Protein embeddings` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `Protein identification / quantification` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to validate protein FASTA inputs, extract deterministic smoke-safe embeddings, and run a reusable sequence-to-function triage flow that can later be swapped onto real ESM-2 or ProtT5 backends.

Use this starter when a task lands in the `Protein structure cross-links` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `PTM analysis` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `Sequence-to-function modeling` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to fetch a UniProtKB accession from the official UniProt REST API and summarize its sequence features into compact JSON.

Use this starter when a task lands in the `Conda / Mamba / Pixi / uv` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to author and run a minimal Common Workflow Language CommandLineTool and one-step workflow with cwltool. Do not use it for containerized production execution or complex scatter/gather workflows.

Use this starter when a task lands in the `CWL workflows` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `Docker / Apptainer / Singularity` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `Environment locking` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to generate a repository-aware GitHub Actions workflow that runs validation, site generation, tests, and a small smoke subset for this project.

Use this skill to run a minimal Nextflow workflow through the repo-managed Java and Nextflow prefix, either locally or on the Slurm cluster. Do not use it for containerized production pipelines.

Use this skill to verify the repo-managed nf-core tools install and retrieve a cleaned summary of available pipelines. Do not use it for interactive launch flows or full pipeline downloads.

Use this skill to execute a tiny parameterized notebook with Papermill and capture a deterministic summary plus the rendered output notebook.

Use this skill to run a tiny Snakemake workflow through the repo-managed Snakemake prefix and inspect deterministic toy outputs.

Use this skill to author and run a minimal WDL task and workflow with miniwdl. Do not use it for Cromwell-specific backends or large imported workflow graphs.

Use this starter when a task lands in the `WDL workflows` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `Workflow interoperability and translation` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `Active-learning experiment loops` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `Automated microscopy acquisition` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to generate a deterministic Autoprotocol JSON plan for a small liquid-handling experiment and inspect a concise execution summary.

Use this starter when a task lands in the `Closed-loop optimization for experiments` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `ELN / LIMS / sample-tracking integration` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `Laboratory robotics safety and monitoring` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to generate a minimal Opentrons Protocol API transfer script and verify it through the local simulator.

Use this skill to run a tiny deterministic parameter sweep with `QCoDeS`, persist the measurements to a local dataset database, and summarize the recorded sweep.

Use this starter when a task lands in the `Code-generation agents for scientific tasks` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to run a deterministic Inspect evaluation harness over toy scientific-agent cases and compare a candidate solver against a weaker baseline.

Use this skill to decompose a scientific task into deterministic step queries, route each step to candidate local skills, and return an execution-ready plan.

Use this starter when a task lands in the `Literature-to-hypothesis agents` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `Long-horizon agent memory and provenance` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to route a free-text scientific task query to the most relevant skills in the local registry.

Use this starter when a task lands in the `Tool-using analysis agents` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `Workflow generation agents` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `Automatic differentiation for scientific models` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to run a deterministic uncertainty-propagation toy workflow with Chaospy and inspect a machine-readable summary of the propagated response distribution.

Use this starter when a task lands in the `Differentiable programming for simulators` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to solve a tiny 1D diffusion problem with `FiPy` and summarize the evolution of the profile.

Use this starter when a task lands in the `Inverse problems and data assimilation` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this starter when a task lands in the `Numerical benchmarking and verification` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Use this skill to integrate a deterministic predator-prey ordinary differential equation with `scipy.integrate.solve_ivp` and return a compact trajectory summary.

Use this starter when a task lands in the `Sparse / iterative linear algebra` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.

Parse small benchmark markdown tables from paper notes and summarize datasets, metrics, and best-performing methods.

Use this starter when a task lands in the `Claim / assumption / limitation extraction` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.