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datalad

Wissenschaftliche Datensätze mit DataLad und git-annex abrufen, versionieren und veröffentlichen sowie die Berechnungsherkunft mit datalad run, rerun und containers-run erfassen.

Was ist datalad?

Diese Skill beschreibt DataLad, eine Datenverwaltungsschicht über Git und git-annex, die speziell für wissenschaftliche Datensätze entwickelt wurde. DataLad trennt die Struktur eines Datensatzes (die in Git verwaltet wird) von den großen Dateiinhalten (die mit git-annex verwaltet werden), sodass riesige Datensätze schnell geklont werden können, während die eigentlichen Dateninhalte erst bei Bedarf mit 'datalad get' heruntergeladen werden. Ein zentrales Merkmal ist die Nachvollziehbarkeit (Provenienz): Mit 'datalad run' ausgeführte Befehle zeichnen Befehle, Eingaben und Ausgaben maschinenlesbar auf, sodass sie später mit 'datalad rerun' reproduziert werden können. Dies macht die Wissenschaft reproduzierbar, da die gesamte Verarbeitungshistorie zusammen mit den Daten gespeichert wird. Die Skill unterstützt mehrere Plattformen wie OpenNeuro, DANDI und datasets.datalad.org, arbeitet mit Containerisierung durch 'datalad-container' und erlaubt die Veröffentlichung auf verschiedenen Remote-Zielen (GitHub, S3, SSH) mit einer speziellen 'publish-depends'-Konfiguration, um sicherzustellen, dass Dateninhalte immer vor der Git-Historie veröffentlicht werden.

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Dokumentation

Was macht datalad?

Überblick

DataLad ist eine Datenverwaltungsschicht über Git und git-annex. Git verfolgt die Struktur des Datensatzes, kleine Textdateien und die Historie. git-annex verfolgt den Inhalt großer Dateien, indem es jede Datei als Schlüssel speichert und die Bytes an einem Ort aufbewahrt, der nicht unbedingt das lokale Repository ist.

Diese Aufteilung ist das mit Abstand Wichtigste, was man verinnerlichen sollte, denn sie bedeutet, dass ein frisch geklonter Datensatz die vollständige Historie und die vollständige Dateiliste enthält, aber fast keine der Daten. Ein 100 TB großer Datensatz wird in Sekunden geklont und belegt ein paar Megabyte. Die Bytes kommen erst auf Anfrage, pro Datei, mit datalad get.

Das zweite, was DataLad hinzufügt, ist die Herkunft (Provenienz). datalad run führt einen Befehl aus und übernimmt das Ergebnis zusammen mit einem maschinenlesbaren Datensatz des Befehls, seiner Eingaben und seiner Ausgaben. datalad rerun liest diesen Datensatz zurück und führt ihn erneut aus. Dies macht aus der Frage „Wie wurde diese Abbildung erstellt?

Individual skills in this repo

This repo contains 20 individual skills — each has its own dedicated page.

adaptyv

How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.

aeon

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 ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.

alphagenome

Look up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC, ChIP-TF, ChIP-histone, CAGE, PRO-cap, splicing, polyadenylation and contact-map tracks), score variants or scan windows on demand with the AlphaGenome model for human and mouse (variant scoring, in silico mutagenesis, REF-versus-ALT track prediction), and build Atlas website deep links. Use when the user mentions AlphaGenome, AlphaGenome Atlas, AVI or AlphaGenome Variant Impact, DeepMind variant effect prediction, or wants to prioritise or mechanistically interpret non-coding, regulatory, splicing, enhancer, promoter, or chromatin-accessibility effects of SNVs from a VCF, credible set, or region. Research use only; not a clinical tool.

analytical-method-validation

Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand binding or cell-based assays whenever the question is whether a procedure is fit for its intended purpose. Triggers include

anndata

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

arbor

Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without overfitting — e.g.

arboreto

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

astropy

Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing or debugging astronomical data analysis code with Astropy.

autoskill

Observe the user

benchling-integration

Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or the v2 API.

bgpt-paper-search

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.

bids

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biopython

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

bioservices

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

bulk-rnaseq

End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathway-enrichment), and publication figures (scientific-visualization). Use whenever the user has bulk RNA-seq reads or quant output and wants a complete, reproducible differential-expression workflow — e.g.

cellxgene-census

Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.

cirq

Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.

citation-management

Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.

clinical-decision-support

Prepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Use for aggregate or synthetic research documentation and traceability—not patient care or live clinical operation.

clinical-reports

Create safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with synthetic, de-identified, or aggregate inputs and verified source-fact manifests; every output requires qualified review.

Verwandte Skills

steipete/video-frames

Extract frames or short clips from videos using ffmpeg.

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steipete/summarize

Summarize or transcribe URLs, YouTube/videos, podcasts, articles, transcripts, PDFs, and local files.

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openclaw/openclaw

Use when testing, fixing, or extending the OpenClaw Control UI GUI with Vitest + Playwright end-to-end checks, mocked Gateway WebSocket flows, mocked dashboard runs, screenshots/videos, or agent-verifiable browser proof.

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obra/superpowers

Obra superpowers agent skills.

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affaan-m/ECC

See, Understand, Act on video and audio. See- ingest from local files, URLs, RTSP/live feeds, or live record desktop; return realtime context and playable stream links. Understand- extract frames, build visual/semantic/temporal indexes, and search moments with timestamps and auto-clips. Act- transcode and normalize (codec, fps, resolution, aspect ratio), perform timeline edits (subtitles, text/image overlays, branding, audio overlays, dubbing, translation), generate media assets (image, audio...

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affaan-m/everything-claude-code

End-to-end marketing campaign planning and execution. Covers audience research, positioning, campaign angle definition, landing page copy, email sequences, social posts, ad copy, short-form video scripts, and content calendars. Use as the orchestration layer for multi-channel product launches. Use when planning or executing a multi-channel product launch, or producing landing page, email, social, or ad copy.

community