research-agent-skills

In the author's own words, from each skill's SKILL.md — showing the first 30 of 281 files.

• 13c-metabolic-flux

  Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart fitting, and flux-profile diagnostics. Use for 13C-MFA, carbon tracing, mass isotopomer distributions (MDVs/MIDs), positional isotopomers, parallel tracer experiments, and determining whether labeling data constrain a pathway…

  skills/13c-metabolic-flux/SKILL.md on GitHub (opens in a new tab)

• abstract-and-title

  Write and sharpen research paper titles, abstracts (structured and unstructured), keywords, highlights, significance statements, graphical-abstract text and lay summaries. Use when drafting or revising an abstract to a word limit, turning results into a one-sentence contribution, choosing between candidate titles, writing Cell/Elsevier highlights, a PNAS significance statement or a plain-language…

  skills/abstract-and-title/SKILL.md on GitHub (opens in a new tab)

• academic-plotting

  Generates publication-quality figures for ML papers from research context. Given a paper section or description, extracts system components and relationships to generate architecture diagrams via Gemini. Given experiment results or data, auto-selects chart type and generates data-driven figures via matplotlib/seaborn. Use when creating any figure for a conference paper.

  skills/academic-plotting/SKILL.md on GitHub (opens in a new tab)

• acm-sigconf

  Format ACM conference papers and journal articles with the acmart LaTeX class (sigconf, sigplan, acmsmall, acmlarge, acmtog, manuscript/review/anonymous modes) or the ACM Word template, covering CCS concepts, keywords, ACM Reference Format, rights management and copyright blocks, anonymization for double-blind review, accessibility (alt text), the TAPS production workflow and common acmart errors…

  skills/acm-sigconf/SKILL.md on GitHub (opens in a new tab)

• 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`, `adapt…

  skills/adaptyv/SKILL.md on GitHub (opens in a new tab)

• 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…

  skills/aeon/SKILL.md on GitHub (opens in a new tab)

• 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 sil…

  skills/alphagenome/SKILL.md on GitHub (opens in a new tab)

• analytical-method-validation

  Plans and evaluates analytical method validation, verification, and transfer using Python scripts (plan_validation, check_response, check_accuracy_precision, check_detection_limits, check_bioanalytical_run, compare_methods) under ICH Q2(R2)/Q14, ICH M10, USP 1220/1225/1226, CLSI EP, or ISO/IEC 17025. Covers protocols, linearity, accuracy and precision, DL/QL, M10 run checks, TOST equivalence, Dem…

  skills/analytical-method-validation/SKILL.md on GitHub (opens in a new tab)

• 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.

  skills/anndata/SKILL.md on GitHub (opens in a new tab)

• apa7

  Format papers, theses and references in APA Style 7th edition for psychology, education, social sciences, nursing and business, covering student vs professional papers, title page, abstract and keywords, heading levels, in-text citations, reference list entries (journal articles, books, chapters, datasets, software, webpages, AI tools), tables and figures, bias-free language, and APA via LaTeX (a…

  skills/apa7/SKILL.md on GitHub (opens in a new tab)

• ara-compiler

  Compiles any research input — PDF papers, GitHub repositories, experiment logs, code directories, or raw notes — into a complete Agent-Native Research Artifact (ARA) with cognitive layer (claims, concepts, heuristics), physical layer (configs, code stubs), exploration graph, and grounded evidence. Use when ingesting a paper or codebase into a structured, machine-executable knowledge package, buil…

  skills/ara-compiler/SKILL.md on GitHub (opens in a new tab)

• ara-research-manager

  Records research provenance at the end of a coding or research session by scanning the conversation and writing decisions, experiments, dead ends, pivots, claims, and heuristics into the ara/ directory (exploration_tree.yaml, claims.md, heuristics.md, observations.yaml, session records), each tagged user, ai-suggested, ai-executed, or user-revised. Use when a task is finished and you want a sessi…

  skills/ara-research-manager/SKILL.md on GitHub (opens in a new tab)

• ara-rigor-reviewer

  Performs ARA Seal Level 2 semantic epistemic review of an Agent-Native Research Artifact directory, reading PAPER.md, logic/claims.md, logic/experiments.md, and trace/exploration_tree.yaml. Scores six dimensions (evidence relevance, falsifiability, scope calibration, argument coherence, exploration integrity, methodological rigor) from 1 to 5 and writes a severity-ranked level2_report.json with a…

  skills/ara-rigor-reviewer/SKILL.md on GitHub (opens in a new tab)

• 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. "get my model's eval score up", "improve this agent/harness", "tune this pipeline", "…

  skills/arbor/SKILL.md on GitHub (opens in a new tab)

• 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.

  skills/arboreto/SKILL.md on GitHub (opens in a new tab)

• arxiv-submission

  Prepare and post preprints to arXiv without processing failures or leaks, covering TeX source packaging (.bbl, figures, case-sensitive paths), stripping private comments, choosing categories and license, endorsement, metadata (title, abstract, comments field), versioning and replacements, and linking the journal DOI later. Use when posting a paper to arXiv, when arXiv's TeX compilation fails, bef…

  skills/arxiv-submission/SKILL.md on GitHub (opens in a new tab)

• 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.

  skills/astropy/SKILL.md on GitHub (opens in a new tab)

• audiocraft-audio-generation

  PyTorch library for audio generation including text-to-music (MusicGen) and text-to-sound (AudioGen). Use when you need to generate music from text descriptions, create sound effects, or perform melody-conditioned music generation.

  skills/audiocraft-audio-generation/SKILL.md on GitHub (opens in a new tab)

• autogpt-agents

  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.

  skills/autogpt-agents/SKILL.md on GitHub (opens in a new tab)

• autoresearch

  Orchestrates end-to-end autonomous AI research projects using a two-loop architecture. The inner loop runs rapid experiment iterations with clear optimization targets. The outer loop synthesizes results, identifies patterns, and steers research direction. Routes to domain-specific skills for execution, supports continuous agent operation via Claude Code /loop and OpenClaw heartbeat, and produces…

  skills/autoresearch/SKILL.md on GitHub (opens in a new tab)

• autoskill

  Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing research-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use when the user asks to analyze their recent work and propose skills based on what they actually do. Requires the screenpipe daemon (https://github.com/screenpipe/…

  skills/autoskill/SKILL.md on GitHub (opens in a new tab)

• awq-quantization

  Activation-aware weight quantization for 4-bit LLM compression with 3x speedup and minimal accuracy loss. Use when deploying large models (7B-70B) on limited GPU memory, when you need faster inference than GPTQ with better accuracy preservation, or for instruction-tuned and multimodal models. MLSys 2024 Best Paper Award winner.

  skills/awq-quantization/SKILL.md on GitHub (opens in a new tab)

• axolotl

  Provides guidance for fine-tuning large language models with Axolotl, covering YAML training configs, LoRA and QLoRA, preference training with DPO, KTO, ORPO and GRPO, multimodal models, FSDP and multi-GPU setups, sequence (context) parallelism, NCCL bandwidth tests, dataset formats, compressed model saving for vLLM and llmcompressor, and custom integrations. Use when writing or debugging an Axol…

  skills/axolotl/SKILL.md on GitHub (opens in a new tab)

• 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.

  skills/benchling-integration/SKILL.md on GitHub (opens in a new tab)

• 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.

  skills/bgpt-paper-search/SKILL.md on GitHub (opens in a new tab)

• bibtex-hygiene

  Clean, deduplicate and validate BibTeX/BibLaTeX bibliographies before submission. Use when a .bib file has duplicate keys or works, missing fields, broken DOIs, lost acronym capitalization (e.g. "bert" instead of "BERT"), inconsistent page dashes, arXiv preprints that now have published versions, or when LaTeX/biber emits bibliography warnings. Includes a zero-dependency linter and normalizer.

  skills/bibtex-hygiene/SKILL.md on GitHub (opens in a new tab)

• bids

  Organizes, queries, validates, and converts neuroscience and biomedical datasets using the Brain Imaging Data Structure (BIDS) standard, covering MRI, PET, EEG, MEG, iEEG, EMG, NIRS, microscopy, motion capture, and behavioral data. Covers PyBIDS (BIDSLayout), the bids-validator, HeuDiConv, dcm2bids, BIDScoin, JSON sidecars, dataset_description.json, events.tsv, participants.tsv, .bidsignore, and…

  skills/bids/SKILL.md on GitHub (opens in a new tab)

• biopython

  Provides Biopython (Bio.Seq, Bio.SeqIO, Bio.Align, Bio.Entrez, Bio.Blast, Bio.PDB, Bio.Phylo, Bio.motifs, Bio.SeqUtils, Bio.Restriction) for sequence handling, file parsing, NCBI access, BLAST, structures, and phylogenetic trees in Python. Reads, writes, and converts FASTA, GenBank, FASTQ, PDB, mmCIF, Newick, and NEXUS files. Use when manipulating or translating DNA, RNA, or protein sequences, co…

  skills/biopython/SKILL.md on GitHub (opens in a new tab)

• 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.

  skills/bioservices/SKILL.md on GitHub (opens in a new tab)

• blip-2-vision-language

  Explains how to use Salesforce BLIP-2 (Q-Former bridging a frozen image encoder and an LLM such as OPT or FlanT5) through HuggingFace Transformers and LAVIS for image captioning, visual question answering, image-text matching, and feature extraction. Use when generating captions for images, building a VQA system, doing zero-shot image-text understanding without task-specific training, matching or…

  skills/blip-2-vision-language/SKILL.md on GitHub (opens in a new tab)

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