k-dense-ai/scientific-agent-skills

exa-search

Searches scientific and technical web content with Exa and extracts page or PDF text from URLs in batches.

Voir la source

Mode d’emploi

  1. Copiez la commande et examinez le paquet avant de l’installer dans votre environnement agent.
  2. Consultez le document original pour les outils, identifiants et environnements requis.
  3. Décrivez les entrées et le livrable souhaité ; comparez la sortie aux sources.
npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill exa-search

Avant de commencer

  • L’installation n’inclut ni abonnement au modèle, ni quota API, ni accès aux fichiers.
  • Étoiles et installations reflètent l’activité, pas un test indépendant de qualité ou de sécurité.
Document Skill original

Rendu depuis le dépôt source en conservant titres, exemples, code, tableaux, liens et images.

Exa Web Toolkit

A skill for web-powered research tasks backed by Exa: web search and URL extraction. Exa's index combines high-quality keyword and semantic retrieval, which makes it well-suited to scientific, technical, and conceptual queries.

Routing — pick the right capability

Read the user's request and match it to one of the capabilities below. Read the corresponding reference file for detailed instructions before running commands.

User wants to...CapabilityWhere
Look something up, research a topic, find current infoWeb Searchreferences/web-search.md
Fetch content from a specific URL (webpage, article, PDF)Web Extractreferences/web-extract.md
Install or authenticateSetupBelow

Decision guide

  • Default to Web Search for topic lookups, research questions, or "what is X?" queries. When the topic is scientific or technical, pass --category publication to bias toward scholarly sources, and/or an academic --include-domains allowlist. See references/web-search.md for the two-pass academic strategy.
  • Use Web Extract when the user provides a URL or asks you to read/fetch a specific page. Prefer this over the built-in WebFetch for batch extraction (multiple URLs in one call) and for academic PDFs.

Academic source priority

For technical or scientific queries, prefer academic and scientific sources:

  • Peer-reviewed journal articles and conference proceedings over blog posts or news
  • Preprints (arXiv, bioRxiv, medRxiv) when peer-reviewed versions aren't available
  • Institutional and government sources (NIH, WHO, NASA, NIST) over commercial sites
  • Primary research over secondary summaries

Two levers to steer Exa toward scholarly content:

  1. --category publication biases retrieval toward scholarly sources.
  2. --include-domains with a scholarly allowlist (arxiv.org, nature.com, pubmed.ncbi.nlm.nih.gov, etc.) restricts the domain pool.

Combine both to narrow the source pool; verify publication type and peer-review status on each source. See references/web-search.md for the full pattern.

When citing academic sources, include author names and publication year where available (e.g., Smith et al., 2025) in addition to the standard citation format. If a DOI is present, prefer the DOI link.


Setup

This skill uses the `exa-py` Python SDK. The scripts in scripts/ declare their dependencies via PEP 723 inline metadata, so you can run them directly with uv run without a separate install step:

bash
uv run "$SKILL_PATH/scripts/exa_search.py" --help

If you prefer a persistent install:

bash
uv pip install "exa-py>=2.23.0,<3"

Authentication

All commands read the API key from the EXA_API_KEY environment variable. Get your Exa API key at dashboard.exa.ai/api-keys.

First, check if a .env file exists in the project root and contains EXA_API_KEY. If so, load it:

bash
dotenv -f .env run -- uv run "$SKILL_PATH/scripts/exa_search.py" "your query"

If dotenv isn't available, install it: uv pip install 'python-dotenv[cli]'.

If there's no .env, export the key for the session:

bash
export EXA_API_KEY="your-key"

Use --help to verify installation and CLI parsing; it does not require an API key or validate authentication. Authentication is checked only when a real query is made.

Extraction limits and freshness

The extractor accepts 1–100 URLs per POST https://api.exa.ai/contents call and exports each SDK status (id, status, source). It rejects larger batches. Use --max-age-hours 0 to request fresh content, -1 for cache only, or a positive age up to 720 hours. Omission uses Exa's cache/fallback policy. published_date is estimated publication metadata, not retrieval time. The tested SDK drops per-URL error details, so report failures without inventing a cause. See URL Extraction.

Verified API and SDK scope

Reviewed the Search API, Contents API, and Exa changelog on 2026-09-30. Both routes use JSON POST requests and x-api-key authentication (the SDK sets this header). Search is POST https://api.exa.ai/search; its SDK kwargs use snake_case and are serialized to camelCase. The current scholarly category is publication; research paper is a compatibility alias in this wrapper. No offset or cursor pagination is documented for these endpoints.

Helpers are tested with exa-py==2.23.0, including mocked HTTP transport through the real SDK. Search content flags are explicit: no flags means metadata only; --highlights does not implicitly fetch text. Authenticated search/extraction examples below and in the references are illustrative; no paid live calls were made during this review.

Tracking header

Every script in this skill sets the x-exa-integration request header to k-dense-ai--scientific-agent-skills so Exa can attribute usage from the K-Dense AI scientific-agent-skills repo to this integration. Do not remove or rename this header when adapting the scripts.


Files in this skill

  • SKILL.md — this file (routing and setup)
  • references/web-search.md — detailed web search reference with academic strategy
  • references/web-extract.md — URL content extraction reference
  • scripts/exa_search.py — CLI wrapper around client.search
  • scripts/exa_extract.py — CLI wrapper around client.get_contents
du même dépôt

Autres Skills

Tous les Skills
k-dense-ai
Communauté

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 flux. Distinguishes measured-label inference from COBRA flux balance analysis and flags experiments

installations
0
GitHub Stars
54,6 k
Mis à jour
19 oct.
k-dense-ai
Communauté

adaptyv

Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory progress, and retrieve results. Applies to Adaptyv Foundry, its target catalog, binding screening and affinity assays, thermostability, expression, fluorescence, epitope binning, and enzyme activity workflows, including code using adaptyv or FoundryClient.

installations
0
GitHub Stars
54,6 k
Mis à jour
19 oct.
k-dense-ai
Communauté

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.

installations
0
GitHub Stars
54,6 k
Mis à jour
19 oct.
k-dense-ai
Communauté

alphagenome

Looks 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), scores variants or scans windows on demand with the AlphaGenome model for human and mouse (variant scoring, in silico mutagenesis, REF-versus-ALT track prediction), and builds Atlas website deep links. Use when t

installations
0
GitHub Stars
54,6 k
Mis à jour
19 oct.