Search the bioRxiv preprint server and retrieve paper metadata or download PDFs via its API. Use when finding life sciences preprints by keywords, authors, DOI, date ranges, or categories, or when conducting a biology literature review of not-yet-peer-reviewed work. Part of the AlterLab Academic Skills suite.
EnglishRuns automated LLM-driven hypothesis generation and testing on tabular datasets with HypoGeniC, combining literature insights with data-driven testing. Use when systematically exploring hypotheses about patterns in empirical data (for example deception detection or content analysis). For manual hypothesis formulation use alterlab-hypothesis-gen; for open-ended creative ideation use alterlab-scientific-brainstorm. Part of the AlterLab Academic Skills suite.
EnglishAccess the NIH Metabolomics Workbench via its REST API (4,200+ studies), querying metabolites, RefMet standardized nomenclature, MS/NMR data, m/z mass searches, and study metadata. Use when retrieving public metabolomics study data, standardizing metabolite names with RefMet, running m/z lookups, or doing biomarker discovery. Part of the AlterLab Academic Skills suite.
EnglishMixed methods research design and integration strategies for combining qualitative and quantitative approaches. Use when planning convergent, explanatory sequential, exploratory sequential, embedded, transformative, or multiphase designs; when integrating diverse data sources through merging, connecting, or embedding; when constructing joint displays or meta-inferences; or when evaluating quality criteria specific to mixed methods research. Covers Creswell & Plano Clark frameworks, notation systems, and software tools for integration. For single-strand qualitative coding (thematic analysis, grounded theory, saturation, inter-coder reliability) use alterlab-qualitative-methods; for questionnaire/Likert/instrument-validation mechanics use alterlab-survey-design. Part of the AlterLab Academic Skills suite.
EnglishFormats manuscripts for Turkish journals: TR Dizin submission rules (TR Dizin mandates a set abstract word limit, two referees from different institutions, Latin script for non-Latin-alphabet articles, and only suggests a second-language abstract; bilingual oz/abstract ~200-250 words and 3-5 keywords are common journal house conventions to confirm against the journal's yazim kurallari) and the Turkish adaptation of APA-7 (ve ark./vd. for multi-author cites, ampersand only in the reference list, s. for page, Cev. for translator, t.y. for no date, aktaran for as-cited-in, Turkish capitalization). Use when writing for a Turkish/Turkce journal, preparing a TR Dizin submission, needing Turkce APA 7 in-text or reference formatting, or formatting a bilingual oz. For English-language citation styles prefer alterlab-citation-mgmt or alterlab-venue-templates; for live TR Dizin index status use alterlab-trdizin. Part of the AlterLab Academic Skills suite.
EnglishSearches YÖK Ulusal Tez Merkezi (tez.yok.gov.tr/UlusalTezMerkezi), Turkey's mandatory national graduate-thesis repository, for literature-review discovery and pre-proposal özgünlük (originality) checks. Drives the detailed search form (Tez Adı/Yazar/Danışman/Konu/Anahtar Kelime/Özet, tez türü, year range, language, İzinli/İzinsiz permission status) via the saidsurucu/yoktez-mcp tool, applies Turkish auto-stemming and ve/veya/içermesin boolean operators, runs paired Turkish+English queries, and emits Türkçe APA-7 thesis citations mapping Tez No to the published Yayın No. Use when the user wants to search Turkish theses, ara YÖK tez, check thesis novelty before approving a proposal, find dissertations by advisor (danışman) or university, dedupe a topic against existing tezler, or cite a YÖK thesis; respects the 2000-results-per-search cap and online-view-only access. For non-thesis Turkish journals use alterlab-dergipark or alterlab-trdizin. Part of the AlterLab Academic Skills suite.
English
AGENT SKILLS ATLASIncludes Alterlab Biorxiv, Alterlab Hypogenic, Alterlab Metabolomics Wb, and other workflows.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLISupported by the Atlas install prompt. Skill-specific requirements vary.
Pack stats
What’s included
Alterlab Biorxiv
Search the bioRxiv preprint server and retrieve paper metadata or download PDFs via its API. Use when finding life sciences preprints by keywords, authors, DOI, date ranges, or categories, or when conducting a biology literature review of not-yet-peer-reviewed work. Part of the AlterLab Academic Skills suite.
Alterlab Hypogenic
Runs automated LLM-driven hypothesis generation and testing on tabular datasets with HypoGeniC, combining literature insights with data-driven testing. Use when systematically exploring hypotheses about patterns in empirical data (for example deception detection or content analysis). For manual hypothesis formulation use alterlab-hypothesis-gen; for open-ended creative ideation use alterlab-scientific-brainstorm. Part of the AlterLab Academic Skills suite.
Alterlab Metabolomics Wb
Access the NIH Metabolomics Workbench via its REST API (4,200+ studies), querying metabolites, RefMet standardized nomenclature, MS/NMR data, m/z mass searches, and study metadata. Use when retrieving public metabolomics study data, standardizing metabolite names with RefMet, running m/z lookups, or doing biomarker discovery. Part of the AlterLab Academic Skills suite.
Alterlab Mixed Methods
Mixed methods research design and integration strategies for combining qualitative and quantitative approaches. Use when planning convergent, explanatory sequential, exploratory sequential, embedded, transformative, or multiphase designs; when integrating diverse data sources through merging, connecting, or embedding; when constructing joint displays or meta-inferences; or when evaluating quality criteria specific to mixed methods research. Covers Creswell & Plano Clark frameworks, notation systems, and software tools for integration. For single-strand qualitative coding (thematic analysis, grounded theory, saturation, inter-coder reliability) use alterlab-qualitative-methods; for questionnaire/Likert/instrument-validation mechanics use alterlab-survey-design. Part of the AlterLab Academic Skills suite.
Alterlab Tr Academic Style
Formats manuscripts for Turkish journals: TR Dizin submission rules (TR Dizin mandates a set abstract word limit, two referees from different institutions, Latin script for non-Latin-alphabet articles, and only suggests a second-language abstract; bilingual oz/abstract ~200-250 words and 3-5 keywords are common journal house conventions to confirm against the journal's yazim kurallari) and the Turkish adaptation of APA-7 (ve ark./vd. for multi-author cites, ampersand only in the reference list, s. for page, Cev. for translator, t.y. for no date, aktaran for as-cited-in, Turkish capitalization). Use when writing for a Turkish/Turkce journal, preparing a TR Dizin submission, needing Turkce APA 7 in-text or reference formatting, or formatting a bilingual oz. For English-language citation styles prefer alterlab-citation-mgmt or alterlab-venue-templates; for live TR Dizin index status use alterlab-trdizin. Part of the AlterLab Academic Skills suite.
Alterlab Yok Tez
Searches YÖK Ulusal Tez Merkezi (tez.yok.gov.tr/UlusalTezMerkezi), Turkey's mandatory national graduate-thesis repository, for literature-review discovery and pre-proposal özgünlük (originality) checks. Drives the detailed search form (Tez Adı/Yazar/Danışman/Konu/Anahtar Kelime/Özet, tez türü, year range, language, İzinli/İzinsiz permission status) via the saidsurucu/yoktez-mcp tool, applies Turkish auto-stemming and ve/veya/içermesin boolean operators, runs paired Turkish+English queries, and emits Türkçe APA-7 thesis citations mapping Tez No to the published Yayın No. Use when the user wants to search Turkish theses, ara YÖK tez, check thesis novelty before approving a proposal, find dissertations by advisor (danışman) or university, dedupe a topic against existing tezler, or cite a YÖK thesis; respects the 2000-results-per-search cap and online-view-only access. For non-thesis Turkish journals use alterlab-dergipark or alterlab-trdizin. Part of the AlterLab Academic Skills suite.
Quick start
- Choose your skills. Select individual skills above, or choose the entire pack.
- Copy the install prompt. Use Copy install prompt above the list.
- Send it to your agent. Paste into your coding agent’s chat. Your agent reviews the source and guides the setup.
Try it with your agent
After installation, start with a request like:
Use the Alterlab Biorxiv skill to help with my task.
Ask me for the context you need before getting started.Requirements & license
- A coding agent that can access your project files and install skills.
- Your agent checks each skill’s instructions, dependencies, and permissions during setup.
- Reported license for the skills shown: MIT. The author’s terms apply.