AlterLab-IEU

@alterlab-ieu source repo

418 skills
0 followers
60 repo stars
2 weeks ago last updated

▌
Alterlab Docentlik Eligibility · alterlab-ieu bundle
Runs a PARTIAL pre-screen of a Turkish associate-professorship (doçentlik) publication list against the ÜAK (Üniversitelerarası Kurul) Sağlık Bilimleri TABLO 10 criteria, applying the author-share rule (full; 0.8 + 0.5; lead-author half-the-rest split) and pass-fail checking the four computable minimums (≥100 total, ≥90 post-doctorate, ≥40 SCIE/SSCI article points, ≥3 lead-author Q1–Q4 articles). It deliberately does NOT emit an ELIGIBLE verdict — it lists the unmodelled mandatory minimums (TR Dizin/national article, citation, congress, teaching, per-category caps) for the user to verify. Use when the user wants to estimate doçentlik eligibility, calculate ÜAK points, or audit lead-author (başlıca yazar) requirements; resolve a journal's live TR Dizin status with alterlab-trdizin first, and compute the akademik teşvik (academic-incentive) score with alterlab-akademik-tesvik. Always verify the full live TABLO 10 — criteria change each term and differ per field. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Survey Analysis · alterlab-ieu bundle
Analyzes complex-sample survey data with design-based inference — declares a survey design (weights, strata, PSUs/clusters, FPC) before estimating means, totals, proportions, ratios, and quantiles, computes design-adjusted standard errors via Taylor linearization or replicate weights (BRR, Jackknife, Bootstrap), calibrates with post-stratification / raking / GREG, and fits design-adjusted GLMs (linear, logistic, Poisson). Uses samplics (stable Python), the emerging svy successor, or the field-standard R survey + srvyr via Rscript. Use when analyzing GSS/ANES/ESS/DHS/Eurobarometer or any weighted/stratified/clustered survey, when a dataset ships survey weights, or when someone quotes unweighted percentages from a complex survey. For questionnaire and sampling-plan DESIGN prefer alterlab-survey-design; for the sampling-adequacy gate prefer alterlab-ssci-sampling-gate; for causal identification prefer alterlab-causal-inference. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Causal Inference · alterlab-ieu bundle
Estimates causal effects from observational and quasi-experimental data — difference-in-differences, instrumental variables, regression discontinuity, panel fixed effects, propensity-score / doubly-robust methods, and heterogeneous treatment effects (CATE) — using the verified Python stack: statsmodels and linearmodels (PanelOLS, IV2SLS), pyfixest (feols, event studies, Sun-Abraham, did2s), DoWhy (identify -> estimate -> refute), EconML (LinearDML, CausalForestDML, DRLearner), and rdrobust for RD. It names the identifying assumption before estimating and runs a refutation/robustness check after. Use when the request mentions difference-in-differences, instrumental variables, regression discontinuity, fixed effects / panel causal estimation, propensity scores, or treatment-effect estimation from non-randomized data. For choosing the design first prefer alterlab-ssci-design-gate; for plain regression or descriptive stats prefer alterlab-statistical-analysis. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Ssci Design Gate · alterlab-ieu bundle
Routes a social-science study to its research design — true experiment, quasi-experiment (difference-in-differences, instrumental variables, regression discontinuity, interrupted time series, fixed effects), observational/correlational, qualitative, or mixed — by walking the random-selection and random-assignment decisions, then PINS the identifying assumption the causal claim will rest on (parallel trends, exclusion restriction, continuity at the cutoff, selection-on-observables, or qualitative saturation logic) before any analysis begins. Use when choosing a study design, asking what design to use, framing a causal question from observational data, or deciding experiment vs quasi-experiment vs observational. For executing the analysis prefer alterlab-statistical-analysis; for qualitative design depth prefer alterlab-qualitative-methods; for choosing the statistical test downstream prefer alterlab-test-selection-guard. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Multilevel Models · alterlab-ieu bundle
Fits and reports mixed-effects / multilevel / hierarchical models for clustered, nested, longitudinal, and repeated-measures data — random intercepts and slopes, variance components and the ICC, cross-level interactions, and GLMMs (logistic/Poisson) — using statsmodels MixedLM and bambi (Bayesian on PyMC) in Python, or the field-standard R lme4 / glmmTMB / brms via Rscript. It enforces the reporting items reviews find under-reported: full fixed + random specification, centering, variance components + ICC, estimation method, assumption checks, model comparisons, and effect sizes. Use when data are grouped/nested (students in schools, repeated measures, panel/longitudinal) and the question concerns within- vs between-cluster variation. For general single-level regression prefer alterlab-statsmodels; for panel fixed effects used for causal identification prefer alterlab-causal-inference. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Sem Psychometrics · alterlab-ieu bundle
Fits and evaluates measurement models — confirmatory factor analysis, full structural equation models, exploratory factor analysis, item response theory, and multi-group measurement invariance — using the verified Python stack: semopy (model syntax =~ / ~ / ~~, Model.fit, inspect(std_est=True), calc_stats for CFI/TLI/RMSEA), factor_analyzer (EFA, KMO, Bartlett, ConfirmatoryFactorAnalyzer), and pingouin/girth, computing McDonald's omega from standardized loadings and judging fit against Hu & Bentler cutoffs. Use when the request mentions confirmatory factor analysis, structural equation modeling, a latent variable or construct model, factor loadings, IRT, or measurement invariance across groups. For deciding whether a scale is trustworthy at all prefer alterlab-ssci-measurement-gate; for plain regression prefer alterlab-statistical-analysis. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Ssci Orchestrator · alterlab-ieu bundle
Coordinates a social-science study through the stage-gated methods pipeline — question then design-gate then measurement-gate then sampling-gate then the right analysis module then inference-gate then reporting — holding a single YAML Design Passport that each gate reads and appends, and enforcing gate order with PASS / WARN / BLOCK semantics (design-gate and inference-gate are fail-closed). It is thin: it routes and holds the artifact, it does not run analysis itself. Use when a researcher describes a whole social-science study end to end, asks to run the methods pipeline or a full methodology review, or wants the design-to-inference workflow coordinated rather than a single step. For a single stage trigger that gate directly (alterlab-ssci-design-gate, -measurement-gate, -sampling-gate, -inference-gate); for multi-agent execution mechanics see alterlab-workflow-orchestration. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Ssci Sampling Gate · alterlab-ieu bundle
Gates who is sampled, how, and how many before data collection — checks that the sampling FRAME matches the target population (coverage error), that the METHOD is named (probability vs non-probability: simple random, stratified, cluster, systematic, quota, convenience, snowball), that sample SIZE follows the inference paradigm (an a-priori power analysis for hypothesis tests, a precision/margin-of-error target for estimation, or saturation/information power for qualitative studies — never a rule of thumb or collect-until-significant), and that the generalization claim matches the sample (statistical generalization only from probability samples). Use when asking how many participants are needed, planning recruitment, running or checking a power analysis, or judging whether a sample supports a population claim. For questionnaire items prefer alterlab-survey-design; for choosing the statistical test prefer alterlab-test-selection-guard. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Ssci Inference Gate · alterlab-ieu bundle
Audits final inferential claims against the design, sample, and uncertainty before they are written or published — refuses causal language unless the design's identifying assumption is defended (else downgrades to associational), corrects p-value and confidence-interval misreadings (a p-value is not the probability the null is true, non-significance is not proof of no effect, a 95% CI is not a 95% probability the parameter is inside it), demands effect sizes with intervals rather than significance stars, flags uncorrected multiple comparisons and optional stopping / HARKing, and scopes generalization to the sampling frame. Use when writing or checking a results or discussion section, interpreting a p-value or confidence interval, or deciding whether a finding supports a causal or population claim. For choosing the statistical test prefer alterlab-test-selection-guard; to execute the analysis prefer alterlab-statistical-analysis. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Qualitative Analysis · alterlab-ieu bundle
Analyzes qualitative data as a dispatched pipeline module — codebook development, thematic / framework / content analysis, and inter-coder reliability computed correctly (Krippendorff's alpha as primary via the krippendorff package or a bundled stdlib nominal calculator with bootstrap CIs; Cohen's / Fleiss' kappa via statsmodels) with 95% CIs and thresholds (alpha >= .80 reliable, .667-.80 tentative). It BRANCHES by design: coefficient-based ICR for codebook / content-analytic coding, versus consensus-and-reflexivity for reflexive thematic analysis where a statistic is not the right criterion. Supports human-vs-LLM double-coding with an alpha check against a human gold standard. Use when coding interviews or open-ended text, building a codebook, or reporting intercoder reliability. For topic modeling / embeddings / supervised text classification prefer alterlab-text-as-data; for the reflexivity gate prefer alterlab-ssci-reflexivity-gate. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Ssci Measurement Gate · alterlab-ieu bundle
Gates measurement quality before a scale or instrument is trusted — checks that each construct is defined and operationalized, that reliability is evidenced with McDonald omega (not Cronbach alpha alone, which assumes tau-equivalence and is only a lower bound), that reliability is not confused with validity (content, criterion, convergent/discriminant construct validity), and that measurement invariance is tested before comparing groups. Use when asking whether a scale or survey instrument is valid, reporting a Cronbach alpha, building or adopting a multi-item measure, or comparing a latent construct across groups. For designing the questionnaire items prefer alterlab-survey-design; for running the confirmatory factor analysis prefer alterlab-sem-psychometrics; to execute basic statistics prefer alterlab-statistical-analysis. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Ssci Reflexivity Gate · alterlab-ieu bundle
Gates trustworthiness before qualitative or interpretivist claims are written — the qualitative analog of the measurement gate. Checks that researcher positionality and role are stated, that the four Lincoln & Guba trustworthiness criteria are addressed (credibility via triangulation / member-checking / prolonged engagement, transferability via thick description, dependability via an audit trail, confirmability via reflexive bracketing), and that reflexivity is evidenced rather than asserted. Fail-closed: interpretivist generalizing or causal language is refused without the corresponding warrant. Use when a study is qualitative / ethnographic / interpretivist, when reviewing trustworthiness or reflexivity, or before writing up thematic or grounded-theory findings. For quantitative measurement validity prefer alterlab-ssci-measurement-gate; for running the coding prefer alterlab-qualitative-analysis; for the final claim audit prefer alterlab-ssci-inference-gate. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Mixed Methods · alterlab-ieu bundle
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.

60 repo stars
▌
Alterlab Survey Design · alterlab-ieu bundle
Comprehensive survey and instrument design assistant supporting questionnaire construction, Likert scale design, question types (open/closed/matrix), response bias mitigation, sampling strategies (probability/non-probability), pilot testing, instrument validation (Cronbach's alpha, factor analysis), online survey tools (Qualtrics, REDCap, Google Forms), interview protocol development, focus group facilitation, mixed-mode surveys, and cultural adaptation of instruments. Use when designing a survey or questionnaire, building Likert scales, planning a sampling strategy, pilot testing, validating an instrument (Cronbach's alpha, factor analysis), developing an interview protocol, improving response rates, or working in Qualtrics or REDCap. For analyzing interview/focus-group data use alterlab-qualitative-methods; for qual+quant integration alterlab-mixed-methods; for test selection/power analysis alterlab-statistical-analysis; for IRB/consent alterlab-research-ethics. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Generate Image · alterlab-ieu bundle
Generates or edits raster images via AI models (FLUX.2, Gemini 3.1 Flash Image / "Nano Banana 2") through an OpenRouter API key. Use when the request is to generate or edit a photo, illustration, artwork, concept art, poster hero image, or presentation/slide visual asset — anything that is not a technical diagram or a data chart. For flowcharts, circuits, pathways, neural-net architectures, and technical/methodology diagrams use alterlab-scientific-schematics; for plotting numeric data (scatter, bar, line) use alterlab-matplotlib instead. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Scientific Viz · alterlab-ieu bundle
Orchestrates matplotlib, seaborn, and plotly with opinionated publication styles to produce journal-ready figures. Use when preparing journal-submission figures that need multi-panel layouts with bold panel labels, statistical significance annotations, error bars, colorblind-safe palettes (Okabe-Ito), or specific journal formatting (Nature, Science, Cell). Does NOT cover raw low-level plotting or fine-grained control of individual plot elements; for building custom plots from scratch or tuning every artist and rcParam prefer alterlab-matplotlib instead. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Hypothesis Gen · alterlab-ieu bundle
Formulates structured, testable hypotheses from experimental observations using a scientific-method framework — derives predictions, proposes mechanisms, and designs experiments to test them, then renders a LaTeX report. Use when turning observations or data into falsifiable, mechanistic hypotheses, competing-explanation sets, testable predictions, or experimental designs. For a standalone systematic literature review or evidence synthesis (not a means to hypotheses) use alterlab-literature-review; to evaluate an existing manuscript use alterlab-peer-review. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Citation Graph · alterlab-ieu bundle
Free, key-less ResearchRabbit analog — builds a citation and co-citation graph around one or more seed papers using the OpenAlex API. Walks both directions of the citation network (works the seed cites and works that cite the seed), ranks the discovered neighbourhood by co-citation strength and bibliographic coupling to surface the papers most central to a topic's literature, and exports the network as GraphML (Gephi / Cytoscape / yEd) and JSON. Use when mapping a literature landscape, finding seminal or highly co-cited papers from a seed DOI, snowballing a reference network, building a citation map / co-citation analysis, or visualizing how a research area's papers connect — no API key required (polite mailto only). Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Yok Akademik · alterlab-ieu bundle
Looks up a Turkish academic's official YOKSIS-backed profile, current affiliation, unvan (academic title), publications, research projects, and supervised theses on the YOK Akademik portal (akademik.yok.gov.tr/AkademikArama/), a server-rendered JSP app with no public JSON API, by scraping its verified endpoints (AkademisyenArama POST search, viewAuthor.jsp profile, AkademisyenProjeBilgileri, AkademisyenYonTezBilgileri) keyed by an opaque authorId, with Turkish-character (Iı Şş Ğğ Çç Öö Üü) normalization for name matching. Use when the request is to verify a Turkish academic's current institution, find a researcher on YOK Akademik, confirm affiliation for authorship or a recommendation letter, or list someone's supervised theses or projects. For admission statistics (kontenjan, taban puan) use alterlab-yokatlas; for the national thesis full-text archive use alterlab-yok-tez; for publication metadata enrichment use alterlab-openalex. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Academic Career · alterlab-ieu bundle
Prepares academic career documents and professional-development materials for faculty and researchers. Use when drafting academic CVs, research statements, teaching philosophies, diversity statements, faculty-position cover letters, tenure dossiers, promotion narratives, academic portfolios, or mentorship statements, and when planning conference-networking strategy, building academic web presence, setting up ORCID profiles, or understanding impact metrics. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Research Grants · alterlab-ieu bundle
Writes competitive research grant proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC — applies agency-specific formatting and review criteria, prepares budgets, and drafts broader-impacts, significance statements, and innovation narratives that comply with submission requirements. Use when drafting or revising a grant proposal, aligning a proposal to a funding agency's review criteria, or preparing grant budgets and compliance sections. For Turkey's TÜBİTAK 1001/1002-A national proposals use alterlab-tubitak-proposal; to write a reviewer's critique of someone else's proposal use alterlab-peer-review; for a journal manuscript use alterlab-scientific-writing. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Venue Templates · alterlab-ieu bundle
Provides LaTeX templates, formatting requirements, and submission guidelines for major scientific venues (Nature, Science, PLOS, IEEE, ACM, Cell Press), conferences (NeurIPS, ICML, ICLR, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). Also covers venue-specific writing style (tone, abstract format, what reviewers prioritize). Use when preparing a manuscript, conference paper, poster, or grant proposal and you need the right template, page/word limits, citation style, figure specs, or venue conventions. For substantive prose/content development defer to alterlab-scientific-writing; for grant argumentation defer to alterlab-research-grants. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Qiime2 Amplicon · alterlab-ieu bundle
Runs 16S/ITS amplicon (microbiome) analysis with the QIIME 2 amplicon distribution (2026.1; renamed to "qiime2" in 2026.4) in the correct order: manifest import, cutadapt trim-paired primer removal BEFORE dada2 denoise-paired (trunc-len chosen from the demux quality .qzv), feature-classifier classify-sklearn against a version-matched SILVA 138 or Greengenes2 classifier, and diversity core-metrics-phylogenetic — teaching the .qza/.qzv artifact-and-provenance model and the 2026.1 feature-table summarize change (the former summarize_plus). Use when the request mentions QIIME2, QIIME 2, qiime, 16S, 18S, ITS, amplicon, microbiome, ASV, DADA2 denoising, feature table, taxonomic classification, or core-metrics diversity. For downstream alpha/beta diversity, PCoA, and PERMANOVA on the exported feature table prefer alterlab-scikit-bio; this is conda-only (no pip install). Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Squidpy Spatial · alterlab-ieu bundle
Analyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms correctly: Visium spots use spatial_neighbors(coord_type='grid') and pair with deconvolution, while Xenium/MERFISH single-cell data use coord_type='generic'/Delaunay neighbors and spatialdata-io readers (xenium, visium_hd, merscope). Runs sq.gr.spatial_neighbors, nhood_enrichment, co_occurrence, spatial_autocorr (Moran's I for spatially variable genes), ripley, and ligrec. Use when the user wants spatial transcriptomics, squidpy, Visium/Xenium/MERFISH analysis, neighborhood enrichment, co-occurrence, or spatially variable genes; QC/clustering uses alterlab-scanpy and spot deconvolution (destVI/Tangram) uses alterlab-scvi-tools. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Stable Baselines3 · alterlab-ieu bundle
Trains single-agent reinforcement learning agents with Stable-Baselines3 — PPO, SAC, DQN, TD3, DDPG, and A2C behind a scikit-learn-like API. Use for standard single-agent RL experiments, quick prototyping, well-documented algorithm implementations on Gymnasium environments, or adding callbacks and evaluation. For high-throughput parallel training, multi-agent systems, or custom vectorized environments prefer alterlab-pufferlib. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Imaging Data Commons · alterlab-ieu bundle
Query and download public cancer imaging data from the NCI Imaging Data Commons (IDC) using the idc-index Python package, filtering by metadata, visualizing in-browser, and checking licenses, with no authentication required. Use when obtaining large-scale radiology (CT, MR, PET) or digital pathology DICOM datasets for AI/ML training or cancer imaging research. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Remote Compute · alterlab-ieu bundle
Dispatch long-running GPU/CPU jobs to remote compute with a provider-agnostic submit → poll → harvest pattern across SLURM/HPC (sbatch, squeue, sacct) and managed APIs (Modal, RunPod, GCP Batch / Vertex AI). Use when submitting a batch job to a cluster, polling job status, retrieving result artifacts from a scheduler or cloud GPU provider, or writing a portable job-submission wrapper; the foundation-model skills (alterlab-alphafold, alterlab-boltz, alterlab-rfdiffusion, and siblings) dispatch their GPU work through this pattern. For Modal-specific serverless container deployment and autoscaling prefer alterlab-modal instead. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Accreditation Aol · alterlab-ieu bundle
Scaffolds program-level Assurance-of-Learning (AoL) documentation for AACSB (2020 Standard 5) and ABET (Criterion 3 Student Outcomes, Criterion 4 Continuous Improvement) accreditation — program learning outcomes / competency goals, curriculum-to-outcome mapping matrices, direct- and indirect-assessment plans, rubric design, and closing-the-loop continuous-improvement narratives — and validates the structure of an outcome-mapping matrix with scripts/aol_matrix.py. Use when the user needs AACSB or ABET assurance-of-learning material, a program-learning-outcomes set, a curriculum/outcome map or coverage matrix, a direct/indirect assessment plan, a closing-the-loop report, or accreditation self-study text. For single-course design or course rubrics prefer alterlab-teaching-design; for post-award grant reports prefer alterlab-grant-reporting. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Usfiscaldata · alterlab-ieu bundle
Queries the U.S. Treasury Fiscal Data API across 54 datasets and 182 data tables (no API key required) for federal financial data on national debt, government spending, revenue, interest rates, exchange rates, and savings bonds. Use when working with U.S. federal fiscal data, national debt tracking (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasury securities auctions, interest rates on Treasury securities, foreign exchange rates, savings bonds, or any U.S. government financial statistics. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Research Ethics · alterlab-ieu bundle
International research ethics and compliance assistant supporting IRB/ethics board applications, informed consent drafting, data management plans, Belmont Report principles, Declaration of Helsinki (2024), GDPR compliance for research, HIPAA considerations, vulnerable populations protocols, deception research, confidentiality and anonymity, research integrity (fabrication/falsification/plagiarism), conflict of interest disclosure, and dual-use research oversight. Use when preparing an IRB or ethics board application, drafting informed consent, writing a data management plan, addressing GDPR/HIPAA in research, protecting human subjects or vulnerable populations, handling animal ethics, or disclosing conflicts of interest. For Turkey-specific etik kurul use alterlab-tr-research-ethics; for KVKK data plans alterlab-kvkk-dmp; for survey wording alterlab-survey-design; for qualitative methodology alterlab-qualitative-methods. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Research Lookup · alterlab-ieu bundle
Look up current research and scholarly papers by auto-routing each query to the best backend — the Parallel Web Systems Chat API (general research) or Perplexity sonar-pro-search (academic paper searches) — and save every result with citations to sources/. Use when finding papers, gathering research data, verifying scientific claims, or assembling citation lists and unsure which search backend fits. For plain general web search or extracting content from a known URL prefer alterlab-parallel-web instead (requires PARALLEL_API_KEY and OPENROUTER_API_KEY). Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Glycoengineering · alterlab-ieu bundle
Analyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and reach curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). Use when identifying or designing glycosylation sites, optimizing therapeutic-antibody or biologic glycoforms, or doing glycoprotein engineering and vaccine-design work. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Syllabus AI Policy · alterlab-ieu bundle
Drafts course-level generative-AI use policies and syllabus statements: assigns each graded task a permitted/restricted/prohibited tier (modeled on Cornell's prohibit/allow-with-attribution/encourage framework), writes the disclosure clause with a verbatim APA (OpenAI, 2023) or MLA Works Cited citation template for ChatGPT, and adds assessment-integrity, accessibility, and equity language bound to the institution's own academic-integrity code. Ships scripts/policy_builder.py to emit a paste-ready statement and scripts/policy_lint.py to flag a vague or self-contradicting draft. Use when the request mentions a syllabus AI policy, a course statement on ChatGPT or generative AI, an academic-integrity clause for AI tools, an AI-disclosure rule, or per-assignment permitted/prohibited AI tiers. For full course/backward design, syllabus, or rubrics use alterlab-teaching-design; for human-subjects AI-tool ethics use alterlab-research-ethics. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Alpha Vantage · alterlab-ieu bundle
Accesses real-time and historical stock market data, forex rates, cryptocurrency prices, commodities, economic indicators, and 50+ technical indicators via the Alpha Vantage API (requires a free API key from alphavantage.co). Use when fetching stock prices (OHLCV), company fundamentals (income statement, balance sheet, cash flow), earnings, options data, market news/sentiment, insider transactions, GDP, CPI, treasury yields, gold/silver/oil prices, Bitcoin/crypto prices, forex exchange rates, or calculating technical indicators (SMA, EMA, MACD, RSI, Bollinger Bands). Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Literature Review · alterlab-ieu bundle
Conducts comprehensive, systematic literature reviews across multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar), with PRISMA flow tracking, study screening (title/abstract and full-text), evidence-table extraction, and risk-of-bias assessment, producing professionally formatted markdown documents and PDFs with verified citations in multiple styles (APA, Nature, Vancouver). Use when running a systematic literature review, meta-analysis, research synthesis, or broad literature search, building a PRISMA flow diagram, screening studies, extracting an evidence table, or assessing risk-of-bias across biomedical, scientific, and technical domains. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Scientific Slides · alterlab-ieu bundle
Builds slide decks for research talks in PowerPoint and LaTeX Beamer, providing slide structure, design templates, timing guidance, and visual validation. Use when making conference presentations, seminar talks, research presentations, thesis-defense slides, or any scientific talk deck. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Preprint Deposition · alterlab-ieu bundle
Drives preprint deposition across servers (arXiv, bioRxiv, medRxiv, SSRN, OSF Preprints): picks the right server by field, prepares submission metadata, sets the license (arXiv offers CC BY/BY-SA/BY-NC-SA/BY-NC-ND 4.0, the arXiv non-exclusive license, or CC0; bioRxiv/medRxiv offer CC BY/BY-NC/BY-ND/BY-NC-ND/CC0 or No-reuse), maps arXiv category taxonomy, handles immutable versioning and preprint DOIs, checks a journal's preprint/self-archiving policy via the Sherpa Romeo v2 API, and links the posted preprint to the published article. Reuses alterlab-arxiv and alterlab-biorxiv for metadata and alterlab-open-science for data-repository choice. Use when depositing a preprint, choosing a preprint server, preparing an arXiv or bioRxiv submission, setting a preprint license, or checking journal preprint policy; for Zenodo/Dryad/Figshare data deposition prefer alterlab-open-science, for TÜBİTAK Aperta prefer alterlab-aperta. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Results Transparency · alterlab-ieu bundle
Enforces results-reporting transparency as a discipline gate built on the Iron Law "NO RESULTS CLAIM WITHOUT REPORTING EVERY ANALYSIS RUN" — a numbered Gate Function (IDENTIFY the claim, LIST every test actually run including the ones that did not "work", CHECK assumptions were reported, CHECK effect size with 95% CI is present, CHECK pre-registration deviations are disclosed, ONLY THEN write the sentence), plus an Excuse-vs-Reality table and Red-Flags-STOP list for selective reporting, cherry-picking, and bare p-values. Use when writing up Results, claiming a finding from a subset of analyses, reporting a p-value without an effect size or confidence interval, dropping outliers post hoc, or omitting analyses that did not pan out. Orchestrates alterlab-statistical-analysis (tests, effect sizes), alterlab-preregistration-discipline (the frozen plan), and alterlab-open-science (TOP, disclosure); it does not run the tests itself. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Test Selection Guard · alterlab-ieu bundle
Enforces statistical-test selection as a discipline, holding the Iron Law NO TEST CHOSEN AFTER SEEING THE P-VALUE: routes the choice through a fixed decision tree (outcome type -> groups -> paired? -> normality) terminating in named tests (t-test, Mann-Whitney U, ANOVA, Kruskal-Wallis, Wilcoxon, Friedman, chi-square, Pearson/Spearman, regression), gates interpretation behind a mandatory Shapiro-Wilk/Levene/linearity assumption check, blocks test-shopping with an Excuse-vs-Reality table and Red-Flags-STOP list, and applies a 3+-tests escalation gate forcing Bonferroni/FDR correction or an exploratory label. Use when choosing or switching a statistical test, asking which test to run, dropping a test after a non-significant result, or running many tests hunting for significance. For executing the chosen test prefer alterlab-statistical-analysis or alterlab-statsmodels; for the broader frozen-plan discipline see alterlab-preregistration-discipline. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Abm Mesa · alterlab-ieu bundle
Builds agent-based models of social systems with Mesa 3 — the current AgentSet API (model.agents.shuffle_do('step'), auto-assigned unique_id, mandatory super().__init__(seed=...)), cell spaces (mesa.discrete_space OrthogonalMooreGrid / classic mesa.space grids), the DataCollector, batch_run parameter sweeps, and SolaraViz — for emergence, segregation, diffusion, opinion dynamics, and cooperation models. It uses the Mesa 3.x API (the old mesa.time schedulers like RandomActivation are removed) and treats the model as a generative theory to be validated, not just run. Use when the request mentions an agent-based model, Mesa, simulating interacting agents, or emergent macro behavior from micro rules. For discrete-event (queueing/process) simulation prefer alterlab-simpy; for reinforcement learning prefer alterlab-stable-baselines3. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Akademik Tesvik · alterlab-ieu bundle
Computes the annual Turkish academic-incentive (akademik teşvik) score for Devlet (state) university öğretim elemanı (academic staff) from a classified activity list, applying the verified Akademik Teşvik Ödeneği Yönetmeliği (2018/11834) Faaliyet Hesaplama Tablosu headline puanları (Proje 20, Araştırma 15, Yayın 30, Patent 30, Atıf 30, Tebliğ 20, Ödül 20) with the k (author-count), p (Q1 1/Q2 0.8/Q3 0.5/Q4 0.25), and r (project-role) coefficients via türü puanı = Σ(faaliyet oranları) × headline (MADDE 8/2), then enforcing the per-type headline ceilings, the 100 cap (MADDE 8/3), and the net-30 payment gate (MADDE 10/3) in a deterministic scripts/tesvik_score.py. Use when the user wants to calculate akademik teşvik puanı, check the en az 30 (net-30) threshold, apply TABLO 4 ceilings, or estimate teşvik eligibility; keeps its coefficients separate from doçentlik scoring. For doçentlik point eligibility prefer alterlab-docentlik-eligibility. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Scientific Writing · alterlab-ieu bundle
Writes scientific manuscripts in full flowing paragraphs (never bullet points) via a two-stage process — section outlines with key points using research-lookup, then conversion to prose — applying IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, and reporting guidelines (CONSORT/STROBE/PRISMA). Use when drafting or revising research papers, journal submissions, or any manuscript section (abstract, introduction, methods, results, discussion), or professional/technical reports. For a specific venue's LaTeX template and house style use alterlab-venue-templates; to build a BibTeX bibliography or verify reference metadata use alterlab-citation-mgmt. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Treatment Plans · alterlab-ieu bundle
Generates concise (3-4 page), focused medical treatment plans in LaTeX/PDF format across all clinical specialties — general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management — using SMART goal frameworks, evidence-based interventions with minimal citations, HIPAA compliance, and professional formatting. Use when drafting a brief, actionable patient treatment or care plan with measurable SMART goals and structured follow-up for any specialty. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Statistical Analysis · alterlab-ieu bundle
Guided statistical analysis with hypothesis-test selection, assumption checking, power analysis, and APA-formatted reporting. Use when choosing the appropriate statistical test for data, verifying test assumptions, computing power/sample size, or producing APA-style results for academic research. For implementing specific models programmatically prefer statsmodels. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Astropy · alterlab-ieu bundle
Processes astronomy and astrophysics data with the Astropy Python library — celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, and world coordinate systems (WCS). Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or general astronomical data analysis. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Pyzotero · alterlab-ieu bundle
Interact with Zotero reference management libraries using the pyzotero Python client — retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Aperta · alterlab-ieu bundle
Drives TÜBİTAK Açık Bilim Politikası (Open Science Policy) compliance and deposition into Aperta — TÜBİTAK ULAKBİM's national open archive at aperta.ulakbim.gov.tr — encoding the binding mandates (green-road deposit of the accepted manuscript on acceptance; open access within 6 months for fen/mühendislik (STEM) and 12 months for sosyal/beşeri (SSH); İlke-6 documentation when data must stay closed for KVKK/privacy reasons) and scaffolding a TÜBİTAK Veri Yönetim Planı / VYP (data management plan) at grant-application time. Use when depositing to Aperta, complying with the TÜBİTAK açık bilim policy, preparing a TÜBİTAK data management plan (VYP), reporting open-access compliance in a final report, or documenting a justified data embargo. For Zenodo/Dryad/OSF and international DMPs prefer alterlab-open-science; for the KVKK lawful-basis/anonymisation plan prefer alterlab-kvkk-dmp. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Figure QA · alterlab-ieu bundle
Verify publication figures with a render-then-check QA pass — data-fidelity against every underlying row, axis/label floor-and-ceiling legibility, bounding-box collision detection for overlapping text/markers, and 300-dpi print-readiness. Use when proofing or auditing a finished figure for correctness and print quality, catching mislabeled or overlapping elements, or confirming a plot faithfully represents its data before submission. For CREATING the plot prefer alterlab-matplotlib (or alterlab-seaborn / alterlab-plotly); for multi-panel publication layout prefer alterlab-scientific-viz; for schematic diagrams prefer alterlab-scientific-schematics. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Alphafold · alterlab-ieu bundle
Predict protein 3D structures with AlphaFold2 via ColabFold — MMseqs2-accelerated MSAs, monomer and AlphaFold2-Multimer complex folding, and confidence-based validation (pLDDT, pTM/ipTM, PAE). Use when folding a protein sequence or complex from FASTA, generating a predicted structure with confidence metrics, ranking models, or checking self-consistency of a design. For co-folding a protein WITH a small-molecule ligand or predicting binding affinity prefer alterlab-boltz; for antibody–antigen or one-FASTA multi-entity complexes prefer alterlab-chai; to LOOK UP an already-computed structure prefer alterlab-alphafold-db; for ESM embeddings or inverse folding prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Biopython · alterlab-ieu bundle
Manipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed programmatically via Biopython (Bio.SeqIO, Bio.Entrez, Bio.PDB, Bio.Blast). Use when scripting custom bioinformatics pipelines, batch-processing sequence files, automating BLAST, or fetching records from Entrez — for quick one-off database lookups use gget, for unified multi-service integration use bioservices. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Cellxgene · alterlab-ieu bundle
Query the CZ CELLxGENE Census (61M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public atlas, running population-scale queries, or benchmarking your data against a reference — for analyzing your own dataset use scanpy or scvi-tools. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Deeptools · alterlab-ieu bundle
Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC (multiBamSummary correlation, PCA, plotFingerprint), apply the ATAC-seq Tn5 shift (alignmentSieve --ATACshift), and make TSS/peak heatmaps and profiles (computeMatrix, plotHeatmap, plotProfile). Use for coverage tracks, signal heatmaps/profiles, normalization (RPGC/CPM/RPKM), and effective-genome-size lookups for ChIP-seq, ATAC-seq, MNase-seq, or RNA-seq. NOT for per-read/CIGAR/MAPQ BAM record access — that is pysam. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Tiledbvcf · alterlab-ieu bundle
Store and query genomic variant data at scale with TileDB-VCF — ingest VCF/BCF into compressed TileDB arrays, add samples incrementally, run fast parallel region/sample queries, and export back to VCF. Use when managing population-genomics variant datasets that are too large for flat VCF, building joint variant stores, or querying thousands of samples by region. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Deepchem · alterlab-ieu bundle
Runs molecular machine learning with DeepChem — diverse featurizers, pre-built MoleculeNet benchmark datasets, and pre-trained models (ChemBERTa, GROVER) for property prediction (ADMET, toxicity, solubility) via traditional ML or graph neural networks. Use when running end-to-end molecular ML experiments that need MoleculeNet benchmarks, scaffold splitting, or ready-made models with minimal setup; for building custom PyTorch graph architectures prefer alterlab-torchdrug, and for standalone molecule-to-feature-vector generation prefer alterlab-molfeat. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Diffdock · alterlab-ieu bundle
Predicts protein-ligand binding poses with DiffDock diffusion-based molecular docking from PDB structures and SMILES, producing pose confidence scores for virtual screening and structure-based drug design. Use when docking ligands into a protein, generating binding poses, or screening compounds against a target; not for binding affinity prediction. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Statsmodels · alterlab-ieu bundle
Statistical modeling in Python with statsmodels — OLS, GLM, mixed models, and ARIMA with detailed diagnostics, residuals, and inference. Use when fitting specific model classes for econometrics, time series, or rigorous inference with coefficient tables and confidence intervals. For guided statistical test selection with APA reporting prefer statistical-analysis. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Clinicaltrials · alterlab-ieu bundle
Query ClinicalTrials.gov via its API v2 to search trials by condition, drug, location, recruitment status, or phase and retrieve trial details by NCT ID. Use when finding interventional or observational studies, checking trial status and eligibility for patient matching, or exporting clinical trial records for research. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Fluidsim · alterlab-ieu bundle
Runs computational fluid dynamics simulations with the FluidSim Python framework using pseudospectral FFT methods, with HPC support and output analysis. Use when simulating Navier-Stokes equations (2D/3D), shallow water equations, or stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Pymatgen · alterlab-ieu bundle
Analyzes and manipulates materials with the pymatgen toolkit — crystal structures and molecules, phase diagrams and thermodynamic stability, electronic structure (band structures, DOS), surfaces and interfaces, and Materials Project database access. Use when working with crystal structures in materials science, converting between structure formats (CIF, POSCAR, XYZ), analyzing symmetry or space groups, computing phase diagrams, querying the Materials Project API, or handling VASP, Gaussian, or Quantum ESPRESSO output. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Trdizin · alterlab-ieu bundle
Searches TR Dizin (TÜBİTAK ULAKBİM national citation index) and verifies a journal's current national-index status through its confirmed unauthenticated REST/Elasticsearch API at https://search.trdizin.gov.tr/api/defaultSearch/{publication|journal|author|institution}/ (params q, order e.g. relevance-DESC, page), parsing hits.hits[]._source plus faceted aggregations, and derives indexing status from a journal record's isActive + journalYear coverage vs rejectYearList. Use when the user wants to search TR Dizin, check if a journal is TR Dizin indexed (TR Dizin'de var mı / taranıyor mu), find Turkish-indexed publications, verify national-index status before submitting, or audit doçentlik-eligible venues. For DergiPark hosting prefer alterlab-dergipark; for doçentlik points prefer alterlab-docentlik-eligibility; for teşvik scoring prefer alterlab-akademik-tesvik. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Yok Tez · alterlab-ieu bundle
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.

60 repo stars
▌
Alterlab Matplotlib · alterlab-ieu bundle
Builds plots with the matplotlib Python library (pyplot and the object-oriented Figure/Axes API) for full low-level customization, exporting to PNG/PDF/SVG. Use when fine-grained control over individual plot elements is needed — custom line/scatter/bar/histogram/heatmap/contour/box/violin/3D plots, rcParams and style-sheet tuning, or GridSpec subplot layouts inside a scientific Python workflow. Does NOT cover opinionated journal-ready multi-panel figure workflows (Nature/Science/Cell formatting, colorblind-safe palettes, significance annotations); for those prefer alterlab-scientific-viz instead. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Etetoolkit · alterlab-ieu bundle
Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect duplication/speciation events, infer orthology and paralogy, query NCBI taxonomy, and export PDF/SVG figures. Use when traversing or reformatting tree files, doing phylogenomic comparative analysis, or producing publication tree graphics in Python. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Ligandmpnn · alterlab-ieu bundle
Design protein sequences around bound ligands, metals, and nucleic acids with LigandMPNN (Dauparas 2023) — inverse folding that conditions on non-protein context, so binding-pocket and metal-site residues are chosen to fit the actual ligand. Use when designing a small-molecule or metal binding pocket, redesigning residues that contact a ligand/ion/nucleic acid, or doing enzyme active-site design where the substrate matters. For backbone sequence design with NO ligand/metal context prefer alterlab-proteinmpnn; to GENERATE a backbone or scaffold a functional site prefer alterlab-rfdiffusion; to validate a design by refolding prefer alterlab-alphafold; to co-fold or dock the ligand prefer alterlab-boltz or alterlab-diffdock. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Scikit Bio · alterlab-ieu bundle
Analyze biological data with scikit-bio — sequence analysis and alignments, phylogenetic trees, alpha/beta diversity metrics (including UniFrac), ordination (PCoA), PERMANOVA statistics, and FASTA/Newick I/O. Use for microbiome and community-ecology analysis — computing diversity, distance matrices, and ordination from feature tables. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Scvi Tools · alterlab-ieu bundle
Train deep generative models for single-cell omics with scvi-tools — probabilistic batch correction and integration (scVI), reference-mapping transfer learning (scArches), differential expression with uncertainty, and multimodal models (totalVI for CITE-seq, MultiVI for multiome). Use when correcting batch effects, integrating multimodal data, or doing advanced probabilistic single-cell modeling — for standard analysis pipelines use scanpy. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Torchdrug · alterlab-ieu bundle
Builds PyTorch-native graph neural networks with TorchDrug for molecules and proteins, exposing custom GNN architectures, task/dataset abstractions, molecular generation, retrosynthesis planning, and knowledge-graph reasoning. Use when developing custom graph model layers, predicting protein properties from sequence or structure, or building retrosynthesis and drug-repurposing pipelines; for ready-made featurizers, MoleculeNet benchmarks, and pre-trained models with less code prefer alterlab-deepchem. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Pydicom · alterlab-ieu bundle
Reads, writes, and manipulates DICOM (Digital Imaging and Communications in Medicine) medical imaging files with the pydicom Python library. Use when reading/writing/modifying DICOM data, extracting pixel data from CT, MRI, X-ray, or ultrasound images, anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM to other formats, handling compressed DICOM, or processing medical imaging datasets for PACS systems, radiology workflows, and healthcare imaging applications. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Scikit Learn · alterlab-ieu bundle
Classical machine learning in Python with scikit-learn — algorithms, preprocessing, pipelines, and best-practice reference documentation. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, feature preprocessing, or building ML pipelines. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Transformers · alterlab-ieu bundle
Pre-trained transformer models with Hugging Face Transformers for NLP, computer vision, audio, and multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, or fine-tuning transformer models on custom datasets. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Metabolomics Wb · alterlab-ieu bundle
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.

60 repo stars
▌
Alterlab Markitdown · alterlab-ieu bundle
Convert files and Office documents to clean, LLM-friendly Markdown with Microsoft MarkItDown (markitdown CLI/Python), supporting PDF, DOCX, PPTX, XLSX, images (EXIF + OCR), audio (transcription), HTML, CSV, JSON, XML, ZIP archives, EPUB e-books, and YouTube transcript URLs, with optional AI image descriptions. Use when converting a document, PDF, slide deck, spreadsheet, scanned image, audio file, web page, or e-book into Markdown text for ingestion or LLM processing, extracting text via OCR, transcribing audio, or batch-converting mixed file formats to token-efficient Markdown. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Geomaster · alterlab-ieu bundle
Covers geospatial science across remote sensing, GIS, spatial analysis, and machine learning for earth observation — satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), raster and DEM operations, spectral indices (NDVI/EVI/NDWI), spatial statistics, point cloud processing, network analysis, and cloud-native workflows (STAC, COG, Planetary Computer), with examples across Python, R, Julia, JavaScript, C++, Java, Go, and Rust. Use for remote sensing workflows, satellite/raster image classification, terrain/slope/hillshade analysis, spatial ML on earth-observation data, hydrological modeling, marine spatial analysis, or atmospheric science. For pure tabular vector work with no raster/EO aspect (plain GeoPandas sjoin, buffer, overlay, dissolve, choropleths) prefer the geopandas skill; for celestial-sphere astronomy coordinates (ICRS/galactic, FITS, WCS) prefer the astropy skill. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Hypogenic · alterlab-ieu bundle
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.

60 repo stars
▌
Alterlab Pennylane · alterlab-ieu bundle
Trains and differentiates quantum circuits with PennyLane, a hardware-agnostic quantum machine-learning framework with automatic differentiation and PyTorch/JAX/TensorFlow integration. Use when training quantum circuits via gradients (parameter-shift, backprop, adjoint), building hybrid quantum-classical models or quantum neural networks, or running differentiable variational algorithms (VQE, QAOA). For IBM Quantum hardware and Qiskit Runtime prefer alterlab-qiskit; for Google Quantum AI or NISQ circuits prefer alterlab-cirq; for open-system Lindblad/master-equation dynamics prefer alterlab-qutip. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Redcap Cdisc · alterlab-ieu bundle
Designs validated research data-capture instruments and aligns them to CDISC submission standards. Builds REDCap projects from a requirements spec: instrument and field design, the 18-column data dictionary (Variable/Field Name, Form Name, Field Type, Choices, Branching Logic, Text Validation, Identifier?), field validation (date_ymd, integer, number, email, phone), branching/show-field logic, longitudinal events and survey settings, and lints a data dictionary for common errors. Maps a study to CDISC: CDASH collection fields, SDTM domain mapping (DM, AE, VS, LB, EX, CM, MH across Interventions/Events/Findings classes), and NCI-EVS controlled terminology. Use when the user wants to build a REDCap project, write or lint a data dictionary, set up branching logic or validation, or map a study to CDISC SDTM/CDASH/CDISC CT. For LabArchives ELN bridging use alterlab-labarchive; for Likert/sampling/reliability use alterlab-survey-design. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Denario · alterlab-ieu bundle
Runs Denario (AstroPilot-AI), a multiagent AI system for scientific research assistance that automates end-to-end research workflows from a described dataset through idea, methodology, computational results, and a publication-ready LaTeX paper. Built on AG2 + LangGraph with a cmbagent analysis backend. Use when driving the Denario pipeline (Denario.get_idea/get_method/get_results/get_paper), generating research ideas from a dataset description, auto-developing methodology, executing analysis agents, or emitting a journal-formatted (APS/AAS/JHEP/ICML/NeurIPS/PASJ) LaTeX manuscript. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Dnanexus · alterlab-ieu bundle
Develops and runs genomics pipelines on the DNAnexus cloud platform using the dxpy Python SDK and dx CLI — build apps/applets, write dxapp.json, upload/download data, and execute jobs/workflows over FASTQ/BAM/VCF files. Use when building or running a DNAnexus app, applet, or workflow, writing dxapp.json, using dx-app-wizard or dx build, calling dxpy (find_data_objects, DXApplet.run, upload_local_file), or uploading/downloading sequencing data on DNAnexus. For LatchBio (Latch SDK @workflow/@task, LatchFile) use alterlab-latchbio instead; for Benchling LIMS use alterlab-benchling. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Latchbio · alterlab-ieu bundle
Builds and deploys bioinformatics pipelines on the LatchBio platform using the Latch SDK — author workflows with @workflow/@task decorators, handle LatchFile/LatchDir I/O, register serverless workflows, configure CPU/GPU task resources, organize data in the Latch Registry, and wrap Nextflow/Snakemake pipelines. Use when developing or deploying a Latch SDK workflow, sizing task resources, working with the Registry, or porting a Nextflow/Snakemake bioinformatics pipeline onto LatchBio. Not for DNAnexus (dxpy/dx CLI) or generic Flyte. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Perplexity · alterlab-ieu bundle
Run AI web searches with real-time, citation-grounded answers using Perplexity Sonar models (sonar, sonar-pro, sonar-pro-search agentic search, sonar-reasoning, sonar-reasoning-pro) via LiteLLM and a single OpenRouter API key. Use when searching for current information or recent scientific literature, getting answers grounded in cited web sources, verifying a claim against current evidence, or reaching information beyond the model's training cutoff. Requires an OpenRouter API key. This is the direct single-backend Perplexity tool: for automatic routing between Perplexity and other backends use alterlab-research-lookup, and for structured per-paper experimental-data extraction (sample sizes, effect sizes, quality scores) use alterlab-bgpt-search. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Kvkk Dmp · alterlab-ieu bundle
Produces KVKK-compliant (Law 6698, as amended by Law 7499 — published in the Official Gazette 12 Mar 2024, KVKK provisions effective 1 Jun 2024) data management plans for Turkish research, encoding the açık rıza (explicit consent) default basis, the Art. 28(1)(b) anonymization exemption as the primary compliance lever, the Art. 6 special-category regime for health/genetic/biometric data, Art. 7 deletion/destruction/anonymization at purpose-end, the Art. 13 thirty-day data-subject response window, Art. 9 cross-border adequacy-decision rules for cloud/overseas data, and Art. 16 VERBIS pre-processing registration, with a KVKK-vs-GDPR crosswalk. Use when the user needs a KVKK data management plan, to anonymize a research dataset under Turkish law, a VERBIS check, or to fix EU DMP boilerplate for Turkey; for pure GDPR/HIPAA use alterlab-research-ethics. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Yokatlas · alterlab-ieu bundle
Retrieves Türkiye higher-education program and admission statistics from YÖK Atlas (yokatlas.yok.gov.tr) — quotas (kontenjan), placements (yerleşen), minimum admission scores (taban puan), success ranks (başarı sırası), and per-title academic-staff counts — via the keyless yokatlas-py (>=0.6.0, MIT) wrapper over the JSON API at /api/tercih-kilavuz/ (search, universiteler, universite-programlar), with SearchFilters for puan türü (SAY/SÖZ/EA/DİL/TYT), university type (DEVLET/VAKIF), province, and success-rank ranges. Use when the request mentions YÖK Atlas, program statistics, kontenjan/quota data, taban puan/minimum admission score, başarı sırası/success rank, placement counts, or program staff counts for institutional research, program benchmarking, or student advising. For an academic's CV/profile/affiliation prefer alterlab-yok-akademik; for theses prefer alterlab-yok-tez. Legacy PHP endpoints are dead post-April-2026; only the JSON API is used. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Paper 2 Web · alterlab-ieu bundle
Converts academic papers into promotional and presentation formats — interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster) from LaTeX or PDF sources. Use when disseminating a paper, preparing for a conference, building an explorable academic homepage, generating a video abstract, or producing a print-ready poster from a paper. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Peer Review · alterlab-ieu bundle
Writes structured, checklist-based manuscript and grant peer reviews — assesses methodology, statistical validity, reporting-standards compliance (CONSORT/STROBE/PRISMA), and gives constructive feedback. Use when writing a formal reviewer report, responding to a journal/grant review invitation, or revising a manuscript against reviewer criteria. For evaluating claims/evidence quality prefer alterlab-scientific-thinking; for a multi-reviewer mock-panel verdict use alterlab-paper-reviewer; for quantitative rubric scoring use alterlab-scholar-eval. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Bioservices · alterlab-ieu bundle
Query 40+ bioinformatics web services through one consistent Python API with bioservices (UniProt, KEGG, ChEMBL, Reactome, Ensembl, NCBI and more). Use when a workflow must hit multiple databases together, map identifiers across services, or run cross-database analyses — for quick single-database lookups use gget, for sequence and file manipulation use biopython. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Neuropixels · alterlab-ieu bundle
Analyze Neuropixels 1.0/2.0 extracellular electrophysiology with SpikeInterface — load SpikeGLX/Open Ephys recordings, preprocess and motion-correct, run Kilosort4 spike sorting, compute quality metrics, apply Allen/IBL curation, and do AI-assisted visual inspection. Use when working with neural recordings, spike sorting, or extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Proteinmpnn · alterlab-ieu bundle
Design protein sequences for a fixed backbone with ProteinMPNN (Dauparas 2022) — message-passing inverse folding that outputs sequences predicted to fold to a given structure, with fixed positions, tied/symmetric chains, amino-acid bias, and a soluble-model variant. Use when inverse-folding a backbone PDB into sequences, redesigning selected positions, imposing symmetry across chains, or generating the sequence step of a design→fold→score loop. For pocket/interface design WITH a bound ligand, metal, or nucleic acid prefer alterlab-ligandmpnn; to GENERATE a new backbone prefer alterlab-rfdiffusion; to refold and validate a design prefer alterlab-alphafold; for generative multimodal design prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Rfdiffusion · alterlab-ieu bundle
Generate de-novo protein backbones with RFdiffusion (Watson 2023) — a diffusion model for unconditional monomer generation, motif scaffolding, binder design against a target, and symmetric oligomers. Use when generating a new protein backbone from scratch, scaffolding a functional motif into a fold, designing a binder backbone to a target surface, or building symmetric assemblies; RFdiffusion produces the STRUCTURE, then alterlab-proteinmpnn designs its sequence and alterlab-alphafold validates it. For sequence design of an existing backbone prefer alterlab-proteinmpnn (or alterlab-ligandmpnn with a ligand); to fold a known sequence prefer alterlab-alphafold; for generative multimodal design prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Iso13485 · alterlab-ieu bundle
Prepares ISO 13485 certification documentation for medical device Quality Management Systems (QMS) — gap analysis of existing documentation, Quality Manuals, required procedures and work instructions, and Medical Device Files. Use for ISO 13485 QMS documentation, conducting a documentation gap analysis, drafting a Quality Manual or SOP/work instruction, assembling a Medical Device File, identifying missing documentation for medical device certification, or when medical device regulations, QMS certification, FDA QMSR, or EU MDR are mentioned. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Pyhealth · alterlab-ieu bundle
Develops, tests, and deploys clinical machine learning models with the PyHealth healthcare AI toolkit. Use when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare (RETAIN, SafeDrug, Transformer, GNN). Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab PDF Explore · alterlab-ieu bundle
Explore a single PDF in depth — parse it once, then answer questions across its sections, figures, tables, and appendices — comparing methods across sections, extracting every instance of a pattern within the document, and reading values off its charts and tables. Use when interrogating one paper or report end-to-end, pulling every occurrence of something inside a document, or reading data from a figure/table in a PDF, serving the literature-review and paper-review pipeline. To build a comparison table across MANY papers prefer alterlab-pdf-extract; to simply convert a PDF to Markdown prefer alterlab-markitdown; for reference/citation management prefer alterlab-pyzotero. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Benchling · alterlab-ieu bundle
Integrates the Benchling R&D platform via its REST API and SDK — access the registry (DNA, proteins), inventory, ELN entries and workflows, build Benchling Apps, and query the Benchling Data Warehouse. Use when automating Benchling lab data management, syncing sample registry or inventory records, scripting ELN entries/workflows, or running SQL against the Benchling Data Warehouse. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Opentrons · alterlab-ieu bundle
Writes liquid-handling protocols for Opentrons OT-2 and Flex robots using the official Opentrons Protocol API v2, with full access to v2 features for production-grade, officially compatible protocols. Use when authoring or running protocols specifically for Opentrons hardware. For multi-vendor automation or broader equipment control use pylabrobot instead. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Bgpt Search · alterlab-ieu bundle
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server, returning 25+ fields per paper (methods, results, sample sizes, quality scores, conclusions). Use when running a literature review or evidence synthesis, or when needing experimental details (sample sizes, effect sizes, methods, quality scores) that abstracts alone do not provide. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab PDF Extract · alterlab-ieu bundle
Free Elicit-columns analog — ingest N PDFs (or any MarkItDown-supported document) and build a per-paper evidence table with user-defined columns, one row per paper and one column per attribute/question you want pulled from every source. Use when extracting structured data across many papers into a comparison table or data-extraction sheet (sample size, methods, main finding, effect, population/intervention/outcome, limitations), screening a corpus into a spreadsheet, or pulling the same fields from a stack of PDFs into CSV/Markdown. Routes conversion through MarkItDown; offline heuristic backend by default, optional LLM backend for precise answers. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Dergipark · alterlab-ieu bundle
Harvests article metadata, abstracts, and full-text PDFs from DergiPark (TÜBİTAK ULAKBİM's national journal-hosting platform, ~2,537 journals) via its verified platform-wide OAI-PMH endpoint (https://dergipark.org.tr/api/public/oai/; verbs Identify/ListSets/ListRecords/GetRecord; prefixes oai_dc/oai_mods/oai_marc/oai_etdms; setSpec=journal-slug), parses Highwire citation_* and DC.* meta tags on /pub/{slug}/article/{id} pages, pulls PDFs from the citation_pdf_url path, and emits BibTeX/RIS locally. Use when the user wants to harvest a Turkish journal, fetch DergiPark articles, list a journal archive, get BibTeX/RIS for a DergiPark paper, or read a journal aim-and-scope (öz/kapsam). For TR Dizin indexing status use alterlab-trdizin; for YÖK theses use alterlab-yok-tez; for academic profiles use alterlab-yok-akademik. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Infographics · alterlab-ieu bundle
Creates professional infographics with Nano Banana Pro AI and smart iterative refinement, using Gemini 3 Pro for automated quality review and an optional Perplexity Sonar research phase for accurate, sourced data — supports 10 infographic types, 8 industry styles, and colorblind-safe palettes. Use when the request is for an infographic, data-story graphic, statistical poster, comparison chart, timeline, process/how-to visual, or list/social graphic that pairs a designed layout with figures. Use alterlab-scientific-schematics instead for technical flowcharts, CONSORT/PRISMA, pathways, or architecture diagrams; alterlab-generate-image for non-infographic illustrations. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab PPTX Posters · alterlab-ieu bundle
Creates research posters in HTML/CSS with responsive layouts and easy visual integration, exportable to PDF or PPTX. Use ONLY when the user explicitly requests a PowerPoint/PPTX/PPT poster, an HTML/web-based poster, or a poster they will edit in PowerPoint, or when LaTeX is unavailable. For a standard/conference research poster with no format named, use alterlab-latex-posters instead; for a slide deck/oral-talk presentation, use alterlab-scientific-slides. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Scholar Eval · alterlab-ieu bundle
Evaluates scholarly work with the ScholarEval framework, producing structured assessment across research-quality dimensions (problem formulation, methodology, analysis, and writing) with quantitative rubric scores and actionable feedback. Use when scoring or grading a paper, thesis, or research output against rubric-style criteria, or benchmarking publication readiness across revisions. For checklist-based narrative reviewer reports prefer alterlab-peer-review; for evidence/claim quality and argument soundness use alterlab-scientific-thinking. Part of the AlterLab Academic Skills suite.

60 repo stars
▌
Alterlab Rnaseq Quant · alterlab-ieu bundle
Quantifies bulk RNA-seq transcript abundance with salmon (v1.11.4 selective alignment) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware gentrome index, runs quant with --validateMappings --gcBias -l A, then imports estimates via tximport/tximeta with a tx2gene map and hands differential expression to alterlab-pydeseq2. Warns that salmon's index format changed to SSHash (rebuild pre-v1.11.2 indices) and that 'salmon alevin' was REMOVED (single-cell now uses piscem + alevin-fry). Use when quantifying RNA-seq transcript abundance, running salmon or kallisto, building a decoy-aware index, or wiring tximport to DESeq2; for differential expression use alterlab-pydeseq2, for FASTQ-to-VCF variant calling use alterlab-nf-core-sarek. Part of the AlterLab Academic Skills suite.

60 repo stars

418 published skills · page 3 of 5