Results for “labarchives”

Queries and displays Labstep electronic lab notebook data — experiments, protocols, resources, and inventory — via labstepPy, with an offline demo mode using synthetic biology data.

Query experiments, protocols, resources, and inventory in the Labstep electronic lab notebook using the labstepPy API.

Manage biological datasets and models with LaminDB, an open-source lineage-native lakehouse. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation, collections, branches, storage, and workflow integrations.

Manages biological datasets and models with LaminDB, covering setup, artifact registration, querying, lineage tracking, validation, ontology annotation, collections, branches, storage, and workflow integrations.

Diagnose and root-cause issues with OCI Kubernetes Engine clusters and workloads through evidence-driven investigation.

Look up and read Hugging Face paper pages in markdown, and use the papers API for structured metadata such as authors, linked models/datasets/spaces, Github repo and project page.

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against ontologies (genes, cell types, diseases, tissues), tracking data lineage and computational workflows, building data lakehouses, or wiring integrations with Nextflow, Snakemake, W&B, or MLflow. Part of the AlterLab Academic Skills suite.

Esta habilidade deve ser usada ao trabalhar com LaminDB, um framework de dados de código aberto para biologia que torna dados consultáveis, rastreáveis, reproduzíveis e FAIR. Use ao gerenciar datasets biológicos (scRNA-seq, espacial, citometria de fluxo, etc.), rastrear workflows computacionais, curar e validar dados com ontologias biológicas, construir data lakehouses, ou garantir linhagem de dados e reprodutibilidade em pesquisa biológica. Aborda gerenciamento de dados, anotação, ontologias (genes, tipos de célula, doenças, tecidos), validação de esquema, integrações com orquestradores de workflow (Nextflow, Snakemake) e plataformas MLOps (W&B, MLflow), e estratégias de deployment.

Builds a compact secret-safe repository pack for AI handoff, review, or large analysis; prefers Repomix when available.

Use when searching a local NCBI EDirect archive/postings index with Boolean, title, word, or pair queries inside the `x*` local-cache workflow.

Finds academic papers on arXiv, checks citation counts via Semantic Scholar, and generates BibTeX entries.

Exploratory data analysis (EDA) on a scientific data file — auto-detects the format, runs structure/quality/statistics checks, and writes a markdown EDA report with downstream recommendations. Use when asked to "explore", "analyze", "summarize", "profile", or "QC" a data file, or to understand its structure/content/quality before deciding what analysis to run. Covers tabular (.csv .tsv .xlsx .parquet), arrays (.npy .npz .hdf5 .h5 .mat .fits), sequence/genomics (.fasta .fastq .sam .bam .vcf .bed .gff .gtf .h5ad), microscopy (.tif .nd2 .czi .lif .ims .dcm .nii), spectroscopy/MS (.mzML .mzXML .mgf .fid .jdx), chemistry (.pdb .cif .mol .sdf .xyz .gro), and proteomics/metabolomics (.pepXML .mzid .mzTab). For zero-shot forecasting of a series use alterlab-timesfm; to create/configure a chunked cloud array store use alterlab-zarr. Part of the AlterLab Academic Skills suite.

Save the current diagnosis state to disk for cross-session recall, including conclusions, rejected directions, and next steps.

Search arXiv papers by keyword, author, category, or ID.

Restores the most recent diagnosis snapshot saved by dbs-save, allowing users to continue a previous diagnostic session.

Verifies that every entry in a bibliography ACTUALLY EXISTS by cross-checking it against four keyless public scholarly APIs (Crossref, OpenAlex, Semantic Scholar, arXiv) with a polite mailto identifier, resolving DOI/arXiv IDs, fuzzy-matching title and authors (difflib SequenceMatcher ratio >=0.70), flagging retractions marked in Crossref (update-to) or OpenAlex (is_retracted), and emitting per-entry JSON verdicts mapped to the AlterLab citation-hallucination taxonomy (TF/PAC/IH/PH/SH). Accepts BibTeX, a DOI/arXiv ID list, or free-form references; degrades gracefully offline by emitting 'unverified' verdicts and never silently passing. Use when the request mentions verify citations, check references, fabricated or hallucinated references, fake DOI, retraction check, bibliography audit, or reference existence check. Does NOT write or draft papers — for authoring a manuscript (whose citation-check mode inserts citations) prefer alterlab-paper-writer instead. Part of the AlterLab Academic Skills suite.

Drafts and revises academic papers through a 12-agent pipeline with hardened LaTeX output (apa7 document class, justified text, table column-width formula, centered bilingual abstracts, standardized font stack, PDF compiled from LaTeX), supporting IMRaD, literature review, theoretical, case study, policy brief, and conference paper structures, APA 7.0 (default), Chicago, MLA, IEEE, and Vancouver citation formats, bilingual zh-TW plus EN abstracts, and multi-format output (LaTeX, DOCX, PDF, Markdown). Use when the request mentions write paper, academic paper, paper outline, write abstract, revise paper, check citations, convert to LaTeX, guide my paper, parse reviews, revision roadmap, or 寫論文, 學術論文, 論文大綱, 寫摘要, 修改論文, 檢查引用, 引導我寫論文, 帶我規劃論文, 逐章規劃, 論文架構, 審查意見, 修訂路線圖. Its citation-check mode formats and inserts citations while drafting; for a standalone anti-hallucination check that cited references actually exist prefer alterlab-citation-verifier instead. Part of the AlterLab Academic Skills suite.

Search, browse, and retrieve scientific protocols from protocols.io via REST API, including private protocols with client token authentication.

Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete.

从 PAPER_PLAN 起草 LaTeX 论文：逐 section 从 wiki 取材撰写 + 生成 figures/tables + BibTeX 验证 + de-AI polish

Hunt for adversary abuse of Living Off the Land Binaries (LOLBins) by analyzing endpoint process creation logs for suspicious execution patterns of legitimate Windows system binaries used for malicious purposes.

Search arXiv papers by keyword, author, category, or ID.

Structured data + RAG. NL2SQL hybrid patterns (text-to-SQL then execute vs embed rows), table embedding strategies (row-level, schema-level, hybrid), semantic layer integration (Cube, dbt metrics), LangChain SQLDatabaseChain, LlamaIndex PandasQueryEngine, safe SQL execution (read-only, sandboxed), schema-aware retrieval. Full PostgreSQL + pgvector hybrid code. USE WHEN: user mentions "tabular RAG", "NL2SQL", "text to SQL", "RAG on tables", "database RAG", "SQL RAG", "semantic layer", "structured data RAG" DO NOT USE FOR: unstructured doc RAG - use `rag-architecture`; metadata filtering only - use `self-querying-retriever`; KG retrieval - use `graph-rag`

Search arXiv papers by keyword, author, category, or ID.

Search and retrieve academic papers from arXiv via their REST API, including citation data from Semantic Scholar.

Query NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. Part of the AlterLab Academic Skills suite.

Search and retrieve preprints from arXiv via the Atom API by keywords, authors, arXiv IDs, date ranges, or subject categories. Use when finding or fetching papers in physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering, or economics, or resolving an arXiv ID to its metadata and PDF. Part of the AlterLab Academic Skills suite.

Query and analyze scholarly literature using the OpenAlex API across 240M+ works, retrieving papers, authors, institutions, citations, and open access status. Use when searching academic papers, tracking citations, finding works by author or institution, analyzing research trends, discovering open access publications, or running bibliometric analysis. Part of the AlterLab Academic Skills suite.

Search and summarize papers from ArXiv. Use when the user asks for the latest research, specific topics on ArXiv, or a daily summary of AI papers.

Discovers, audits, repairs, adapts, and designs bounded AI-agent loops with explicit triggers, actions, verification, stopping conditions, guardrails, and handoffs.

Search arXiv papers by keyword, author, category, or ID.

Query ChEMBL via the chembl_webresource_client Python client for curated bioactive molecules and drug-like compound libraries at scale — search compounds by structure or physicochemical properties, retrieve bioactivity measurements (IC50, Ki, EC50), and find inhibitors of a target. Use when screening chemical libraries, mining curated bioactivity for a protein, running SAR studies, or sourcing medicinal-chemistry data; for measured protein-ligand binding affinities (Ki/Kd/IC50) prefer alterlab-bindingdb instead. Part of the AlterLab Academic Skills suite.

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.

Merges multiple diagnosis snapshots from dbs-save into a single, timestamped Markdown report organized by topic.

Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete.