Results for “academic-pipeline”

Orchestrate the complete post-first-draft polishing pipeline for an academic LaTeX paper by invoking five existing skills in fixed order: (1) paper-polish, (2) paper-self-revise, (3) paper-style, (4) paper-polish again, (5) reference-verify. Trigger when user says "paper pipeline" / "paper-pipeline" / "论文流水线" / "全流程打磨" / "一条龙打磨" / "初稿打磨" / "full polish pipeline" / "run the whole pipeline", or wants the entire post-draft polishing sequence run on a paper folder. Use this skill whenever the user asks for several paper-finishing steps (polish + revise + style + reference check) on one manuscript in one go, even if they don't name every individual skill.

Build complete mass-spectrometry workflows with pyOpenMS — feature detection, peptide identification, protein quantification, and full LC-MS/MS pipelines across many MS file formats (mzML, mzXML) and algorithms. Use for comprehensive proteomics and MS data processing — for simple spectral comparison and metabolite identification use matchms. Part of the AlterLab Academic Skills suite.

Chunked, compressed N-dimensional arrays for cloud storage with Zarr — parallel I/O, S3/GCS integration, and NumPy/Dask/Xarray compatibility. Use when storing or reading large N-D scientific arrays, streaming chunked data to/from cloud object stores, or building large-scale scientific computing pipelines. Part of the AlterLab Academic Skills suite.

Route academic-figure work into the lightest workable PaperBanana mode instead of jumping straight to a full multi-agent generation run. Use when the user needs publication-quality methodology diagrams, statistical plots, figure evaluation, polishing an existing figure, batch/sweep generation, or a full-paper figure package from text or PDF. Even if the user does not say "paperbanana" — also triggers on: academic figure, methodology diagram, publication figure, generate diagram from paper, statistical plot from CSV, figure evaluation, polish figure, NeurIPS/ICML figure, arxiv illustration, plan-then-refine diagram pipeline.

Computes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spectra, scoring similarity (cosine, modified cosine), and searching spectral libraries to annotate unknowns. Use when matching MS/MS spectra, identifying metabolites, or library searching; for full LC-MS/MS proteomics pipelines use pyopenms. Part of the AlterLab Academic Skills suite.

Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handling layers/obsm/backed-mode; for the QC, normalization, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for RNA velocity from spliced/unspliced layers prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.

VS-Enhanced Journal Matcher with Journal Intelligence MCP — Real-time journal data pipeline with checkpoint-based human decisions. Uses OpenAlex + Crossref APIs for live metrics. Light VS applied: Avoids IF-centric recommendations + multi-dimensional matching strategy Use when: selecting target journals, planning submissions, comparing publication options Triggers: journal, submission, impact factor, academic journal, publication, submit

Access the European Nucleotide Archive (ENA) via its API and FTP to retrieve DNA/RNA sequences, raw sequencing reads (FASTQ), and genome assemblies by accession, with support for multiple formats. Use when downloading reads or sequences for a study, run, or sample accession, or when sourcing nucleotide data for genomics and bioinformatics pipelines. Part of the AlterLab Academic Skills suite.

Read and write genomic alignment and variant files in Python with pysam (htslib bindings) — SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, plus region extraction and per-base coverage/pileup. Use when scripting NGS data-processing pipelines that parse, filter, index, or compute coverage over BAM/CRAM/VCF files. Part of the AlterLab Academic Skills suite.

Fast in-memory DataFrame analytics with Polars — lazy evaluation, parallel execution, and an Apache Arrow backend for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory, for 1-100GB datasets, ETL pipelines, or a faster pandas replacement. For larger-than-RAM data prefer dask or vaex. Part of the AlterLab Academic Skills suite.

Use when a researcher asks where to start, which project skill fits the current stage of a study, or in what order literature scoping, source access, vault upkeep, drafting, citation verification, disclosure, and review response should run.

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map transcription-factor-to-target-gene regulatory interactions, build adjacency networks, or run the GRN-inference step of a SCENIC pipeline on large datasets. Part of the AlterLab Academic Skills suite.

Universal deep research agent team. 13-agent pipeline for rigorous academic research on any topic. 7 modes: full research, quick brief, paper review, lit-review, fact-check, Socratic guided research dialogue, and systematic review with optional meta-analysis. Covers research question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk of bias assessment, meta-analysis, APA 7.0 report compilation, editorial review, devil's advocate challenges, ethics review, and post-research literature monitoring. Triggers on: research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, guide my research, help me think through, 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 事實查核, 引導我的研究, 幫我釐清, 幫我想想, 我不確定要研究什麼, 研究方向, 研究主題.

Transparent, rigorous research with full methodology — not a black-box API wrapper. Conducts exhaustive investigation through mandated 2-cycle research per theme, APA 7th citations, evidence hierarchy, and 3 user checkpoints. Self-contained using native OpenClaw tools (web_search, web_fetch, sessions_spawn). Use for literature reviews, competitive intelligence, or any research requiring academic rigor and reproducibility.

Designs and implements production-grade ML pipeline infrastructure: configures experiment tracking, creates orchestration DAGs, builds feature store schemas, deploys model registries, and automates retraining and validation workflows.

PRISMA Scoping Review Pipeline

Fork, sanitize, and package private projects for safe public release through a three-stage pipeline.

End-to-end data pipeline for empirical research: fetch economic data from APIs (FRED, World Bank, IMF, BLS, OECD, Yahoo Finance), clean and transform raw data, construct strategy-specific variables, and validate panel structure. Use when asked to fetch data, download data, clean data, merge datasets, prepare analysis-ready data.

Coordinate multi-stage edge research pipelines from candidate detection through strategy design, review, revision, and export.

Runs a three-phase AOI training pipeline: AutoML HPO baseline, DEFT iterative data improvement, and AutoML refinement on the augmented dataset.

End-to-end pipeline for writing ML/AI research papers — from experiment design through analysis, drafting, revision, and submission. Covers NeurIPS, ICML, ICLR, ACL, AAAI, COLM. Integrates automated experiment monitoring, statistical analysis, iterative writing, and citation verification.

Cross-runtime 2-stage pipeline for Claude Code, Codex/OMX, and Gemini/Antigravity/OMA: trace causal hypotheses, inject evidence into deep-interview style requirements crystallization, then hand off to the right runtime planner/executor.

Search, filter, and browse high-signal academic papers using the Paperzilla CLI.

End-to-end content creation workflow that orchestrates research, editorial review, and social distribution agents in sequence. Use when the user wants to create, review, and distribute content through a multi-stage pipeline, or says "/content-pipeline".

2-stage pipeline: trace (causal investigation) -> deep-interview (requirements crystallization) with 3-point injection

Composite skill — safely refactor a module end-to-end with sequencing, parallel implementation, post-refactor cleanup, and rationale capture. Chains refactor-plan (phased plan + rollback) → three-man-team (architect/builder/reviewer in parallel) → fix-the-suite post-refactor → adr-write → docs-sync. Use for non-trivial refactors that need both careful sequencing and durable record.

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.

Analyze recent screen activity via a local screenpipe daemon, detect repeated research workflows, and draft new skills or composition recipes for uncovered patterns.

Provides the shared STORM methodology, artifact layout, stage-gating contract, citation hygiene, and retrieval fallback. Use when executing any /storm:* skill (generate, research, outline, write, polish). Internal knowledge; never user-invocable.

End-to-end source processing -- seed, reduce, process all claims through reflect/reweave/verify, archive. The full pipeline in one command. Triggers on "/pipeline", "/pipeline [file]", "process this end to end", "full pipeline".