Scientific Communication

Plugin scientific-communication from marketplace data-science-skills in jamesjnadeau/data-science-skills. Commands read from the repo's manifest — 1 month ago.

Skills (35)

• dask

  Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; fo

• experimental-design

  Design experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable. Use whenever someone is planning a study, asks how to assign subjects/samples to groups, mentions randomization, blocking, stratific

• exploratory-data-analysis

  Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds.

• geopandas

  Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.

• matplotlib

  Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use p

• networkx

  Create, analyze, and visualize complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks (random, scale-free, small-world), readin

• polars

  High-performance DataFrame library for Python ETL, analytics, and pandas migration. Use for expression-based data manipulation with lazy query optimization, parallel execution, streaming out-of-core processing, Arrow interoperability, and optional GPU execution.

• scientific-visualization

  Create and audit truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use for figure design, multi-panel layouts, uncertainty and missing-data displays, color/contrast review, image metadata validation, and journal export planning.

• seaborn

  Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pair plots, heatmaps. Built on matplotlib. For interactive plots use plotly; for publication styling u

• statistical-analysis

  Guided statistical analysis for research data - test selection, assumption checking, effect sizes, power analysis, Bayesian alternatives, and APA-formatted reporting. Use whenever a user wants to compare groups, test a hypothesis, analyze experimental or survey data, check statistical assumptions, c

• statistical-power

  Sample-size and statistical power calculations for planning studies. Use whenever someone asks "how many subjects/samples/replicates do I need", wants an a priori power analysis, a minimum detectable effect (MDE), a power curve, or needs to justify a sample size for a grant, IRB protocol, or pre-reg

• uncertainty-and-units

  Track physical units and propagate measurement uncertainty in scientific calculations using pint and uncertainties. Use for unit conversion and dimensional checking, GUM uncertainty budgets, Type A and Type B evaluation, coverage factors and expanded uncertainty, Monte Carlo propagation, significant

• vaex

  Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to

• xlsx

  Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary deliverable. Use for formulas, formatting, financial models, multi-sheet workbooks, and tabular cleanup exported to Excel. Also applies to .csv/.tsv when the user wants spreadsheet outpu

• analytical-method-validation

  Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand

• iso-standards-readiness

  Prepares and structurally reviews readiness evidence for ISO management-system and laboratory-competence standards - ISO 13485 medical device QMS, ISO 14971 device risk management, ISO/IEC 17025 testing and calibration laboratories, and ISO 15189 medical laboratories. Use when organizing declared sc

• consciousness-council

  Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants diverse viewpoints, needs help making a tough decision, asks for a council/panel/board discussion, wants to explore a problem from multiple angles, requests devi

• hypothesis-generation

  Formulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, measurements, and preregistration-ready analysis plans. Use when turning observations or preliminary findings into transparent, testable research pla

• market-research-reports

  Build evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for market definition, industry and customer evidence, competitive landscapes, TAM/SAM/SOM reconciliation, forecast sensitivity, and auditable report scaffolds.

• research-grants

  Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.

• scholar-evaluation

  Provide qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes research-assessment rubrics with optional local quality controls. Never use for ranking people or consequential decisions.

• scientific-brainstorming

  Facilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation, adversarial review, and decision logs. Use for early-stage research brainstorming or prioritizing candidate directions; hand off empirical validation, stud

• scientific-critical-thinking

  Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For for

• what-if-oracle

  Run structured What-If scenario analysis with 4–6 branch possibility exploration (best, likely, worst, wild card, contrarian, second-order). Use when the user asks speculative what-if questions about uncertain futures, strategic forks, contingency planning, or stress-testing a decision before commit

• citation-management

  Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert

• docx

  Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', '.dotx', or requests to produce professional documents with formatting like tables of conte

• liteparse

  Local document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; running OCR on scans; producing layout-preserved JSON for RAG; batch-ingesting folders of papers; or rendering pages to PNG for multimodal agents. Distingu

• literature-review

  Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical,

• markdown-mermaid-writing

  Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based diagrams as the default documentation standard with full style guides (markdown + mermaid), 24 diagram type references, and 9 document templ

• markitdown

  Convert heterogeneous documents and selected URIs to Markdown with Microsoft MarkItDown for text analysis, search, and LLM/RAG ingestion. Covers safe local conversion, streams, Office/PDF/data formats, batch workflows, plugins, vision OCR, Azure extraction, and the official MCP server.

• paper-lookup

  Search 11 academic literature APIs for papers, preprints, citations, and open-access full text, and return results with reproducible provenance. Covers PubMed, PMC (full text), Europe PMC (full-text and preprint search), bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall.

• pdf

  Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rotating pages, adding watermarks, creating new PDFs, filling PDF forms, encrypting/decrypting PDFs, ext

• peer-review

  Prepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Use for authorized review of scientific manuscripts, protocols, preprints, or research proposals; reporting-guideline selection; claim–evidence checks; methods, statistics, reproducibility, ethics, figur

• pptx

  Use this skill any time a .pptx or .potx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from any .pptx or .potx file (even if the extracted content will be used elsewhere, like in an em

• scientific-writing

  Draft, revise, and audit scientific manuscripts or reports with explicit evidence provenance, reporting-guideline coverage, authorship accountability, confidentiality controls, and local consistency checks. Use for manuscript sections, references, declarations, tables, figures, or submission prepara

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