TobiasBlask/open-paper-machine
Command
Strategic project triage — should you continue, pivot, or kill your current research project? Evaluates 5 signals (results, competition, impact, effort, motivation) and delivers a clear Continue/Pivot/Kill recommendation. For Pivot: suggests concrete new framing. For Kill: suggests what to salvage.
TobiasBlask/open-paper-machine
Command
Verify all citations by fetching source abstracts/full-text and checking claims against actual content.
TobiasBlask/open-paper-machine
Command
START THE PAPER MACHINE. Give a title, topic, or research question — the autonomous agent takes over and runs the complete 5-phase pipeline: Reconnaissance → Framing → Architecture → Production → Assembly. You approve at checkpoints, the machine does the work.
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
Comprehensive citation management for academic research. Search Google Scholar and PubMed 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 DOIs to BibTeX, or ensure…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
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 devil's advocate…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
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, scientific, and…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
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 templates.
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
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 plotly; for…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
Interactive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, and presentations. For static publication figures use matplotlib or scientific-visualization.
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
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 this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
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.
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback.
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific observations yet. For formulating testable hypotheses from data use…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
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 formal peer review…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
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 use…
TobiasBlask/open-paper-machine
Skill Claude CodeCodex
Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power analysis, and APA-formatted results. Best for academic research reporting, test selection guidance. For implementing specific models programmatically use…