Braselog

Quick capture for thoughts, observations, or ideas during research sessions. Use when the user types /note or wants to capture a quick thought without context-switching. Logs timestamped notes to activity.md. Supports both explicit /note command and natural language like "make a note" or "jot down".

Conduct comprehensive, systematic literature reviews using multiple databases (PubMed, bioRxiv, Semantic Scholar, OpenAlex). Creates documented searches, synthesizes findings thematically, verifies citations, and generates professional markdown reports with multiple citation styles (APA, Nature, Van

Conduct a monthly review of project alignment and progress toward aims. Use when the user types /monthly_review, at the start of a new month, after completing a major milestone, or when uncertain about project direction.

Assess current project state and suggest the most valuable next action. The primary entry point for users who aren't sure what to do. Analyzes context, checks for issues, and recommends specific skills or actions.

Systematic peer review and self-evaluation toolkit. Evaluate methodology, statistics, experimental design, reproducibility, ethics, and reporting standards. Use during the REVIEW phase to assess manuscript quality before submission, or when reviewing others' work.

Create a focused weekly plan based on tasks, priorities, and your work patterns. Use when the user types /plan_week, after a weekly review, at the start of a new week, or when feeling overwhelmed by options.

Conduct a quarterly review of your overall research mission and direction. This is a user-level review stored in ~/.researchAssistant/. Use when the user types /quarterly_review, every 3 months, after major project milestones, or when questioning research direction.

Create publication-quality scientific figures with matplotlib, seaborn, and plotly. Includes multi-panel layouts, error bars, significance markers, colorblind-safe palettes, and journal-specific export (PDF/EPS/TIFF). Use when creating figures for manuscripts, presentations, or any research visualiz

Write scientific manuscripts with proper structure (IMRAD), citations (APA/AMA/Vancouver), figures/tables, and reporting guidelines (CONSORT/STROBE/PRISMA). Use when drafting any manuscript section, improving writing clarity, or preparing for journal submission.

Draft or update the background/introduction section based on literature in .research/literature/. Use when the user types /write_background, after completing literature review, or when background.md is empty but literature files exist.