Software
Open-source tools developed to support research workflows. These projects are available on GitHub and can be adapted for use in other research settings.
Lab Data Manager
A web application for managing mouse experiment data, including subject tracking, daily observations, sample collection, freezer storage organization, and data visualization with Kaplan-Meier survival curves.
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Key Features
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Experiment Management
Create experiments with treatment groups, track individual subjects with ear tags, and record outcomes (deaths, sacrifices, exclusions) -
Daily Observations
Tablet-friendly interface for recording weight and clinical condition scores (CSS) with automatic alerts for weight loss and health thresholds -
Sample Tracking
Collect and manage samples (blood, serum, tissue) linked to subjects; browse samples across all experiments with filtering -
Freezer Storage
Visual box layouts for organizing samples in freezers, racks, and boxes with drag-and-drop assignment and position tracking -
Data Visualization
Interactive plots including Kaplan-Meier survival curves, weight timeseries, and CSS tracking with cross-experiment comparison by treatment group
Technical Details
Built with React, TypeScript, and Node.js. Uses SQLite for local data storage and Recharts for visualization. Designed for self-hosting on a local network or Raspberry Pi.
Literature Monitor
An automated literature tracking system that searches PubMed and bioRxiv/medRxiv weekly, uses AI to rank papers by relevance to your research projects, and delivers organized email digests with one-click Zotero integration.
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Key Features
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Automated Search
Configurable queries search PubMed and preprint servers weekly, with date-range filtering and deduplication -
AI-Powered Ranking
Claude analyzes each paper's title and abstract, scoring relevance (0-1) against your defined research projects and generating brief summaries -
Weekly Email Digest
Papers organized by priority (high/moderate/low) delivered to your inbox with summaries and rationale for each ranking -
One-Click Zotero Integration
Add papers directly to your Zotero library from the email digest with a single click, using secure signed URLs -
Capacities Integration
Optionally sync digests and papers to Capacities for personal knowledge management
Available Versions
| Version | Hosting | Best For |
|---|---|---|
| Literature Monitor | GitHub Actions | Serverless, no hardware required |
| Literature Monitor (Pi Edition) | Raspberry Pi / Self-hosted | Local control, permanent database |
Technical Details
Built with Python, using SQLite for paper storage and tracking. The Zotero integration uses a Cloudflare Worker to handle secure paper addition.
Configurable via YAML for search queries, watched authors, journal weights, and research project definitions. The AI ranking considers your specific research interests to surface the most relevant papers.