Real-time infectious disease modelling. Developing tools and methods for outbreak response, routine surveillance, and pandemic preparedness.
Sam Abbott's skills help an agent with academic work, including reviewing and editing manuscripts against peer-review writing standards and summarising papers from a URL, DOI or file. They also cover software upkeep, such as code review, linting, improving test coverage, auditing local code directories, and analysing GitHub repository activity. A notable feature is an automated pull request quality gate that monitors CI and review feedback in the background.
Claude
1 skills · 8 stars
Julia Repl Evaluate Julia through the warm AgentREPL MCP session rather than `julia -e`, hot-reload edits wi…
Skills
54 skills · 6 stars · MIT
Academic Writing Standards Expert knowledge of academic writing standards for peer-reviewed papers, including citation integ…
Add Bot Add the bot account as a collaborator with push permissions to a repository
Analyzing Research Papers Expert methodology for analyzing and summarizing research papers, extracting key contributions, m…
Bot Report Report on what the unattended agent bots have been doing — what the review bot has posted, what i…
Bot Tasks Check bot notifications for tasks requested by the repo owner, then execute them using a team
Code Cleanup Audit and clean up ~/code directory structure, archiving stale repos, fixing folder names, and re…
Commit Create a well-structured commit with conventional format and proper git identity
Conductor View what all active Claude Code sessions are doing and optionally send instructions to them via…
Create Note Import a markdown file into Obsidian library and format it as a note
Daily Summary Summarise today's Claude Code activity across all repos into a dated log file
Docs Check that all code has appropriate documentation and fix gaps
Format Note Format an Obsidian note with tags and link it from today's daily note
Github Dashboard GitHub dashboard update with notifications, PR status, issue triage, and action items
Grant Application Setup Expert guidance for setting up and organising research grant applications following established p…
Grant Compliance Checking Expert knowledge of research grant compliance requirements, deliverables tracking, and funder exp…
Improve Coverage Improve test coverage by identifying gaps and generating meaningful tests
Issue Reply Post a helpful reply to a GitHub issue
Issue Summary Summarise a GitHub issue conversation with focus on the last message
Julia Development Julia package development on a warm REPL session, verifying each edit with Revise and TestItemRun…
Lint Lint, format, and optionally commit changes
Literature Search Search local bibliography files and Paperpile for relevant papers
Minutes Create structured meeting minutes from a transcript
Org Ci Health Quick scan of CI status across all repos in an org, flagging failures and stale workflows
Org Deps Audit cross-repo dependencies within an org and flag outdated or breaking changes
Org Issues Do Scan org repos for easy issues opened by contributors and resolve a few via worktree PRs
Org Issues Tidy Add clarity and structure to open issues across an org's repos without repeating previous work
Org Maintenance Clean up stale worktrees and help stuck PRs across an org's repos
Org Orchestrate Set up and run full org automation including repo cloning, script generation, cron scheduling, an…
Org Releases Check which packages in an org are overdue for release and draft release PRs
Org Standards Scan repos in an org for standards drift and propagate fixes via worktree PRs
Paper Summary Summarise an academic paper from URL, DOI, or file path
Patch Release Plan a patch release from recent issues.
Pi Delegate a self-contained task to pi (cheap local AI coding agent) and report back.
Pr Create a pull request based on a GitHub issue with analysis, implementation, QA, and PR creation
Pr Automate Run as a background subagent after a PR is created or pushed.
Pre Pr Checks Run the full pre-PR verification routine (format, lint, tests, type/package checks, coverage) in…
Preprint Search Search for new preprints in infectious disease modelling from arXiv, medRxiv, and bioRxiv
Project Organization Expert guidance for setting up and organizing research software projects following established pa…
R Development Expert guidance for R package development following best practices for devtools, testthat, roxyge…
Repo Activity Analyse GitHub repository activity including issues, PRs, contributors, and engagement
Repo Summary Analyse a GitHub repository combining activity metrics with code development insights
Repo Watch Detect active repos by the owner not cloned locally and request confirmation before acting
Review Perform a code review with linting, standards checking, and priority-ranked findings
Scan Issues Scan repositories and identify issues that Claude Code can efficiently handle
Setup Scripts Generate or regenerate all helper scripts used by org automation skills
Show Diff Open a tmux split running diffview.nvim so the user can review the agent's recent changes.
Stan Development Expert guidance for Stan probabilistic programming language development, including modern syntax,…
Taskfile Automation Expert guidance for using Task (taskfile.dev) automation tool to discover and execute project dev…