A platform for orchestrating Claude Code agents across research projects. Bipartite provides a bip CLI and a library of Claude Code skills that coordinate multi-agent workflows: spawning workers on GitHub issues, tracking manuscript progress across repositories, managing paper libraries, and keeping a research team informed via Slack digests.
The core of bipartite is the EPIC orchestration system — a conductor/worker pattern for managing multiple Claude Code sessions across clones and worktrees. The conductor session stays on main, scans GitHub for open issues, and spawns workers in dedicated tmux windows. Workers implement, test, and create PRs autonomously; an issue-lead subagent evaluates progress and escalates only when human judgment is needed.
Key skills: /bip.epic, /bip.epic.spawn, /bip.epic.poll, /bip.epic.handoff, /bip.epic.tuckin
Manuscript sessions (/bip.ms) monitor tracked EPIC issues in remote code repositories and react when new results arrive — pulling data, importing figures, and drafting text. This separates the "writing the paper" concern from the "running experiments" concern.
Key skills: /bip.ms, /bip.ms.poll, /bip.ms.tuckin
An agent-first reference manager: JSON output, CLI interface, git-backed JSONL storage, Semantic Scholar and Asta search. Your library is mergeable across collaborators with standard git workflows.
Guide: Reference Management
Themed narrative digests, cross-repo check-ins (spawn dedicated tmux windows), Slack integration, and server resource scouting via SSH.
Key skills: /bip.checkin, /bip.digest, /bip.narrative, /bip.spawn, /bip.scout
This installs the bip CLI plus Claude Code agents and skills:
git clone https://github.com/matsen/bipartite
cd bipartite
make installPrerequisites:
- Go 1.24+
- Claude Code
Verify with bip --help.
If you just want the bip CLI without agents/skills:
go install github.com/matsen/bipartite/cmd/bip@latestNote: This installs to $GOBIN if set, otherwise $HOME/go/bin. Ensure the appropriate directory is in your PATH.
- Create your private nexus — the repository that stores your paper library, workflow config, and project context. Click "Use this template" on nexus-template, then clone:
git clone https://github.com/YOUR_USERNAME/nexus ~/re/nexus- Point bip to your nexus (minimal config to get started):
mkdir -p ~/.config/bip
echo 'nexus_path: ~/re/nexus' > ~/.config/bip/config.yml- Build the index and try it out:
bip rebuild
bip search "phylogenetics" --human
bip s2 add DOI:10.1038/s41586-021-03819-2See the Getting Started guide for full setup instructions.
For full functionality, add API keys (Semantic Scholar, Asta, GitHub, Slack) to your config:
nexus_path: ~/re/nexus
s2_api_key: your-key
asta_api_key: your-key
github_token: ghp_...
slack_bot_token: xoxb-...See the Configuration Guide for all options.
MIT