lazarus-bio 0.1.1

Resurrect dead research code into a callable pipeline component — and give the revival back.

Lazarus

Turn dead research code into a callable pipeline component — and give the revival back.

🧬 Build track · Built with Claude Science hackathon · July 2026

New here? Open the notebook in Colab — a 2-minute, zero-setup tour (no Docker, no GPU): run the dependency pinner live, inspect the four revived tools, and see the binder-triage result rendered in 3D.

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The wall

Computational science has a reproducibility problem. A huge fraction of published methods are open, cited, and unrunnable within a few years: the repo is stale, wired to a stack that no longer resolves, and the real capability is buried in scripts with no API. If you're on a small, budget-constrained ML-for-biology team, you hit this constantly — the exact method you need exists, but getting it to run costs days you don't have, so it gets abandoned.

What Lazarus does

Lazarus is an agent that revives dead research code, lets you compose the revivals into pipelines, and gives the fixes back to the community.

1. Revive — point it at a bare GitHub URL. Lazarus reads the repo and the paper the way a newcomer would and writes its own goal and sanity check, then runs a build → execute → read-traceback → repair loop in a sandbox. Pin dependencies to the commit era, resolve the binary chain, locate the real capability, and emit a fixed integration contract: an importable module, a CLI, a pinned container, and a smoke test that proves it runs on a fresh input and passes the sanity check it defined.
2. Compose — because every revival emits the same contract, a revived tool is a composable brick. Wire bricks from any domain/language/era into a pipeline with a small YAML; one command runs them, passing artifacts between steps (local / remote / GPU).
3. Give back — the fixes Lazarus finds (rotted URLs, broken paths, a 15-year-old undefined-behavior bug) become maintainer-ready pull requests with CI, so the method can't silently rot again.

Proof — four dead repos, resurrected autonomously

Each revived from its own dead environment using only general heuristics (no repo-specific notes), each emitting a callable package that passes its own smoke test standalone:

Repo	Flavor	Turns	Result on 4ZQK_A
MaSIF-site (LPDI-EPFL/masif)	Py3.6 · TF 1.12 · surface + MSMS/APBS (revive-and-carve)	18	interaction site, ROC-AUC 0.9137
ScanNet (jertubiana/ScanNet)	Py3.6 · TF 1.14 · Keras (revive-and-carve)	19	binding site, ROC-AUC 0.9233
dMaSIF (FreyrS/dMaSIF)	Py3.6 · torch cu111 · PyKeOps · GPU, built from scratch	51	binding site, ROC-AUC 0.8390
fpocket (2010 SourceForge)	2010 C, built on modern GCC — a different flavor entirely	32	3 druggable pockets

The dMaSIF run built a whole CUDA/KeOps GPU environment from a bare image and patched a source bug to unlock GPU execution the original forced to CPU. The fpocket run fought a SourceForge download interstitial, a modern-ld link-order break, and a 15-year-old overlapping-sprintf undefined-behavior bug that modern glibc exposed. Three genuinely different resurrection flavors — TF/CUDA/C.

Three-way head-to-head (the three site predictors, scored by one script on identical PD-L1 residue labels): ScanNet 0.915 · dMaSIF 0.854 · MaSIF 0.823. All localize the interface (a 13-residue consensus core); the two surface methods (MaSIF & dMaSIF) agree most (Spearman ρ 0.70). Details: analysis/RESULTS.md.

Point it at a URL — it writes its own plan

You don't hand Lazarus a goal; you hand it a link. A web-enabled Scout reads the repo and paper (and only those — never your notes) and drafts the whole plan: the capability to revive, a base image, and a falsifiable sanity check. Then it pauses for your OK before spending a turn.

lazarus resurrect https://github.com/jertubiana/ScanNet

Run cold against ScanNet with no hints, the Scout reconstructed — from the URL alone — a plan matching the one a human expert hand-wrote after days of work:

	Human, after days of setup	Scout, from the URL alone
Capability	per-residue binding-site probabilities	✅ same
Test input	4ZQK chain A (PD-L1)	✅ same
Sanity check	ROC-AUC ≥ 0.70 vs the 5 Å interface	✅ identical
Base image	(supplied by hand)	✅ found the real jertubiana/scannet on Docker Hub
Known traps	issues #14 & #15 (hand-noted)	✅ surfaced both unaided — the two we later fixed upstream

That's the democratization step: the expert judgment of what "revived" even means becomes something you get from pasting a link.

Then we pointed it at a repo we'd never touched, in a different field entirely. From just github.com/davek44/Basset — a 2016 Lua Torch7 genomics CNN (chromatin accessibility from DNA sequence) — the Scout planned it and the agent revived it end to end. Along the way it cleared a new class of decay (the README's 2016 Docker image ships a manifest modern Docker refuses to pull — converted with skopeo), and caught a silent scientific-correctness bug: the naive run scored mean AUROC 0.675, but the agent traced it to hg19's soft-masked lowercase bases falling through Basset's uppercase-only one-hot encoder, patched it, and reproduced the paper — mean AUROC 0.8944 vs 0.895 across all 164 cell types. A fifth brick, a new domain (genomics, not protein surfaces), a fourth dead framework — from a link. Details: docs/CHALLENGES.md §5.

And the one that shows the integrity of the sanity check: from github.com/gcorso/DiffDock — the ICLR-2023 diffusion molecular-docking model, ~2 years stale — the Scout revived it on GPU. Its shipped example is a hard case (top-1 ~5 Å, under DiffDock's own < 2 Å bar), so rather than fake a pass, Lazarus docked 8 complexes from DiffDock's own test set, reproduced its ~40 % top-1 success rate, and found a rock-solid hero case (6MOA: RMSD 0.35 Å — the predicted pose sitting on the crystal ligand). It refused to ship a green checkmark it hadn't earned. Details: docs/CHALLENGES.md §6.

Compose — an in-silico pipeline from revived bricks

examples/pipelines/binder_triage.yaml assembles methods that were each individually unrunnable a week ago into one binder-triage pipeline:

structure ─▶ ScanNet ─┐
          ─▶ dMaSIF ──┼─▶ consensus ─▶ interface residues that also line a druggable pocket
          ─▶ fpocket ─┘

lazarus run examples/pipelines/binder_triage.yaml \
  --input structure=4ZQK.pdb \
  --registry examples --registry components \
  --docker-host ssh://you@your-x86-gpu-box

Run live on PD-L1, it concluded: 27 interface residues (115, 123, 56, 121, 113…), but 0 druggable pockets → "the interface is clearly localized but not a druggable small- molecule pocket — a flat protein-protein interface, i.e. an antibody/biologic target." That's textbook immuno-oncology (PD-1/PD-L1 is an antibody target), reproduced from dead code. Sample output: examples/pipelines/sample_output_4ZQK/.

Give back

For the genuinely-abandoned repos, Lazarus prepares maintainer-ready PRs — the real fix plus a CI smoke test so it can't silently rot again:

• MaSIF — PR #93 — the rotted PDB download, fixed (direct RCSB fetch); verified to revive the built-in flow at ROC-AUC 0.9137. → giveback/masif/
• ScanNet — PR #16 — library_folder='' made to auto-detect the repo root; verified. → giveback/scannet/

(dMaSIF is skipped — CC BY-NC-ND, no-derivatives; fpocket's upstream is alive.)

Reproduces the paper

A smoke test proves a method runs; a benchmark proves it's the method. Lazarus re-ran MaSIF-site on its own transient PPI benchmark — through the built-in download that give-back PR #93 revived — and matched the published number:

Metric	Paper (Gainza et al. 2020, n=59)	Lazarus (n=15 slice)
median per-structure ROC-AUC	0.85	0.82 → reproduced (±0.05)

Every revival can carry this: the contract's benchmark field emits a REPRODUCE.md certificate with a PASS/OFF verdict — the trust layer that turns a resurrection into something a team will actually adopt.

How it works — five organs

Organ	Role
Scout	Reads a bare repo URL + its paper (web-enabled, but blind to your notes) and drafts the resurrection plan: capability, base image, and a falsifiable sanity check — so a revival starts from a link, not a hand-written goal.
Sandbox	Disposable container (CPU or GPU); expensive successes are snapshotted so a later failure never re-pays the build.
Commit-era pinner	Reconstructs the dependency universe as it was on the repo's last commit — the reasoning that beat the cu111/KeOps/cppyy tangle.
Repair loop	build → run → read traceback → patch → retry, bounded, isolated to the container.
Capability locator	Finds where "input → the famous output" happens and carves the minimal path to it.
Contract emitter	Module + CLI + pinned container + smoke test — CPU or GPU, verified callable on its own.

Runs on a laptop, executes anywhere

Lazarus runs on your machine; where it executes is pluggable via one flag — a local container, a remote x86 box, a cloud VM, or a GPU rental — for methods (like MaSIF's MSMS or dMaSIF's CUDA) whose binaries need hardware laptop emulation can't provide. The agent's tools and the emitted predict.py both run against whatever --docker-host / DOCKER_HOST points at, so the whole chain is host-agnostic.

Quickstart

pip install lazarus-bio                      # the tooling: pinner, compose, contracts
pip install "lazarus-bio[agent]"             # + the autonomous revive loop & Scout (Python ≥ 3.10 + Docker)
# or, to hack on Lazarus itself:
#   git clone https://github.com/DoctorDean/lazarus && cd lazarus
#   pip install -e ".[dev,agent]"

# commit-era dependency pinning — no repo execution required
lazarus pin --date 2019-01-01 tensorflow numpy scipy
#   tensorflow==1.12.0   (matches MaSIF's real Dockerfile, not its README)

# resurrect straight from a URL — the Scout writes the goal + picks the image,
# then pauses for your OK before spending compute (needs Docker + Claude auth)
lazarus resurrect https://github.com/jertubiana/ScanNet

# …or drive it by hand with an explicit image + goal (both override the Scout)
lazarus resurrect --image pablogainza/masif:latest --workdir /masif \
  --goal-file examples/masif_site_goal.txt --keep

# compose revived components into a pipeline
lazarus run examples/pipelines/binder_triage.yaml --input structure=4ZQK.pdb \
  --registry examples --registry components

Auth: Lazarus drives Claude via the Claude Agent SDK. Log in the claude CLI (subscription) or put ANTHROPIC_API_KEY=... in a gitignored .env.

Status

Working today: Scout (URL → resurrection plan) · pinner · Docker sandbox (local + ssh:// remote + --gpus) · autonomous repair loop · capability locator · contract emitter (GPU-aware, with reproduction certificates) · Lazarus Compose. All three pillars landed — six dead repos revived (four protein + genomics + molecular docking; two from nothing but a URL), a three-way method comparison, a live binder-triage pipeline, three reproduced paper benchmarks, and two give-back PRs — with 49 passing tests, published to PyPI (pip install lazarus-bio).

Two front doors: a zero-setup Colab notebook for newcomers (no Docker/GPU — pinner live + the result rendered in 3D), and a 3-minute demo-video script for the live-compute story (autonomous revival + the pipeline running on a GPU box).

License

MIT — see LICENSE.