PepMLM

1-5 minutesPaperCodeProduction Ready

Design linear peptide binders

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_ready_real_pepmlm_shared_sif_slurm_validated
Storage: 5-20GB
Strategy: shared python312_slim.sif + mrnabert_runtime_py312_site + shared Hugging Face model cache
Next: Monitor runtime cost and optionally add HF_TOKEN for higher Hugging Face rate limits; keep shared model cache at /media/nik/seagate_nik/bio_server/cache/huggingface.

Batch B evidence: source cloned at /media/nik/seagate_nik/bio_server/tools/pepmlm/source, commit 3169c49. Storage reached about 1.4GB after partial pip --target dependency/cache attempt. Uses Hugging Face model TianlaiChen/PepMLM-650M. Normal venv creation under Seagate failed because the mount disallows lib64 -> lib symlinks; pip --target install was stopped per instruction before a real Slurm benchmark. 2026-07-07 16:05 +0800: SOP Runner Adapter Pending audit: demoted from Runner Adapter Pending because only placeholder pepmlm-smoke is configured and no real PepMLM Slurm benchmark has passed; source/model target are staged/identified but runtime and model cache remain incomplete. 2026-07-07 SOP reclassification: agent audit confirmed PepMLM uses public ungated TianlaiChen/PepMLM-650M but the shared PyTorch/Transformers runtime and model cache are incomplete. Partial install/cache already reached ~1.4GB, and only pepmlm-smoke is wired. Moved from Production Blocked to Need >5GB shared runtime/model lane. 2026-07-16T20:35:00+08:00 SOP Need >5GB resolution: built real PepMLM adapter using shared python312_slim.sif, mrnabert_runtime_py312_site PyTorch/Transformers stack, and Hugging Face model ChatterjeeLab/PepMLM-650M cached under /media/nik/seagate_nik/bio_server/cache/huggingface. Deployed cluster_runner.py and cluster_tools/cpu_tools.py to /home/nik/bio_mega_runner. API Slurm job b3945aba12d5 completed with non-proxy artifacts results.csv, pepmlm_metadata.json, per-position probability JSON, and summary.json; top peptide SSL, runtime_seconds 7.157 after cache warmup.