Readiness
- Readiness
- Production Ready
- Smoke
- passed
- Artifacts
- passed
- Production
- ready
- Storage
- <5
- Strategy
- shared python312_slim.sif + paragraph_py312_site + palm_py312_site CPU Torch/scientific layer + upstream Paragraph pretrained weights
- Next
- Production Ready for scoped paired/heavy/light Paragraph paratope prediction using staged or bundled PDB/key CSV inputs. Optional expansion: richer GUI upload mapping for custom PDB batches.
No obvious large model/database dependency identified; validate upstream docs before install. 2026-07-05 triage: upstream Paragraph needs source checkout, Python 3.8-era scientific stack, trained_model/example assets, and a direct Slurm paratope smoke before runner wiring. 2026-07-05 SOP recheck: backend inventory has no staged Paragraph source/env/assets and runner audit is not_configured. Kept Smoke Pending. 2026-07-05 SOP batch recheck: backend inventory has no staged Paragraph source/env/assets and runner audit is not_configured. Kept Smoke Pending. 2026-07-05 18:19 +08:00 backend re-audit: no staged Paragraph source/env/assets found under shared backend paths; runner remains not configured and no direct Slurm smoke exists. Agents agreed Smoke Pending remains correct. 2026-07-06 implementation pass: cloned upstream oxpig/Paragraph at /media/nik/seagate_nik/bio_server/tools/paragraph-paratope-prediction/source/Paragraph rev 1052d66faf52a18460e4624d12ad0bcac0803d75; bundled pretrained paired/heavy/light weights and example PDB assets are present. Staged Paragraph plus einops into /media/nik/seagate_nik/bio_server/envs/paragraph_py312_site, reusing shared python312_slim.sif and palm_py312_site CPU Torch/scientific packages. Direct Slurm job 455 passed at /media/nik/seagate_nik/bio_server/runs/paragraph-paratope-prediction/smoke_20260706_154000 using bundled 4EDW example and paired pretrained weights, producing 72 prediction rows for H/L chains with probabilities in [0.002776, 0.989193], plus summary.json, results.csv, paragraph_predictions.csv, copied input CSV/PDBs, stdout/stderr, job.log, slurm.out, and empty slurm.err. 2026-07-07T21:47:44+08:00 SOP runner-adapter pass: added real backend adapter using shared python312_slim.sif, Paragraph source at /media/nik/seagate_nik/bio_server/tools/paragraph-paratope-prediction/source/Paragraph, and paragraph_py312_site overlay. Ubuntu runner API job d7b0c7beb417 / Slurm job 521 passed for paired pretrained paratope prediction on bundled 4EDW example with 72 H/L-chain prediction rows, probability range 0.002776-0.989193, summary.json, results.csv, paragraph_predictions.csv, paragraph_runtime.json, stdout/stderr captures, job.log, slurm.out, and zero-byte slurm.err.