N-Linked Glycosylation Prediction

secondsPaperCodeProduction Ready

Predict N-Linked Glycosylation sites

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: ready
Storage: <5
Strategy: shared python312_slim SIF with mounted TensorFlow/Keras/Pandas site-packages
Next: Production Ready for bundled LMNglyPred feature-CSV scoring. Optional hardening: add raw sequence feature generation and richer UI controls for user-provided feature CSVs.

LMNglyPred source identified from KCLabMTU/LMNglyPred rev 106a74d1eea8c176d2e52918fbddfeb1e55a7171; tied to Glycobiology LMNglyPred paper. Staged dir ~449 MB with .h5 model files/notebooks/CSV/test data, but clone was interrupted and git status was inconsistent with tracked files deleted/untracked. No env/install or Slurm smoke completed. 2026-07-04 backend update: verified LMNglyPred source at /media/nik/seagate_nik/bio_server/tools/n-linked-glycosylation-prediction/source/LMNglyPred, rev 106a74d1eea8c176d2e52918fbddfeb1e55a7171, with clean git status and bundled .h5/assets present. Source clone inconsistency is cleared; runtime/Slurm validation remains pending. 2026-07-05 SOP recheck: LMNglyPred source and bundled .h5 assets are staged cleanly, but compatible TensorFlow/Keras runtime and direct Slurm prediction smoke remain pending. Kept Smoke Pending. 2026-07-05 SOP batch recheck: LMNglyPred clean checkout and bundled .h5 assets are present, but TensorFlow/Keras runtime and direct prediction Slurm smoke remain pending. Kept Smoke Pending. 2026-07-05 SOP recheck: LMNglyPred clean checkout and bundled .h5 assets are present, but TensorFlow/Keras runtime and direct prediction Slurm smoke remain pending. Kept Smoke Pending. 2026-07-05 SOP batch recheck: LMNglyPred clean checkout and bundled .h5 assets are present, but compatible TensorFlow/Keras runtime and direct prediction Slurm smoke remain pending. Kept Smoke Pending. 2026-07-05 18:19 +08:00 backend re-audit: LMNglyPred source/assets remain staged under tools/n-linked-glycosylation-prediction (~854 MB), but no compatible TensorFlow/Keras SIF/overlay or direct prediction Slurm smoke exists. Agents agreed Smoke Pending label remains correct despite readiness_status still recording production_blocked history. 2026-07-05 22:38 +08:00 backend implementation pass: direct Slurm job 428 completed using shared python312_slim.sif with deepsp_py312_site TensorFlow/Keras and palm_py312_site Pandas. It loaded bundled NGlyDE_Prot_T5_Final.h5 and scored 8 rows from Glycobiology_NGlyDE_Independent_Positive_202_Negative_100.csv, producing summary.json and results.csv under /media/nik/seagate_nik/bio_server/runs/n-linked-glycosylation-prediction/model_smoke_20260705_223822. Reclassified to Runner Adapter Pending; runner/API adapter still missing. 2026-07-07 17:56 +08:00 production validation: runner adapter wired and deployed to Ubuntu backend. Runner API remote job f64e3d2627ec / Slurm job 499 completed using shared python312_slim.sif with deepsp_py312_site and palm_py312_site on PYTHONPATH, loaded bundled NGlyDE_Prot_T5_Final.h5, scored 8 rows, and produced summary.json, input_features.csv, results.csv, job.log, slurm.out, and slurm.err artifacts. Runtime 23.31s; predictions ranged 0.076139 to 0.923861.