Readiness
- Readiness
- Production Ready
- Smoke
- passed
- Artifacts
- passed
- Production
- api_validated_production_ready
- Storage
- <5
- Strategy
- shared python312_slim.sif + TNP py312 target overlay + host HMMER/DSSP/PSA binds
- Next
- Monitor longer nanobody sequences and multi-sequence FASTA submissions; current production adapter is validated for single-sequence GUI submissions with full TNP metrics and model artifacts.
Batch D evidence: source cloned at /media/nik/seagate_nik/bio_server/tools/tnp-therapeutic-nanobody-profiler/source, storage 93MB. Upstream CLI is TNP --name <name> --output <outdir> --seq <nanobody_sequence>. Blocked by missing complete compatible environment: ANARCI, NanoBodyBuilder2/ImmuneBuilder, DSSP, and Biopython 1.77. No Slurm production job has passed yet. 2026-07-07 16:05 +0800: SOP Runner Adapter Pending audit: demoted from Runner Adapter Pending because only placeholder tnp-therapeutic-nanobody-profiler-smoke is configured and no real TNP Slurm benchmark has passed; ANARCI/NanoBodyBuilder2 or ImmuneBuilder/DSSP/Biopython runtime is still missing. 2026-07-10 SOP implementation: built TNP runtime overlay at /media/nik/seagate_nik/bio_server/tools/tnp-therapeutic-nanobody-profiler/py312_site using shared python312_slim.sif, staged ANARCI 2026.2.13.2, ImmuneBuilder 1.2/NanoBodyBuilder2, pdbfixer 1.12.0, OpenMM 8.5.2, einops, requests, and a small sitecustomize Biopython compatibility shim for Bio.PDB.Polypeptide.three_to_one/one_to_three. Bound host HMMER binaries hmmscan/hmmpress/hmmsearch/hmmalign into the container and reused /home/nik/bio_server_venvs/alphacutter_runtime DSSP with LD_LIBRARY_PATH plus upstream TNP source/bin/psa. Direct validation at /media/nik/seagate_nik/bio_server/artifacts/tnp-therapeutic-nanobody-profiler/direct_full4_20260710_011434 completed upstream bin/TNP on a nanobody sequence in 13.23 s and produced TNP JSON metrics, NanoBodyBuilder2 model PDB, annotated PDB, modelling details, numbering, and sequence liabilities. Metrics: Total CDR Length 20 amber, CDR3 Length 5 amber, CDR3 Compactness 0.5734570634086757 amber, PSH 72.2108 red, PPC 0.0059 green, PNC 0.0 green. 2026-07-10T01:18+08:00 SOP production validation: promoted from Production Blocked to Production Ready after adding real runner adapter and validating through Ubuntu runner API remote job bf73f9e21c0d / Slurm job 686. API run completed in 13.454 s with sequence_length 111, model_pdb_bytes 68,291, annotated_pdb_bytes 56,414, and metrics Total CDR Length 20, CDR3 Length 5, CDR3 Compactness 0.572099253701283, PSH 72.3683, PPC 0.0064, PNC 0.0. Verified artifact manifest: summary.json, results.csv, tnp_result.json, tnp_summary.json, tnp_nanobody_model.pdb, tnp_nanobody_model_annotated.pdb, tnp_model_details.json, tnp_sequence_liabilities.json, tnp_stdout.txt, tnp_stderr.txt, slurm.out, slurm.err, and job.log.