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bio-nexus-api / bioai-platform /backend /app /tools

289 kB

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History: 131 commits

Samad14

feat: techspec additions — de novo tier-6 branch, structure export, page capture + final synthesis

4939f56 about 1 month ago

__init__.py

0 Bytes
Initial commit: Bio Nexus pipeline engine — BLAST + UniProt + AlphaFold + AI interpretation (Phase 1) 4 months ago
admet.py

36.8 kB
Fix pipeline MSA/AI stall, add SwissADME-parity ADMET panel, PubChem search, docking ligand data 2 months ago
alphafold.py

2.56 kB
fix: AlphaFold lookup for NCBI RefSeq accessions 2 months ago
base.py

313 Bytes
Initial commit: Bio Nexus pipeline engine — BLAST + UniProt + AlphaFold + AI interpretation (Phase 1) 4 months ago
blast.py

4.38 kB
fix(pipeline): stop abandoning slow NCBI BLAST jobs + EBI fallback about 2 months ago
castp.py

5.93 kB
feat: optimize CASTp SASA with KDTree, add sequence input to CASTp + Structure Prep, ESMFold integration for unknown genes about 1 month ago
docking.py

16.8 kB
Docking: flatten multi-chain obabel receptor output to a single model 2 months ago
domain_analysis.py

19 kB
feat(uniprot,domains): reviewed/organism filters + debounce/fast-path, PROSITE raw-sequence scan UI (3c,3d) 2 months ago
dotplot.py

10.7 kB
feat(results): in-app share dialog + self-normalized dotplot scoring about 2 months ago
ebi_msa.py

4.74 kB
Fix pipeline MSA/AI stall, add SwissADME-parity ADMET panel, PubChem search, docking ligand data 2 months ago
function_predict.py

4.54 kB
fix(function-predict): add BP term, real AA composition, JSON export, UniProt distinction, and /learn topic about 2 months ago
md_config.py

7.45 kB
feat(md): verified force field/solvent menu (ff14SB/ff15ipq/ff19SB/amberfb15/CHARMM36 x OBC1/OBC2/GBN2) with alanine-dipeptide createSystem startup probe; explicit errors for invalid combos; dynamic frontend menu 2 months ago
md_sim.py

40.9 kB
feat(md): verified force field/solvent menu (ff14SB/ff15ipq/ff19SB/amberfb15/CHARMM36 x OBC1/OBC2/GBN2) with alanine-dipeptide createSystem startup probe; explicit errors for invalid combos; dynamic frontend menu 2 months ago
motif_scanner.py

12.9 kB
feat(seq-tools): motif categories & structure overlay, dot-plot scoring & features, cross-tool links about 2 months ago
msa_fallback.py

6.27 kB
Fix pipeline MSA/AI stall, add SwissADME-parity ADMET panel, PubChem search, docking ligand data 2 months ago
ngs.py

41.5 kB
fix: NGS fallback to Python aligner when native tools missing; add missing re import in sequence_utils about 1 month ago
oligo_qc.py

9.83 kB
feat(primers): add NCBI gene search + sequence retrieval, oligo QC and in-silico PCR verification with recharts graphs about 2 months ago
pairwise_alignment.py

4.66 kB
feat(alignment): pairwise global/local alignment via BLAST hit 'Align pair' (3a) 2 months ago
protox.py

6.81 kB
feat(admet): ProTox 3.0 ML toxicity prediction — backend client + endpoint, frontend ProTox tab, restored sidebar chevron about 2 months ago
pubchem.py

2.96 kB
Fix pipeline MSA/AI stall, add SwissADME-parity ADMET panel, PubChem search, docking ligand data 2 months ago
sequence_fetch.py

3.72 kB
feat(alignment): pairwise global/local alignment via BLAST hit 'Align pair' (3a) 2 months ago
sequence_utilities.py

8.76 kB
feat(seq-tools): add sequence utilities, motif scanner and dot plot tools with frontend pages about 2 months ago
sequencing.py

17 kB
feat: add full 6-step NGS pipeline + fix sequencing WinError 193 about 2 months ago
structure_prep.py

15.5 kB
feat: techspec additions — de novo tier-6 branch, structure export, page capture + final synthesis about 1 month ago
uniprot.py

5.44 kB
feat(uniprot,domains): reviewed/organism filters + debounce/fast-path, PROSITE raw-sequence scan UI (3c,3d) 2 months ago