Trust documentationDisclosed before asked
Dependency licensing
PetriDish runs on a curated stack. Every dependency below has its commercial-use status verified and recorded. Non-commercial models are firewalled to the research lane — they do not appear in any customer-facing endpoint. Pending licenses (most importantly the IndiGen commercial conversation with CSIR-IGIB) are disclosed openly rather than buried.
Source: Build & Launch Reference §3 (Licensing Decision Matrix) + §7 (Indian Data Layer).
DISCLOSED — INDIGEN COMMERCIAL LICENSING IN PROGRESS
The IndiGen 1,029-genome panel (CSIR-IGIB) is the foundation of India-specific allele frequencies in the platform. Research-tier use is free. Commercial licensing with CSIR-IGIB Business Development is in active conversation and will be resolved before paid product launch. We disclose this because — per Build & Launch Reference §7 — discovered late it reads as a gap; disclosed early it reads as rigor.
Production · Commercial OKPending — CSIR-IGIBVerify before usePaid license requiredResearch lane only
Production · Commercial OK
15| Asset | Category | Purpose | License | In shipped product |
|---|---|---|---|---|
Llama 3.3 70B (via Groq) Used under threshold for commercial deployment | Reasoning LLM | Cypher generation + grounded synthesis | Llama Community License | ✓ |
Neo4j AuraDB | Knowledge graph | 4.4M+ edges India-weighted | Commercial | ✓ |
PrimeKG (Harvard) | Knowledge graph | Precision-medicine KG seed | MIT | ✓ |
OpenTargets | Knowledge graph | Target-disease evidence + PharmGKB widget | Open / permissive | ✓ |
ESM-2 (Meta) | Protein LM | Protein variant function (planned integration) | MIT | — |
BioMedLM (Stanford) | Clinical LM | Biomedical reasoning (planned) | Apache 2.0 | — |
IGVDB | Variant DB | Indian variant frequency context | Open | ✓ |
FAERS | Drug safety | Adverse event reporting reference | Public domain (FDA) | — |
IMPPAT 2.0 (IIT-M curated subset) 100 of 17,967 compounds ingested; ACTREC expansion in progress | Phytochemistry | Ayurvedic compound knowledge layer | Academic / CC-BY (curated subset) | ✓ |
MHCflurry 2.0 Planned production integration. 91% of alleles ≥0.90 AUC. Pan-allele works on Indian HLA without Indian-specific training data. | Peptide-MHC presentation (Class I) | Open-source pan-allele HLA Class I binding prediction for Protein Atlas | Apache 2.0 — open | — |
BepiPred / DiscoTope Planned integration for Protein Atlas Layer 3 (autoantigens) when real-time inference layer ships. | B-cell epitope prediction | Linear / conformational B-cell epitope candidates for autoantigen layer | Open | — |
ACMG/AMP Variant Interpretation Standards Public clinical-genomics standard. IndoVar applies as the decision-support framework. | Classification framework | ACMG-2015 BS1/BA1/PM2/PP3/BP4 rule logic for IndoVar reclassification | Public standard | ✓ |
gnomAD v4 The Western baseline IndoVar improves on. Critical reference for BS1 reclassification logic. | Western baseline reference | Reference allele frequencies that IndoVar compares against | Open · MIT | ✓ |
ClinVar (NCBI) ClinVar is the existing baseline IndoVar concords with or reclassifies when Indian frequency justifies. | Variant database | Existing clinical-significance calls that IndoVar concords with or reclassifies | Open · public domain (NIH) | ✓ |
Evo 2 (Arc Institute + NVIDIA) Planned integration as the production variant-effect model (§5). | DNA foundation model | Variant-effect backbone (planned production) | Open · commercially usable | — |
Pending — CSIR-IGIB
1| Asset | Category | Purpose | License | In shipped product |
|---|---|---|---|---|
IndiGen (CSIR-IGIB) Currently used under research framing. Commercial licensing conversation with CSIR-IGIB Business Development required before paid product launch (Build & Launch Ref §7). | Population genomics | 1,029 Indian whole genomes; India allele frequencies | Research free · Commercial license required | ✓ |
Verify before use
6| Asset | Category | Purpose | License | In shipped product |
|---|---|---|---|---|
AlphaMissense (DeepMind) Not currently in shipped product; verify before adoption | Variant pathogenicity | Missense pathogenicity scores | Weight/artifact license requires verification | — |
PharmGKB redistribution Annotations referenced only; not bulk-redistributed | PGx annotations | Variant-drug-response references | Free access · commercial redistribution requires verification | — |
ESM-3 / ESM-C (EvolutionaryScale) Default to ESM-2 unless commercial terms confirmed | Protein LM | Next-gen protein function | Tiered — commercial terms vary | — |
SIDER drug-side-effect DB | Drug safety | Side-effect knowledge | Commercial terms require verification | — |
NetMHCpan-4.1 / NetMHCIIpan-4.0 Class II auROC ~0.91. Default to MHCflurry + ESMCBA (open) for production unless DTU commercial terms confirmed. | Peptide-MHC presentation (Class I + II) | Field-standard pan-allele binding prediction (DTU) | Academic license — commercial terms require verification | — |
ESMCBA (2025) | Peptide-MHC presentation | ESM-C-based Class I prediction — new SOTA direction (median Spearman 0.62 vs NetMHCpan 0.56) | Academic — verify | — |
Paid license required
1| Asset | Category | Purpose | License | In shipped product |
|---|---|---|---|---|
DrugBank (full) Open subset only is shipped; full DrugBank requires paid commercial license at scale | Drug compendium | Comprehensive drug data | Paid commercial license required | — |
Research lane only
3| Asset | Category | Purpose | License | In shipped product |
|---|---|---|---|---|
AlphaFold3 (DeepMind) Per autoimmune_protein_deep_research.md §9: best structural tool but firewalled to research lane. Used for paper-grade structural confirmation; never inside any customer-facing endpoint. | Structure / TCR-pMHC | Best HLA-peptide-TCR structural model — research papers and validation only | Non-commercial server + weights | — |
MsgaBpred / AlphaEpi Inherits AF3 non-commercial restriction. Research lane only. | B-cell epitope (research) | AF3-based epitope prediction for research-paper validation | Research (uses AF3) | — |
AlphaGenome (DeepMind) Firewalled to validation paper analysis. Will not appear in any customer-facing endpoint. | Regulatory variants | Regulatory variant analysis (research papers) | Non-commercial API only | — |
License discipline
Per Build & Launch Reference §3: every dependency's commercial-use status is verified at the moment of adoption and recorded in this matrix. Non-commercial models (AlphaGenome) are firewalled to the research lane. Paid-license dependencies (DrugBank full) are not shipped until the commercial agreement is in place.