The pipeline

Open-source models, all the way down.

SciRouter routes every step of the analysis through the same biomedical model stack already in production for our drug-discovery customers. No proprietary black box — every variant call, every neoantigen rank, every drug recommendation is reproducible. Below, the route table the oncology product runs against.

Task	Model / pipeline	Layer
Variant calling from BAM	GATK HaplotypeCaller, Mutect2, Strelka, Manta	Genomics
Variant annotation	ANNOVAR, Funcotator, VEP, OncoKB-canine alignment	Genomics
RNA-seq quantification	Salmon, STAR, RSEM aligned to canFam4 (UU_Cfam_GSD_1.0)	Transcriptomics
Differential expression	DESeq2, GSVA, ssGSEA	Transcriptomics
DLA typing (canine MHC)	DLA-typing pipeline (research collaboration; partnership opportunity)	Immunogenomics
Neoantigen prediction	pVACtools, NetMHCpan-4.1, MHCflurry — calibrated for DLA	Immunogenomics
Protein structure for mutated peptides	AlphaFold 3, ESMFold, Boltz-1	Structure
Drug–target binding	DiffDock, Boltz-2, Chai-1	Structure
Drug property prediction (ADMET)	ADMET-AI (already on SciRouter)	Cheminformatics
Generative analog design	REINVENT4 (already on SciRouter)	Cheminformatics
Histopathology slide analysis	UNI, Virchow, CONCH + canine fine-tunes	Imaging
Radiology interpretation	MedSAM, SAM-Med, canine-trained foundations	Imaging
Free-text → structured	Gemma 4 26B MoE (RunPod serverless)	Language
Owner-facing explainer	Gemma 4 4B (always-on, Railway)	Language

Why this matters

FidoCure, Vidium, and ImpriMed each ship a slice of this stack as a closed product. SciRouter Oncology treats genomics as data we ingest, not a product we sell exclusively. That means a vet using ImpriMed's chemosensitivity assay alongside a Vidium 120-gene panel — both feeding a single canonical patient record, with a single drug-mutation matrix in the vet view.

Personalized mRNA neoantigen vaccines (SciRouter mRx) follow the same pattern: WES + RNA-seq → DLA typing → neoantigen ranking via pVACtools → AlphaFold-3 confirmation of peptide-MHC binding → mRNA construct → LNP formulation via a manufacturing partner (Vernal Biosciences in Vermont, or UNSW RNA Institute in Sydney for the Rosie protocol). Administered under USDA-CVB conditional licensure or university IACUC trial wrappers.

The two-tier Gemma 4 deployment maps cleanly to the product: Gemma 4 4B always-on for the conversational owner-side explainer; Gemma 4 26B MoE serverless on RunPod for vet-side decision synthesis, document parsing, and the tumor-board agent committee.

For deeper technical reading on the SciRouter platform, see the SciRouter homepage and engineering blog.