Platform capabilities

Everything your team needs to move faster.

BioMate is built for real scientific work, not demos. Every capability is QC-gated, auditable, and reproducible — whether the result is going into a paper, a regulatory submission, or the next experiment.

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Workflow routing

Describe a goal in plain English. BioMate picks the right pipeline.

The routing engine maps loose research questions to validated workflows with 94.6% accuracy — from AlphaFold structure prediction to GATK variant calling to CryoSPARC particle picking. No bioinformatics rote required.

  • Ranks candidate pipelines with explicit confidence scores
  • Surfaces alternative workflows when the top choice has a known limitation
  • Refuses ambiguous queries instead of guessing
  • Falls back to human triage with a reasoning trace attached
router · resolved 0.94 confidence
> predict structures of 38 variants of human IL23R extracellular domain
AlphaFold2 multimer · v2.3.2 0.94 ✓
ESMFold · v1 0.71
OmegaFold 0.62
Inputs auto‑prepared from a Benchling sequence collection · 38 jobs queued · 12.4 GPU‑h estimated.
Parameter management

Pre‑filled parameters, validated before they run.

BioMate auto‑fills workflow parameters from your query context, file type and research domain. Required inputs are flagged. Optional ones show evidence‑based defaults — with the citation that justified the value.

  • Parameter validation at submit, not at runtime
  • Defaults grounded in published benchmarks, not folklore
  • Per‑lab overrides preserved across runs
  • Diff view between an old run and the next
params · GATK HaplotypeCaller · germline
--min-base-quality20
--standard-min-confidence30.0
--emit-ref-confidenceGVCF
--ploidy2 ⚠ override?
--referenceGRCh38.p14
Why this default?
Min base quality of 20 follows GATK best practices for germline short‑variant discovery (Van der Auwera & O'Connor, 2020).
Evidence‑graded QC

GOLD / SILVER / BRONZE — so you always know where your result stands.

Every run is evaluated against 32 domain‑specific QC profiles. BioMate grades outputs, explains which metrics passed or failed, and gives you the cited standard behind every threshold — so the result is defensible whether it goes into a paper, a regulatory filing, or a CRO handoff.

  • Per‑profile thresholds, version‑pinned
  • Reviewer overrides require a written justification
  • Explicit “needs human review” state — never silently passes
qc · run #c2f9 · cryo-EM single particle
SILVER
3 of 4 gates passed · CTF resolution at threshold
defocus range (μm)1.0–2.4 ✓
CTF resolution (Å)3.8 ⚠
particle count142,108 ✓
FSC 0.143 (Å)3.1 ✓
Reproducibility & audit

A complete record of every decision — forever.

BioMate maintains an immutable audit trail for every run: parameters set, parameters overridden, retrieved sources, reviewer comments, and a deterministic re‑run hash. Export to PDF or JSON, or pipe directly to your DMS.

  • Regulatory-grade audit trail & GxP compliance alignment
  • Tenant‑managed key rotation
  • Bit‑identical re‑run from a single hash
  • Reviewer surface separate from the executor
audit · run #c2f9 · history (14 events)
Run submitted by Dr. Sara Kim
2026‑04‑08 09:14:22 UTC · sha 7b21…f3c
QC profile cryo-em.singleparticle.v3 applied
2026‑04‑08 09:14:23 UTC
Reviewer J. Thiele requested re‑run with override
“Defocus drift on 18% of micrographs — tighten range.”
Compliance signature applied
e‑sig · J. Thiele · 09:42:11
Literature survey

From a research question to a synthesized evidence summary in minutes.

BioMate searches and synthesizes primary literature across PubMed, bioRxiv, ChEMBL, ClinicalTrials.gov, and PDB — returning ranked, cited summaries grounded in actual sources, not hallucinated references.

  • Retrieval-grounded answers: every claim links to a source
  • Structured summaries by study type, sample size, and outcome
  • Conflict detection — flags contradictory findings across studies
  • Export to DOCX or BibTeX for grant applications and manuscripts
literature · KRAS G12C resistance mechanisms
Synthesis (23 studies, 2020–2026)
Acquired resistance to KRAS G12C inhibitors (sotorasib, adagrasib) most commonly involves secondary KRAS mutations (Y96D, H95R) reported in 11/23 studies, followed by bypass signalling via EGFR/MET amplification (8/23). Three studies report co-occurring STK11 loss as a primary resistance driver in LUAD.
PMID 38901234 Fell et al. 2025 — KRAS Y96D covalent pocket mutation in 6/32 adagrasib-treated patients.
PMID 38712098 Awad et al. 2025 — MET amplification as co-resistance mechanism, combinatorial EGFR blockade partially rescues.
+21 sources · Export BibTeX · Export DOCX summary
Protocol generation

Experimental protocols written from your workflow results — not from a template.

BioMate generates step-by-step wet-lab and computational protocols grounded in the actual parameters used in your analysis — reagent concentrations, instrument settings, QC checkpoints, and safety notes all derived from the run record, not generic boilerplate.

  • Auto-generated from run provenance: parameters match what actually ran
  • Structured per-step format: materials, procedure, QC pass/fail criteria
  • SOP-ready: formatted for direct upload to Benchling, Notion, or Word
  • Protocol versioning tied to the workflow version that produced it
protocol · RNA extraction from PBMC · run #f4a1
STEP 1 · Cell isolation
Dilute whole blood 1:1 with PBS (no Ca²⁺/Mg²⁺). Layer 30 mL over 15 mL Ficoll-Paque PLUS. Centrifuge 400 × g, 30 min, 18–20 °C, brake off.
QC: PBMC viability ≥ 90% by Trypan blue before proceeding.
STEP 2 · RNA extraction
Lyse 1 × 10⁶ cells in 350 µL RLT buffer + 1% β-ME. Process with Qiagen RNeasy Micro kit. Elute in 14 µL RNase-free water.
QC: RIN ≥ 7.0 · A260/A280 1.8–2.1 · Yield ≥ 50 ng
6 steps total · Derived from run #f4a1 params · Export SOP (DOCX) · Export Benchling entry
All capabilities

Built for production research.

Every feature ships production‑tested — not as a prototype.

Workflow catalog

4,000+ indexed workflows across 36 biomedical domains.

Container‑pinned and version‑locked, spanning 36 biomedical domains. Bring your own when you need to.

Integrations & connectors

Plug into every layer of your stack.

BioMate connects to AI assistants, messaging platforms, sequencers, and laboratory instruments — so analysis starts where your data lives.

AI & Protocol
Communication
Lab Instruments
Data sources

60+ named live databases — queried in real time, not cached.

Every BioMate analysis draws from primary biological and chemical databases at query time. No stale snapshots. Results are always current.

Protein & Structure

UniProt / Swiss-Prot PDB AlphaFold DB InterPro Pfam CATH / SCOP2 ModBase

Genomics & Variant

Ensembl gnomAD ClinVar NCBI Gene dbSNP COSMIC ClinGen GWAS Catalog OMIM

Transcriptomics & Omics

GEO SRA ArrayExpress PRIDE MetaboLights cBioPortal TCGA

Chemistry & Drug Discovery

ChEMBL ChEBI PubChem DrugBank BindingDB ZINC OpenFDA DailyMed

Pathways, Ontology & Disease

KEGG Reactome Gene Ontology STRING-db BioGRID DisGeNET HPO Orphanet

Literature & Clinical

PubMed / MEDLINE Europe PMC bioRxiv / medRxiv ClinicalTrials.gov FDA labels (DailyMed) EMA EPAR
All queried live at analysis time — not cached snapshots
Security & compliance

Designed for the most regulated science on earth.

BioMate is the rare AI tool your QA lead approves on the first call. GxP audit support, an immutable trail, and controls you can inspect.

Aligned to
SOC 2 Type II · ISO 27001
Aligned to
HIPAA · GDPR · 21 CFR Part 11
Tenant data
Customer‑managed keys, in‑region
Training policy
Never on your data. Never co‑mingled.

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