Projects

Projects and apps we have built for our clients.

Beyond direct data analysis, we create custom scientific software: automated analysis pipelines, bespoke databases, visualization tools, and internal platforms that outlive the project they were written for.

Below we show a few examples of what we have delivered most often. The details vary between implementations — the data, the assay, the question being asked — but the core tends to transfer.

DrugREV

molecular engine

DrugRev is a molecular engine we developed to explore the chemical binding activity, pharmacokinetics, and side effects of drug-like molecules. It draws on public and licensed sources — PDB, DrugBank, ChEMBL, and FAERS among them — alongside whatever in-house data a client brings, with 3D visualization, docking, and molecular dynamics on one side and statistical and deep learning models on the other.

Together these have helped our clients predict whether a molecule will engage its intended target in a clean and efficacious fashion. DrugRev also offers generative capabilities: designing small molecules and de novo binders — macrocycles, peptides, and mini-proteins — with a specified activity profile against a particular set of targets, including the option to ensure the result does not engage designated off-targets.

docking · molecular dynamics PDB · ChEMBL · DrugBank · FAERS · in-house ADME/T off-target prediction de novo binder design generative design
DrugRev · docking + de novo design selective · 1 of 14 active
binding site KRAS G12C · switch II 2.9 Å 3.1 Å 3.4 Å O N N de novo macrocycle · 9 residues ΔG bind kcal/mol -9.4 poses 128/128 selectivity pIC50 pred cut 6.0 KRAS hERG CYP2D6 SRC CYP3A4 ADRB2 EGFR LCK MAO-A 5-HT2B ABL1 PXR AURKB D2R 4 6 8
  • on-target
  • off-target flag
  • predicted contact
  • de novo binder

BAYESIC

data integration

Multiple datasets spanning various data types — GWAS, transcriptomics, proteomics, binary screens, and other specialized measurements — are common in genomics, and integrating them is challenging. The process often gets reduced to a rigid funnel where only genes with positive results in every dataset are considered.

Bayesic selects an appropriate prior for each data type and converts each contribution into a weighted posterior probability. This enables a more flexible evaluation, where a negative result in one dataset does not automatically disqualify a gene, and you can see exactly how much each dataset moved it.

Bayesian integration priors per data type posterior ranking GWAS · RNA-seq · proteomics
Bayesic · priors → posterior priors set · P 0.19
evidence · point ± 1 s.d. null GWAS p 4.7e-12 w 0.34 RNA-seq q 8.3e-04 w 0.26 proteomics q 2.6e-05 w 0.28 CRISPR screen FDR 0.62 negative w 0.12 effect (z) posterior · P(target | data) prior 90% CrI P(target) 0.19 CrI 0.05–0.78 sd 0.227 rank by P(target | all data) top 9 of 1,842 candidates gene Δrank P(target) GCKR·0.34 TCF7L2·0.31 CDKAL1·0.29 HNF1A·0.26 KCNJ11·0.24 ADCY5·0.22 SLC30A8·0.19 MTNR1B·0.17 GLP1R·0.15 an AND-funnel would drop SLC30A8
  • GWAS
  • RNA-seq
  • proteomics
  • CRISPR · negative evidence
  • posterior · SLC30A8

Targette

target discovery

Target identification and validation is where a great many programs begin. Targette is our implementation of how that work tends to shape up: splice junctions, chromatin accessibility, single-cell expression, and perturbation screens pulled into one place, with sequence-to-function models tying the layers together and the chain of evidence from a variant to a phenotype kept visible throughout.

Where the target product profile is already settled, it drives that work: a small molecule, a gene edit, and a nanobody do not need the same evidence behind them.

splice junctions chromatin accessibility single-cell perturbation screens sequence-to-function models target product profile
Targette · locus → cell type → pathway scanning · 1.1M variants
A · gwas meta-analysis B · single-cell atlas C · pathway graph
  • locus → population → path
  • genome-wide significance
  • background variants & cells

Grimoire

AI assistant

Every research organization has more written down than anyone can hold in their head: assay results, protocols, internal reports, and the literature around all of it. Grimoire is the assistant we build over that corpus — retrieval-augmented, running on a client-specific cloud deployment, and inheriting the same data access privileges as the account asking the question.

The design constraint that matters is provenance. Every answer names the chunks it came from, so a claim can be traced back to the report it came out of rather than taken on trust.

RAG LangChain private corpus per-account access control cited answers
Grimoire · retrieval, with sources idle · 8,431 chunks
corpus 8,431 chunks embedding n = 164 shown context 5 chunks · 3,140 tok assay data3,182 protocols1,046 reports2,417 literature1,786 8,431 chunks · 214 docs scoped to your account UMAP-1 UMAP-2 k = 5 · cosine 768-d · umap query why did IC50 shift in rep 3? answer 4 of 5 cited · 0 unsupported mmr λ 0.5 · 3,140 / 8,192 tok
  • assay data
  • protocols
  • reports
  • literature
  • retrieved
02Stack

The tools we work with.

Our expertise encompasses the computational tools and best practices used by leading biopharmaceutical companies as well as top tech-bio and software organizations, so that whatever we hand over can be picked up and run by your own team.

Languages and pipelines

  • Python
  • R
  • C++
  • SQL
  • Nextflow
  • Snakemake
  • Git

Modeling and ML

  • PyTorch
  • JAX
  • scikit-learn
  • Stan
  • PyMC
  • XGBoost
  • LangChain

Biology and chemistry

  • Scanpy
  • Seurat
  • Bioconductor
  • RDKit
  • OpenMM
  • GROMACS
  • AutoDock

Data and delivery

  • PostgreSQL
  • DuckDB
  • Docker
  • AWS · GCP
  • Plotly Dash
  • R Shiny
  • React

A representative selection rather than a complete list.

How to get started with MatGen

Much of what we build is smaller than the platforms above: an analysis pipeline, a database replacing a folder of spreadsheets, or a dashboard a few people use every day. Navigate here to learn how the engagement process with MatGen works.