Vivofold Research
Validated Methods & Scientific Software
We implement published bioinformatics and cheminformatics methods from their papers, test them against simulated data with a planted truth, and ship them in Nayancode software with their limits documented. The aim is analysis software that is private, reproducible and honest about what it can do.
Questions
What we want to know
- How much of standard genomics and cheminformatics can run privately in a web browser, and at what scale?
- How should scientific software prove that it gives correct answers, release after release?
- How can every analysis produce its own methods section and provenance automatically?
Approach
How we work on it
- Clean-room re-implementation from the primary literature, under permissive licences
- Planted-truth simulations and regression tests on real reference data
- Web Workers and WebAssembly for local, private computation
- Automatic provenance capture and methods generation
Methods already implemented
Global and local alignment with affine gapsRead mapping and SNV calling (minimap2 + samtools, WebAssembly)Maximum-likelihood phylogenetics with model selectionSNN-Louvain clustering with clean-room UMAP and t-SNEComBat batch correction, ORA and preranked GSEAInteraction profiling, pockets, SASA and TM-score
Open projects
Projects you can join
01
Browser-scale read mapping benchmarks
Characterise accuracy, memory and runtime of WebAssembly mapping across genome sizes and devices.
02
Numerical regression suites for analysis kernels
Extend planted-truth tests to every statistical kernel and publish the suite.
03
Accessible scientific visualisation
Keyboard and screen-reader access for interactive plots of large datasets.
Across Vivofold
Learn it, use it, commission it
Vedicgen courses
Algorithms for BioinformaticsUp to 4 weeks, about 32 hours live (customisable)Dry labfrom ₹4,499 + GSTResearch Software EngineeringUp to 4 weeks, about 32 hours live (customisable)Dry labfrom ₹4,499 + GSTHigh-Performance Scientific Programming: C++, Rust & WebAssemblyUp to 4 weeks, about 32 hours live (customisable)Dry labfrom ₹5,999 + GST
Scientific Software Engineering Internship (Nayancode) Collaborate