Coding Toolbox

Hopefully, this coding toolbox will grow into a collection of source code enabling students, researchers and developers to jump-start their own projects. Contributions are highly welcome.

General Libraries

  • Microsoft
    Simple Encrypted Arithmetic Library (SEAL)
    ‘is an easy-to-use homomorphic encryption library, developed by researchers in the Cryptography Research Group at Microsoft Research. SEAL is written in C++, and contains .NET wrappers for the public API. It has no external dependencies, so it is easy to compile in many different environments. SEAL uses the Microsoft Research License Agreement, and is free for research use.’

More specific tools and implementations

  • Bonnie Berger
    ‘is a tool for finding significantly correlated SNPs which uses a dynamic boundary approach to deal with accuracy problems. In addition, using a convex analysis based approach it calculates, for a given SNP, the neighbor distance in constant time, overcoming the major computational bottleneck in the neighbor method.’

  • Bonnie Berger
    ‘is a set of two methods for performing privacy preserving GWAS in the presence of population stratification: PrivSTRAT and PrivLMM. Both methods allow researched to generate GWAS results while protecting private phenotype information about participants. In particular, researchers can: (1) return highly associated SNPs (2) estimate association statistics and (3) estimate the number of significant SNPs.’

  • Bonnie Berger
    ‘is a test that can be used on minor allele frequency data to determine how much releasing the minor allele frequencies from the study will compromise the privacy of those who participated in the study.’

GitHub Repositories

Code provided in papers’ supplements

  • Huang Z, Ayday E, Lin H, Aiyar RS, Molyneaux A, Xu Z, Fellay J, Steinmetz LM, Hubaux JP
    A privacy-preserving solution for compressed storage and selective retrieval of genomic data
    Genome Research. 2016. Volume 26. Issue 12. Pages 1687-1696.
    (Abstract, PDF, Supplement including source code)

  • He D, Furlotte NA, Hormozdiari F, Joo JWJ, Wadia A, Ostrovsky R, Sahai A, Eskin E
    Identifying genetic relatives without compromising privacy
    Genome Research. 2014. Volume 24. Issue 4. Pages 664–672.
    (Abstract, PDF, Source Code)

  • Cho H, Wu DJ, Berger B
    Secure genome-wide association analysis using multiparty computation
    Nature Biotechnology. 2018. Online May 07.
    (Abstract, PDF, Source Code)