Contents

• OCaml Math/Machine Learning
• Bioinformatics Workflows
• Smaller OCaml Libraries
• Contact

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Documentation of Software Projects

OCaml Math/Machine Learning

Swiss Army Knives for math, statistics and machcine learning in OCaml.

• Oml
  The OCaml Math Library
  See: the repository on Github.

Bioinformatics Workflows

These projects are building blocs for running big computational workflows that use bioinformatics tools from the community.

• Ketrew
  Workflow Engine for complex computational experiments.
  See:
  • the documentation for version 1.1.1,
  • the documentation for version 2.0.0,
  • the documentation for version 3.0.0,
  • the documentation for version 3.1.0,
  • the documentation for version 3.2.0,
  • the documentation for the master branch,
  • and the repository on Github.
• Biokepi
  Framework for building Bioinformatics Pipelines based on Ketrew.
  See:
  • the documentation for the master branch,
  • and the repository on Github.
• Coclobas
  Configurable HPC cluster scheduler (for now, based on gcloud and Kubernetes).
  See: the repository on Github.
• Epidisco
  Personalized cancer epitope discovery and peptide vaccine prediction pipeline.
  See: the repository on Github.

Smaller OCaml Libraries

Over the years we have developped small, self-contained, generic OCaml libraries.

• Nonstd
  Nano-library providing very few Core-like modules (like List, Option).
  See:
  • the documentation for the master branch,
  • the documentation for version 0.0.1,
  • and the repository on Bitbucket.
• Sosa
  The “Sane OCaml String API” library is a set of APIs (module types) that define what a string of characters should be, and a set of modules and functors that implement them.
  See:
  • the documentation for the master branch,
  • the documentation for version 0.1.0,
  • the documentation for version 0.2.0,
  • the documentation for version 0.3.0,
  • and the repository on Github.
• Docout
  The functor Docout.Make_logger creates a nice embedded DSL on top of the smart-print library.
  See:
  • the documentation for the master branch,
  • the documentation for version 0.0.1,
  • and the repository on Bitbucket.
• Pvem
  The "Polymorphic Variants-based Error Monad", Pvem (pronounce /pi:vɛm/), is a module providing simple handling of an error monad type based on polymorphic variants.
  See:
  • the documentation for the master branch,
  • the documentation for version 0.0.1,
  • and the repository on Bitbucket.
• Pvem_lwt_unix
  Pvem_lwt_unix provides a high-level API on top of Lwt_unix, with comprehensive error types.
  See:
  • the documentation for version 0.0.1,
  • the documentation for the master branch,
  • the documentation for version 0.0.2,
  • and the repository on Bitbucket.
• Oredoc
  Build documentation websites for some OCaml projects.
  See:
  • the documentation for the master branch,
  • and the repository on Github.
• Trakeva
  Transactions, Keys, and Values: an API describing key-value storage with ACID transactions and different backends.
  See:
  • the documentation for the master branch,
  • the documentation for version 0.0.0,
  • the documentation for version 0.1.0,
  • and the repository on Github.
• Genspio
  EDSL to generate complex POSIX shell scripts.
  See:
  • the documentation for the master branch,
  • and the repository on Github.

Contact

Please use if possible the issue trackers of the corresponding repositories. See also http://www.hammerlab.org/contact/.