AIBench is a lightweight, non-intrusive, MVC-based Java application framework that eases the connection, execution and integration of operations with well defined input/output. This basic idea provides a powerful programming model to fast develop applications given that:

  • The logic can be decoupled from the user interface.
  • The interconnection of operations can also be decoupled based in the idea of “experiments”.
  • The programmer is forced to “think-before-program”, easing the code reuse.

jARVEST (Java web harvesting library)

jARVEST (Java web harvesting library) is a simple web harvesting or web scraping framework. jARVEST is implemented via a powerful JRuby-based domain specific language (DSL), allowing you to develop harvesters with minimum code

PileLine & PileLineGUI

PileLine is a flexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files produced by next-generation sequencing experiments (i.e. pileup, BED,GFF, or VCF files). PileLine is designed to be memory efficient by performing on-disk operations over sorted GP files directly.

PileLine GUI is a front-end of the PileLine toolkit, plus a genome browser. With this intuitive graphical desktop application you can run the following tasks:

  1. Processing commands of GP files, like seek, join, annotate and filtering.
  2. Perform 2-samples and n-samples point somatic mutation calling (via the
  3. PileLine 2smc and nsmc commands).
  4. Browse GP files in an interactive local genome browser.

ALTER (ALignment Transformation EnviRonment) is a public tool for MSA (Multiple Sequence Alignment) file format conversion. It performs a program-oriented conversion between different DNA and protein MSA formats.


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