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Open Source projects

  • GenomeView is an interactive genome browser and annotation editor that can deal with a multitude of sequencing and (comparative) genomics data sets.[1]
  • Java-ML is a collection of machine learning algorithms aimed at software engineers and programmers. It has well documented source code and provides plenty of code samples and tutorials.
  • GitHub repositories GitHub listing with recent software
  • Abeel Java Toolkit (AJT): Toolkit with useful Java classes
  • Abeel Toolkit (ATK): Successor of ATJ, toolkit with useful Java and Scala classes
  • PHP-agenda: Online agenda and calendering tool
  • EPSGraphics: Utility library that provides an easy way to create EPS figures from Java code.
  • GenomeTools: Family of command-line tools to convert between various genomics data formats.

Closed source scientific software

  • EP3: Eukaryote core promoter prediction program[2]
  • ProSom: Eukaryote core promoter prediction program[3]
  • pppBenchmark: Core promoter prediction evaluation program [4]

Random tips & tricks


  1. Abeel et al.: GenomeView: a next-generation genome browser. Nucleic Acids Res. 2012;40:e12. PMID: 22102585. DOI.
  2. Abeel et al.: Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res. 2008;18:310-23. PMID: 18096745. DOI.
  3. Abeel et al.: ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics 2008;24:i24-31. PMID: 18586720. DOI.
  4. Abeel et al.: Toward a gold standard for promoter prediction evaluation. Bioinformatics 2009;25:i313-20. PMID: 19478005. DOI.