The workshop "Bioinformatics for Biotechnology Applications (HavanaBioinfo 2012)", held December 8-11 2012 in Havana, aimed at exploring new bioinformatics tools and approaches for large-scale proteomics, genomics and chemoinformatics. Major conclusions of the workshop include the following: (i) Development of new applications and bioinformatics tools for proteomic repositories analysis is crucial; current proteomic repositories contain enough data (spectra/identifications) that can be used to increase the annotations in protein databases and to generate new tools for protein identification; (ii) spectral libraries, de novo sequencing and database search tools should be combined to increase the number of protein identifications; (iii) Protein probabilities and FDR are not yet sufficiently mature; (iv) computational proteomics software needs to become more intuitive; and at the same time appropriate education and training should be provided to help efficient exchange of knowledge between mass spectrometrist and experimental biologists with bioinformaticians in order to increase their bioinformatics background, especially statistics knowledge.