Software Development for Bioinformatics

We provide resources for software development of bioinformatics applications for VIB scientists. Via two calls per year, we invite the bioinformatics community at VIB to submit proposals on software projects with significant impact and track records over the past years.

You can also hand in proposals at any time during the year using this template. An overview presentation can be found here.

Examples of delivered applications are:

  • PTM Viewer: an intuitive protein-centric PTM viewer (De Smet Lab)
    submitted to JPR, in rebuttal

  • Through collaboration with the VIB Bio Imaging Core (BIC), Frank Vernaillen from the VIB Bioinformatics Core designed and implemented a software ‘bridge’ that allows ‘Quasar’ code to be called from within Java. He also designed and developed a user-friendly plugin for de-noising electron microscopy (EM) images. It was added to the broadly used Image analysis software ImageJ. 
    Release is envisaged in 2019 as well as a publication.

  • Furthermore, together with Sebastian Munck, he developed an analysis technique which allows characterizing of the surface of the cell membrane over tens of micrometers with a resolution on the nanometer scale in a label free manner. MATLAB scripts have been developed to interpret the gray level information of the measured interferometric patterns to deduce the nanotopography of the membrane.
    A manuscript is currently in preparation.

Current projects are:

  • Beerome (Verstrepen Lab)

  • Flow Cytometry - automated gating strategies (Liston Lab)

  • Protein Homeostatis DB (Switch Lab)

  • Reliably estimating the quality and completeness of your plant genome/transcriptome (Vandepoele Lab)
  • SnpEffect 5.0, an updated version online tool online tool for analysing the effect of coding mutations on the structure and folding of proteins (Switch Lab).

  • Toucan.JS: a re-written and extended web browser-based version of Toucan, workbench for regulatory sequence analysis (Aerts Lab)