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:

  • PhyD3: a new online tool for phylogenetic tree visualization - https://phyd3.bits.vib.be
    This tool has been integrated in the PLAZA framework (http://bioinformatics.psb.ugent.be/plaza/), and published in the journal of Bioinformatics: http://dx.doi.org/10.1093/bioinformatics/btx324
    The preprint version is available here: https://doi.org/10.1101/107276

  • SCope: An online tool to explore and compare single-cell datasets across species - http://scope.aertslab.org
    This tool has been published in the article: A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain Cell 2018 https://doi.org/10.1016/j.cell.2018.05.057
    The preprint version is available here: https://doi.org/10.1101/237420

  • ConTra V3: an update of the online tool for the exploration of predicted transcription factor binding sites - http://bioit2.irc.ugent.be/contra/v3/
    The article on ConTra 3 has been published in the 2017 Web Server edition of Nucleic Acids Research: https://dx.doi.org/10.1093/nar/gkx376

  • TriForC: an online database for high-value triterpenes - http://bioinformatics.psb.ugent.be/triforc/
    This tool has been published in the datase issue of Nucleic Acids Research: https://doi.org/10.1093/nar/gkx925

  • WgDotPlot: a plugin for visualization of colinear regions between and/or within species - https://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/dotplot/index
    This tool has been integrated in the PLAZA framework (https://bioinformatics.psb.ugent.be/plaza/) and publised in the Nucleic Acids Research https://doi.org/10.1093/nar/gkx1002

  • iRefIndex WS: an update of consolidated protein interaction data and their supporting evidence - https://irefindex.vib.be
    It is also available via the PSICQUIC Viewer at EBI: PSICQUIC Viewer

  • TTFD: a metabolic network based guidance tool for the setup and interpretation of stable isotope metabolomics experiments.
    The development of the tool has been outsourced to ENPICOM, and was financially supported (around 40 %) by the BioInformatics @ VIB initiative.
    The tool is part of a manuscript in preparation that will be submitted to a journal of Nature group soon.

  • Pladipus 2: Design and implementation of a full rewrite of the Pladipus workflow tool, a platform for distributed proteomics pipelining.
    The project will be finalized in October 2018 and wil be made available for download via the Compomics web site.

  • 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 early 2018.

  • 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.

  • Scop3D 2.0 – online visualization of mutation rates on protein structure (Martens Lab)
    Soon online...

  • PTM Viewer: an intuitive protein-centric PTM viewer (De Smet Lab)
    Soon online...

  • Mobile application for Vlaams Darmflora project (Raes Lab) on Android devices, for participants data gathering.
    Inhouse development.

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)