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 - Scop3D 2.0 – online visualization of mutation rates on protein structure (Martens Lab)
https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00681 - “A Label-free Multicolor Optical Surface Tomography (ALMOST) imaging method for nontransparent 3D samples”
Axelle Kerstens; Nikky Corthout; Benjamin Pavie; Zengjin Huang; Frank Vernaillen; Greetje Vande Velde; Sebastian Munck
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-018-0614-4 - “Modernization of Golgi staining techniques for high-resolution, 3-dimensional imaging of individual neurons”
Katlijn Vints, Dorien Vandael, Pieter Baatsen, Benjamin Pavie, Frank Vernaillen, Nikky Corthout, Vasily Rybakin, Sebastian Munck, and Natalia Gounko
https://www.nature.com/articles/s41598-018-37377-x - Mobile application for Vlaams Darmflora project (Raes Lab) on Android devices, for participants data gathering.
Inhouse development.
- 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)
