# Internships

## Links
* https://www.howest.be/en/events/2021-09-16-online-internship-market-ict-profiles
* https://www.howest.be/nl/events/2021-09-16-online-stagemarkt-voor-ict-profielen

## Questions
1. Beschrijving van uw bedrijf of organisatie.
Deze informatie nemen we op in de overzichtbrochure voor alle deelnamers. (_Description of your company or organization.
We will include this information in the overview brochure for all participants._)

1. Wij zoeken volgende profielen of werken aan volgende projecten.
Deze informatie nemen we op in de brochure voor studenten. Wees creatief en zorg voor een attractieve en wervende beschrijving.
(_We are looking for the following profiles or working on the following projects.
We will include this information in the brochure for students. Be creative and provide an attractive and appealing description._)

## Description of VIB

VIB is the premier biotech research organisation in Belgium. VIB employs 1600 research scientists, technicians, and engineers from more than 70 nationalities, working on the cutting edge of biology and engineering. They do fundamental research in life sciences with great value to society, such as finding innovative cures for cancer, or better understand the brain and help treat debilitating brain diseases like Alzheimer's. Life science research is no longer the exclusive domain of chemists and biologist in lab coats, but needs talented computer scientists to design algorithms, build websites, handle big data, and apply modern AI to hard biological problems.

## Intern profile
We are looking for motivated software engineers to work on open-source software used directly by researchers for cutting-edge science. Do you want people to use the software you create? Do you want to interact with scientists? If your answer is 'yes' to those questions then VIB bioinformatics core is for you!

## Project Ideas
1. Request: Acinetobase (Charles Van der Henst)
1. ProBio: database for metabolites (Geert Goeminne)
1. web interface including submission (?) for SnpEffect pipeline (Switch, based on Guy's work)
1. Add specialised visualisations to a popular single-cell research tool (SCope)
1. Modernise a popular web-browser based tool to visualise phylogenetic trees (PhyD3).
1. Integrate a neuroscience visualisation tool with popular open source lab notebook software (Falcon / Falcon Client).
1. Integrate advanced protein folding (FoldX) support into popular visualisation tools (Pymol and Chimera).
1. Integrate advanced protein comparison (MMLigner) support into popular visualisation tools (PyMOL and Chimera).
1. Allow researchers to use alternative data formats in a popular single-cell research tool (SCope)
1. Create a general purpose library for using a neuroscience research tool (Falcon / Falcon Client).
1. web interface for iRefIndex
1. Make Inkscape more useful for life sciences.

## Refined Project ideas
> [name=Frank] Our target audience almost certainly has virtually no knowledge of life sciences and its problems. The refined project ideas try to rephrase our projects in an accessible way to students with no biology background.
> [name=Frank] I wonder if for each project we also need to hint at the specific profile of the ideal student? Would it help to attract students? Or do we intentionally keep it vague to appeal to as many students as possible, filling in details only later during the internship fair?
> [name=James] This will be somewhat answered by having examples (I've already sent an email). That said, we're asked "Wij zoeken volgende profielen" and a single profile may cover all projects?

1. You may have heard about the completion of the human genome. In fact, the DNA sequence for this genome is an "averaging" and biologists actually use data at different resolutions: from this whole-genome view down to the level of individual cells. This project will allow you to work on a tool that researchers use to visualise and interact with single-cell resolution sequence data.
2. Researchers use advanced 3D visualization software to study the structure and interaction of large, complex biological molecules. The goal of this internship project is to extend two popular visualization applications (PyMOL and Chimera) with algorithms for protein folding and protein comparison. Protein comparison is a fundamental task upon which understanding of disease and drug discovery are among the important applications, and protein folding is a central unsolved problem in biology, a solution would revolutionise humanity's understanding of life. [Didn't Google DeepMind "solve" protein folding? :-) ][ Shhhh! ]
1. The "tree of life" traces the origins or ancestry of all species of life on earth. But how are these trees constructed? In this project you will work on software that draws interactive phylogenetic trees that biologists use to visualise not only ancestral relationships between species, but even individual biological molecules.
1. Neuroscientists track small fluctuations in brain patterns to understand their effects or purpose. In this project you will work on software for experimenting with these patterns: visualising them in real-time, stimulating the brain in response to certain patterns, and understanding results.

## Questions
- [name=Frank] Will this brochure be a printed one, or online?
- [name=Frank] Do we have an example of what it looked like in previous years?