Category Archives: Hints and Tips

Singularity: a guide for the bewildered bioinformatician

Have you ever worked with a piece of software that is awfully difficult to set up? That legacy code written on FORTRAN 77, that other one that requires significant modifications to compile, or any of those that require a long-winded bash script with a thousand dependencies (which you also have to install!). Would it not be helpful if, when that red-eyed PhD student, that one that just spent three months writing up their thesis, says that they absolutely must use that server where you have installed all your stuff, you could just relocate to another one without trouble? Well, you may be able to do that now. You just need to use containerization.

The idea behind containerization is rather simple. The best way to ensure anyone can reproduce your work is to, well, ship your entire system to whomever needs to use it. You could, for example, pack up your desktop in a box, and ship it to your collaborators anywhere in the world. Unfortunately, this idea is quite unpractical, not only because of tedious logistics (ever had to deal with customs?), but also because suddenly you won’t be able to run your own pipeline. However, it is a good enough thought that at some point made a clever engineer wonder whether there was a way to ship an entire system without physically delivering the computer. And that’s exactly what they designed.

40ft x 8ft (9ft 6") One trip high cube shipping container bl
Best way to make sure your collaborators on the other side of the world can run your pipeline — just pack your desktop in one of these, and ship it away!
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Commercialising your research: Where to start?

If you look at some of the biggest technology companies in the world, from Google and Facebook to hardware companies like Dell or even biotech unicorns like Oxford’s own Oxford Nanopore, all of them started on university campuses. If you are a researcher interested in finding out how to make the first steps to commercialise your research here is a quick guide:

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Peer Review: reviewing as an early career researcher

Peer review is an important component of academic research and publishing, but it can feel like an opaque process, especially for those not directly involved. I am very fortunate to have been able to participate in the peer review of multiple papers, despite being very early in my career, through support from my supervisors and a mentoring program run by Sense about Science with Nature Communications. Here are some of the things I have learned.

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Making Pretty Pictures with PyMOL

There’s few things I like more in our field than the opportunity to make a really nice image of a protein structure. Don’t judge me, but I’ve been known to spend the occasional evening in front of the TV with a cup of tea and PyMOL open in front of me! I’ve presented on the subject at a couple of our research group retreats, and have wanted to type it up into a blog post for a while – and this is the last opportunity I will have, since I will be leaving in just a few weeks time, after nearly eight years (!) as an OPIGlet. So, here goes – my tips and tricks for making pretty pictures with PyMOL!

Ray Tracing

set ray_trace_mode, number

I always ray trace my images to make them higher quality. It can take a while for large proteins, but it’s always worth it! My favourite setting is 1, but 3 can be fun to make things a bit more cartoon-ish.

You can also improve the quality of the image by increasing the ‘surface_quality’ and ‘cartoon_sampling’ settings.

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BioDataScience101: a fantastic initiative to learn bioinformatics and data science

Last Wednesday, I was fortunate enough to be invited as a guest lecturer to the 3rd BioDataScience101 workshop, an initiative spearheaded by Paolo Marcatili, Professor of Bioinformatics at the Technical University of Denmark (DTU). This session, on amino acid sequence analysis applied to both proteomics and antibody drug discovery, was designed and organised by OPIG’s very own Tobias Olsen.

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Enhance your presentation by using virtual webcams and scene transitions

If you haven’t checked out Matt’s post on using OBS for recording video, I highly recommend doing so. OBS is a terrific way to present your work online. It can provide (amongst many, many other things) the ability to create live picture-in-picture scenes, so you can move through your powerpoint deck whilst overlaying video of your tiny talking head in the corner.

Continuing on from Matt’s post, I’d like to promote the OBS virtual camera plugin and Touch Portal.

Every company, department or course has its own favourite video conferencing application and whilst they all have their strengths, consistency is not one of them. If you want to consistently display your presentation and your live video regardless of the platform in use, this quickly gets into the “messy” territory. This is where the virtual camera comes in.

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Graphical abstracts that spark joy on a gloomy day

Have you ever read a paper just because it had a funny, endearing, or utterly bizarre graphical abstract? Ever since a colleague showed me the ‘Graphical abstracts that I gone and found’ Facebook page, I have definitely come across a few, and I thought I would share some of my favourite ones below. If you enjoy this kind of thing, I strongly suggest visiting their page for more – it makes for a wonderful distraction from pretty much anything. Continue reading