Category Archives: Software & Services

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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The Coronavirus Antibody Database: 10 months on, 10x the data!

Back in May 2020, we released the Coronavirus Antibody Database (‘CoV-AbDab’) to capture molecular information on existing coronavirus-binding antibodies, and to track what we anticipated would be a boon of data on antibodies able to bind SARS-CoV-2. At the time, we had found around 300 relevant antibody sequences and a handful of solved crystal structures, most of which were characterised shortly after the SARS-CoV epidemic of 2003. We had no idea just how many SARS-CoV-2 binding antibody sequences would come to be released into the public domain…

10 months later (2nd March 2021), we now have tracked 2,673 coronavirus-binding antibodies, ~95% with full Fv sequence information and ~5% with solved structures. These datapoints originate from 100s of independent studies reported in either the academic literature or patent filings.

The entire contents CoV-AbDab database as of 2nd March 2021.
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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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Prerecording Conference Talks and Posters using OBS Studio

Seemingly every conference due to take place this year has either been cancelled or will be run virtually due to the COVID-19 pandemic. Many organisers have decided that running entirely live virtual programmes causes more trouble than it’s worth (e.g. due to unforseeable IT and internet issues disrupting the schedule), and so are asking their presenters to prerecord their talks, which are then broadcast “live” on the day.

I recently “presented” two virtual prerecorded talks at the ISMB conference using Open Broadcast Software Studio (OBS Studio), a free open-source software package most commonly used by live-streamers on Twitch and Youtube. It is super simple to use and achieves a professional output, with video overlaying a presentation slide deck/poster PDF. This blog is a “how-to” on getting started with OBS for conference talks/poster presentations.

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The Coronavirus Antibody Database (CoV-AbDab)

We are happy to announce the release of CoV-AbDab, our database tracking all coronavirus binding antibodies and nanobodies with molecular-level metadata. The database can be searched and downloaded here: http://opig.stats.ox.ac.uk/webapps/coronavirus

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TCRBuilder: Multi-state T-cell receptor structure prediction

Hello friends of OPIG,

From my last blopig blog post [link: https://www.blopig.com/blog/2019/10/comparative-analysis-of-the-cdr-loops-of-antigen-receptors/], I summarised our findings that TCR CDRs are more flexible than their antibody counterparts. Because of this observation, we believe that it is more appropriate to represent TCR binding sites using an ensemble of conformations.

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Lightning-fast Python code

Scientific code is never fast enough. We need the results of that simulation before that pressing deadline, or that meeting with our advisor. Computational resources are scarce, and competition for a spot in the computing nodes (cough, cough) can be tiresome. We need to squeeze every ounce of performance. And we need to do it with as little effort as possible.

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Considering Containers? – Go for Singularity

Docker is an excellent containerisation system ideally suited to production servers.  It allows you to do one small thing but do it well.  For example, breaking a large blog up into individually maintained containers for a web-server, a database and (say) a wordpress instance. However due to inherent security woes, Docker doesn’t play nicely with multi-tenanted machines, the kind which are the bread and butter for researchers and HPC users.  That’s where Singularity steps in.   

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SAbBox – the easy way to obtain our antibody tools

A significant part of the work we do here in OPIG revolves around antibodies, the proteins of the immune system that bind to and help remove any foreign entities that find their way into the body. Since antibodies can be developed that target basically anything, they have become extremely useful as therapeutics. In our research, we develop computational tools that can be incorporated into various points along the antibody discovery pipeline. These tools include our database of antibody structures, SAbDab, and a series of predictive tools (e.g. structural modelling algorithms like ABodyBuilder) which are known collectively as SAbPred.

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