Author Archives: Benjamin McMaster

Testing python (or any!) command line applications

Through our work in OPIG, many of our projects come in the form of code bases written in Python. These can be many different things like databases, machine learning models, and other software tools. Often, the user interface for these tools is developed as both a web app and a command line application. Here, I will discuss one of my favourite tools for testing command-line applications: prysk!

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Conference Summary: AIRR Community Meeting VII – Learnings and Perspectives

At the start of June, we (Lewis and Benjie) attended the AIRR Community meeting in beautiful and sunny Porto, Portugal. This meeting was focused on collecting and analysing adaptive immune receptor repertoires. This comprised of two rivalling factions at the conference: the antibody (Ab) people or the T cell antigen receptor (TCR) people. The split was nearly fifty-fifty between these two topics throughout the conference. Overall, the conference was a fairly comfortable size, with approximately a hundred people in attendance, making it easy to visit all of the posters and talk with many people in your area, without feeling too niche. There was a wide variety of content formats throughout the conference including posters, scientific talks, lightning talks, software demos, and hands-on tutorials. In the following section, we highlight some of our favourite sessions to give a flavour of what this meeting entails.

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How to write a review paper as a first year PhD student

As a first year PhD student, it is not an uncommon thing to be asked to write a review paper on your subject area. It is both a great way to get acquainted with your research field and to get the background portion of your thesis completed early. However, it can seem like a daunting task to go from knowing almost nothing about your research field to producing something of interest for experts who have spent years studying your subject matter.

In my first year, I was exactly in this position and I found very little online to help guide this process. Thus, here is my reflective look at writing a review paper that will hopefully help someone else in the future.

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Working with PDB Structures in Pandas

Pandas is one of my favourite data analysis tools working in Python! The data frames offer a lot of power and organization to any data analysis task. Here at OPIG we work with a lot of protein structure data coming from PDB files. In the following article I will go through an example of how I use pandas data frames to analyze PDB data.

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A match made in heaven: academic writing with latex and git

Alternative titles:

  • A match made in heavenhell: academic writing with latex and git
  • Procrastinating writing by over-engineering my workflow

If you are like me, you can happily write code for hours and hours on end but as soon as you need to write a paper you end up staring at a blank page. Luckily, I have come up with a fool proof way to trick myself into thinking I am coding when in reality I am finalling getting around to writing up the work my supervisor has been wanting for the last month. Introducing Latex and git- this was my approach to draft a review paper recently and in this blopig post I will go through some of the ups and downs I had using these tools.

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Can AlphaFold predict protein-protein interfaces?

Since its release, AlphaFold has been the buzz of the computational biology community. It seems that every group in the protein science field is trying to apply the model in their respective areas of research. Already we are seeing numerous papers attempting to adapt the model to specific niche domains across a broad range of life sciences. In this blog post I summarise a recent paper’s use of the technology for predicting protein-protein interfaces.

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