Author Archives: Guy Durant

Slurm and Snakemake: a match made in HPC heaven

Snakemake is an incredibly useful workflow management tool that allows you to run pipelines in an automated way. Simply put, it allows you to define inputs and outputs for different steps that depend on each other, Snakemake will then run jobs only when the required inputs have been generated by previous steps. A previous blog post by Tobias is a good introduction to it – https://www.blopig.com/blog/2021/12/snakemake-better-workflows-with-your-code/. 

However, often pipelines are computationally intense and we would like to run them on our HPC. Snakemake allows us to do this on slurm using an extension package called snakemake-executor-plugin-slurm.

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OP-uns

As a long-standing social sec of the OPIG research group, the key part of the job is to ensure that the event name includes some kind of pun around OPIG (and then maybe organise something). Notable ones include OPIGmas, the annual Christmas party that I am neglecting to organise at the moment, and O’Punting, our annual punting trip. For the next generation of social secs, I have proposed some new activities with even worse names.

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Tracking the change in ML performance for popular small molecule benchmarks

The power of machine learning (ML) techniques has captivated the field of small molecule drug discovery. Increasingly, researchers and organisations have employed ML to create more accurate algorithms to improve the efficiency of the discovery process.

To be published, methods have to prove they have improved upon others. Often, methods are tested against the same benchmarks within a field, allowing us to track progress over time. To explore the rate of improvement, I curated the performance on three popular benchmarks. The first benchmark is CASF 2016, used to test the accuracy of methods that predict the binding affinity of experimental determined protein-ligand complexes. Accuracy was measured using the Pearson’s R value between predicted and experimental affinity values.

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250 Trips on the Oxford Tube: what I’ve learnt

The Oxford Tube is a bus service that shuttles people between Oxford and London taking approximately 1 hour and 30 minutes. I have now taken the bus over 250 times which is approximately 375 hours or a fortnight of my life.

In this time spent on the bus, I have discovered some tips and tricks that make the journey ever so slightly more bearable. I shall share them so that others can optimise their experience. Enjoy!

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GitHub.dev: Just press “.”

GitHub.dev is an incredibly useful feature in GitHub which allows you to view and edit code directly on the browser as a remote VSCode session.

To access this remote VSCode session, either:

  1. Press “.”
  2. Change “.com” to “.dev” in the URL

This is a great way to quickly explore someone’s code without having to clone it onto your machine or go through the GitHub UI.

Coding a Progress Bar for your Google Slides Presentation

Presentations are a great opportunity to explain your work to a new audience and receive valuable feedback. A vital aspect of a presentation is keeping the audience’s attention which is generally quite tricky I have found (from experience).

One thing that I have noticed other presenters using, which has helped maintain my focus, is an indication of the progression of the presentation. Including in your slides information that there are only a few slides remaining, encourages the listeners to keep their focus for a little longer.

Instead I will show you how to do it using Apps Script, Google’s cloud platform that allows you to write JavaScript code which can work with its online products such as Docs or Slides.

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Code your own molecule sketcher in 4 easy steps!

Drawing molecules on your laptop usually requires access to proprietary software such as ChemDraw (link) or free websites such as PubChem’s online sketcher (link). However, if you are feeling adventurous, you can build your personal sketcher in React/Typescript using the Ketcher package!

Ketcher is an open-source package that allows easy implementation of a molecule sketcher into a web application. Unfortunately, it does require TypeScript so the script to run it cannot be imported directly into an HTML page. Therefore we will set up a simple React app to get it working.

The sketcher is very sleek and has a vast array of functionality, such as choosing any atom from the periodic table and being able to directly import molecules from either SMILES or Mol2/SDF file format into the sketcher. These molecules can then be edited and saved to a new file in the chemical file format of your choosing.

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Meeko: Docking straight from SMILES string

When docking, using software like AutoDock Vina, you must prepare your ligand by protonating the molecule, generating 3D coordinates, and converting it to a specific file format (in the case of Vina, PDBQT). Docking software typically needs the protein and ligand file inputs to be written on disk. This is limiting as generating 10,000s of files for a large virtual screen can be annoying and hinder the speed at which you dock.

Fortunately, the Forli group in Scripps Research have developed a Python package, Meeko, to prepare ligands directly from SMILES or other molecule formats for docking to AutoDock 4 or Vina, without writing any files to disk. This means you can dock directly from a single file containing all the SMILES of the ligands you are investigating!

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ORDER!: Returning bond order information to your docked poses

John Bercow Order Remix - YouTube

Common docking software, such as AutoDock Vina or AutoDock 4, require the ligand and receptor files to be converted into the PDBQT format. Once a correct pose has been identified, the pose will be produced also as a .pdbqt file.

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