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
Using Python in PyMOL
Decades later, we owe Warren DeLano and his commitment to open source a great debt. Warren wrote PyMOL, an amazingly powerful and popular molecular visualization tool, but it has many hidden talents.
Perhaps its greatest strength is the use of the open source language, Python, as its control language.
Continue readingBuilding More Useful Bash Scripts
If there is some set of keystrokes that you find yourself using day in, day out, you can almost certainly write something that can automate the process. This could be something simple that could be achieved by putting a bash alias somewhere in your ~/.bashrc:
Cryo-EM reaches atomic resolution in protein structure determination
The end of the era of crystallography has been long predicted also on this blog, but has it come now with the recent report of an atomic resolution protein structure solved by cryo–electron microscopy (cryo-EM)?
Continue readingA new Graduate students (unexperienced) guide to academic literature.
Given this is my first ever attempt at a blog post, let alone one on such a highly regarded platform I feel it’s proper that I introduce myself. Hi, my name is Maranga, I am a second-year SABS student starting my DPhil project in Small molecules, and honestly, I really don’t like reading. Especially, scientific journals. Now I can appreciate this does not bode well given my chosen career path, however, my aversion for reading is not new (shoutout to Biff, Chip and Kipper) and hopefully not permanent.
Continue reading3 Useful UNIX commands you might not know
nohup
The command nohup (stands for “No hang up”) allows your script to run even if you quit the terminal. It can be very useful, especially if your terminal has been opened through ssh and you have a dodgy connection. It can be used as follows:
nohup python my_script.py > log.out &
nohup will automatically append the output from your script to a file named nohup.out. By adding the > log.out part of the command you can save the output to a different file of your choice.
NeurIPS 2020: Chemistry / Biology papers
Another blog post, another look at accepted papers for a major ML conference. NeurIPS joins the other major machine learning conferences (and others) in moving virtual this year, running from 6th – 12th December 2020. In a continuation of past posts (ICML 2020, NeurIPS 2019), I will highlight several of potential interest to the chem-/bio-informatics communities
The list of accepted papers can be found here, with 1,903 papers accepted out of 9,467 submissions (20% acceptance rate).
In addition to the main conference, there are several workshops highly related to the type of research undertaken in OPIG: Machine Learning in Structural Biology and Machine Learning for Molecules.
The usual caveat: given the large number of papers, these were selected either by “accident” (i.e. I stumbled across them in one way or another) or through a basic search (e.g. Ctrl+f “molecule”). If you find any I have missed, please reach out and I will update accordingly.
Continue readingSpeaking about Sequence and Structure at a Summit
A couple of weeks ago I was lucky enough to be asked to speak at the 5th Computational Drug Discovery & Development for Biologics Summit. This was my first virtual conference – it was a shame I didn’t get to visit Boston, and presenting to my empty room was slightly bizarre, but it was great to hear what people have been working on, and there’s definitely something to be said for attending a conference in fluffy socks…
Improving your Python code quality using git pre-commit hooks
Intro
I recently completed an internship during which I spent a considerable amount of time doing software engineering. One of my main take-aways from this experience was that in industry, a lot more attention is spent on ensuring that code committed to a GitHub repo is clean and bug-free.
This is achieved through several means like code review (get other people to read your code), test-driven development (make sure your code works as you are adding functionality) or paired development (have two people work together on the same piece of code). Here, I will instead focus on a useful tool that is easy to integrate into your existing git workflow: Pre-commit hooks.
Continue readingThe 10 Commandments of OPIG (Lockdown edition)
The start of Michaelmas Term means some new faces on our Zoom screens and lots of things for our new group members to get used to. To help them settle in quickly I thought I’d put together an updated edition of the 10 Commandments of OPIG, tailored towards our new reality.
Continue reading