With the university now working remotely, and our group working entirely on linux systems, I figured that now would be a good time to share some useful SSH commands to streamline remote access. This is far from an exhaustive list, but will hopefully serve as a useful starting point for anybody who finds themself needing to work remotely on a linux system.
Continue readingCategory Archives: How To
Using SLURM a little bit more efficiently
Your research group slurmified their servers? You basically have two options now.
Either you install all your necessary things on one of the slurm nodes within an interactive session, e.g.:
srun -p funkyserver-debug --pty --nodes=1 --ntasks-per-node=1 -t 00:10:00 --wait=0 /bin/bashand always specify this node by adding the ‘#SBATCH –nodelist=funkyserver.cpu.do.work’ line to your sbatch scripts or you set up some template scripts that will help you to install all your requirements on multiple nodes so you can enjoy the benefits of the slurm system.
Here is how I did it; comments and suggestions welcome!
Step 1: Create an sbatch template file (e.g. sbatch_job_on_server.template_sh) on the submission node that does what you want. In the ‘#SBATCH –partition’ or ‘–nodelist’ lines use a placeholder, e.g. ‘<server>’, instead of funkyserver.
For example, for installing the same conda environment on all nodes that you want to work on:
Continue readingConsistent plotting with ggplot
Unlike other OPIGlets (looking at you, Claire), I have neither the skill nor the patience to make good figures from scratch. And making good figures — as well as remaking, rescaling and adapting them — is incredibly important, because they play a huge role in the way we communicate our research. So how does an aesthetically impaired DPhil student do her plotting?
Continue readingA few more reasons why UNIX is awesome
One could easily find dozens of reasons for which UNIX — mainly Ubuntu — is simply, the best operating system. Although I remember people in my proximity mentioning this for ages, it’s been only a few months that I’ve realized what are the true advantages. Helpful for this were all the people teaching/demonstrating in various modules during my first year in SABS/DTC: quite often we would be asked to do something in the console rather than by clicking the mouse. In the meanwhile, I’d wonder why using the console can be better from a nice, user-friendly GUI (i.e. Windows…). Tools like sed, grep, tar and of course alias-ing form a quick answer. I will not argue more about these but demonstrate two more tools/tricks.
Continue readingCombining Inset Plots with Facets using ggplot2
I recently spent some time working out how to include mini inset plots within ggplot2 facets, and I thought I would share my code in case anyone else wants to achieve a similar thing. The resulting plot looks something like this:
Python Handout
Many OPIGlets extensively use Jupyter (in either Notebook or Lab flavour) to prototype and present their work. However, as project progress frequently notebooks are converted into regular python files for a number of reasons, losing the notebook functionality.
Wouldn’t it be nice if we could combine some of the benefits of Jupyter notebooks (not least the ability to present both code & results naturally) with regular python files?
Enter Python Handout.
Python Handout was recently (5th August 2019) released by Danijar Hafner and allows Python scripts to be converted into handouts with Markdown comments and inline figures (see above picture).
Installation is via pip (pip3 install -U handout) and Python Handout supports python 3 scripts.
While I’ve not used Handout much (yet), I will definitely be experimenting more in the coming weeks.
How to Iterate in PyMOL
Sometimes pointing-and-clicking just doesn’t cut it. With PyMOL’s built-in Python interpreter, repetitive actions are made simple.
Continue readingConstrained Embedding with RDKit
This blog post explores the RDKit function ConstrainedEmbed.
Continue readingA Brief Introduction to ggpairs
In this blog post I will introduce a fun R plotting function, ggpairs, that’s useful for exploring distributions and correlations.
Quick Python tricks
It’s always fun when you stumble across something in your programming toolkit that you had never noticed. Here are three things I’ve recently enjoyed learning.
- Ternary syntax
a = int(raw_input()) is_even = True if a % 0 == 0 else False
- Enumerate
I’ve been looping over the length of my list, all these years, like a chump. It turns out you can do this:
for index, item in enumerate(some_list):
# now the index of each item is available as well as the item
# Don't do do this
for index in range(len(some_list)):
item = some_list[index]
- for… else
Every so often, you really need to know that a for loop has run to completion. That’s what for…else is for!
for item in iterable:
if item % 0 == 0:
first_even_number = item
else:
raise ValueError('No even numbers')