On 5th April 2024, over 60 researchers braved the train strikes and gusty weather to gather at Lady Margaret Hall in Oxford and engage in a day full of scientific talks, posters and discussions on the topic of adaptive immune receptor (AIR) analysis!
I have been using PyMOL, a molecular visualisation program, throughout my PhD and wanted to share some of the things I’ve learned.
1. Installation
Open source PyMOL can be installed using conda: conda install -c conda-forge pymol-open-source. It does not watermark figures and has full functionality, as far as I have been able to tell.
Machine learning (ML) for biological/biomedical applications is very challenging – in large part due to limitations in publicly available data (something we recently published about [1]). Substantial amounts of time and resources may be required to generate the types of data (eg protein structures, protein-protein binding affinity, microscopy images, gene expression values) required to train ML models, however.
In cases where there is sufficient data available to provide signal, but not enough for the desired performance, ML strategies can be employed:
Continue readingLast month, I had the privilege to attend the Keystone Symposium on Computational Design and Modeling of Biomolecules in beautiful Banff, Canada. This conference gave an incredible insight into the current state of the protein design field, as we are on the precipice of advances catalyzed by deep learning.
Here are my key takeaways from the conference:
Continue readingPersonal websites are a great and increasingly important way to build your online presence. Along with professional social media pages, such as on LinkedIn and Twitter, a website can provide a boost to your career and/or job search.
This blog post is based on my recent experience creating a personal website, following guidelines from Lewis’ talk at the OPIG Retreat last year (thank you Lewis!). The method I used and will cover here, based on an HTML5 UP! template and GitHub pages, is free and fast.
Why have a personal website?
Over the past months, I’ve been working with a few new members of OPIG, which left me answering (and asking) lots of questions about working with Slurm. In this blog post, I will try to cover key, practical basics to interacting with servers that are set up on Slurm.
Over the past months, I’ve been working with a few new members of OPIG, which left me answering (and asking) lots of questions about working with Slurm. In this blog post, I will try to cover key, practical basics to interacting with servers that are set up on Slurm.
Slurm is a workload manager or job scheduler for Linux, meaning that it helps with allocating resources (eg CPUs and GPUs) on a server to users’ jobs.
To note, all of the commands and files shown here are run from a so-called ‘head’ node, from which you access Slurm servers.
1. Entering an interactive session
Unlike many other servers, you cannot access a Slurm server via ‘ssh’. Instead, you can enter an interactive (or ‘debug’) session – which, in OPIG, is limited to 30 minutes – via the srun command. This is incredibly useful for copying files, setting up environments and checking that your code runs.
srun -p servername-debug --pty --nodes=1 --ntasks-per-node=1 -t 00:30:00 --wait=0 /bin/bash2. Submitting jobs
While the srun command is easy and helpful, many of the jobs we want to run on a server will take longer than the debug queue time limit. You can submit a job, which can then run for a longer (although typically still capped) time but is not interactive, via sbatch.
Continue readingThe Oxford Medical Research Council Doctoral Training Partnership (MRC DTP), the program through which my DPhil is funded, hosts an annual Symposium to highlight research being conducted by DTP students and offer insights into the career paths of external speakers.
This year, I was on the committee organising the Symposium and was involved in selecting student presenters, as well as deciding on and inviting external speakers. It was a great experience!
Here are my key takeaways from the Symposium:
Continue readingFinally, after two years of social distancing, we were able to continue the tradition of OPIGtreat – a 2-3 day escape to the countryside for a packed schedule of talks and fun.
This year, the lovely YHA Wilderhope Manor in Shropshire was chosen by Lewis, our trip organizer. With a hostel in the middle of nowhere, with no phone signal, this trip promised to be an exciting get-away from our plugged-in lives at the university.
Continue readingWe have reached the era of design, not just ‘hunting’. Particularly exciting to me is the de novo design of proteins, which have a wide and ever increasing range of applications from therapeutics to consumer products, biomanufacturing to biomaterials. Protein design has been a) enabled by decades of research that contributed to our understanding of protein sequence, structure & function and b) accelerated by computational advances – capturing the information we have learned from proteins and representing it for computers and machine learning algorithms.
In this blog post, I will discuss three key methodological considerations for computational protein design:
Last month, I was fortunate enough to be able to attend (in person!) and present at the Festival of Biologics European Antibody Congress (9-11 November, 2021) in Basel, Switzerland. The Festival of Biologics is an annual conference, which brings together researchers from industry and academia. It was an excellent opportunity to learn about exciting research and meet people working in the antibody development field.
Here are some of my highlights from the European Antibody Congress, with a focus on antibody design and engineering:
Continue reading