Introducing a Vegan to Protein

Introducing a Vegan to Protein

As a vegan, I am undoubtedly familiar with protein and how important it is to our survival – even more so now that I have been studying it for my PRACE Summer of HPC Internship. More specifically, I have been researching KRAS, a protein that is an oncogenic mutant – with an oncogene being something with the potential to cause cancer and a mutant being an organism resulting from an instance of mutation.

Since my introductory blog post last week, I have learnt so much! Our training week at CINECA consisted of learning an array of useful skills that were all new to me – but which I hope become much more familiar as I progress through this internship. The week started with an introduction to Linux and progressed to parallel programming with MPI and also to OpenMP later on. The training period in Bolgna then finished with an introduction to GPU‘s and to some visualisation programs called Paraview and Blender. I very much enjoyed this visualisation aspect after having concentrated on pure coding earlier on in the week- especially because I enjoy making and looking at scientific simulations. During our visit to CINECA, we were also able to visit the supercomputer there.

This is a photo of myself and the other 2019 PRACE Summer of HPC interns and coordinators. This was on our first day at CINECA, Italy. Source: CINECA.
This photo is from the supercomputer at CINECA, Italy. I was fascinated by the sheer number of cables required for each of the machine units!

The first institution I was introduced to after arriving in Greece was the Biomedical Research Foundation, BRFAA, where the majority of my time will be spent. My first task was to write a report on the various inter- and intramolecular forces found in proteins and in protein-ligand complexes. Proteins consist of multiple amino acids that are all held together via peptide bonds. These proteins can fold and hence form an enormous range of differnet structures. It is these configurations of the chains of amino acids that helps to determine the protein type.

After finishing this report, the second assigned task was to complete an online tutorial in order to learn about NAMD, a parallel molecular dynamics code, and molecular dynamics simulations. This tutorial gave such useful insight into the world of simulations and introduced me to the range of possibilities available with this program, and others like it.

This is a video I made on my first day before I arrived at the BRFAA in Athens.

My third week of the Summer of HPC internship was located at GRNET, where the supercomputer, ARIS, is managed. The week consisted of learning a multitude of new skills and the continued support and guidance increased my confidence when using new software. We completed tutorials in Gromacs and were taught about important parameters and initialisation steps when creating and studying proteins. In addition, we were also lucky enough to be able to visit ARIS, the supercomputer, itself. Thanks to PRACE Summer of HPC, this visit made it the second supercomputer I had visited in just three weeks! A photo of me visiting ARIS is the featured photo for this blog!

Next week, from Monday 22nd July, I will return to work at the Biomedical Research Foundation. The week will consist of learning more about my final project and becoming more familiar with the molecular dynamics simulations that I will be working with. This will be the final training week, before officially starting work on my final project and I am very excited to continue learning more about KRAS, the protein I will be studying.

I am very much looking forward to the upcoming weeks and would love to share my journey with you. You can stay updated with my blog posts throughout the summer and I would love to hear what you are doing this summer as well! Is it related to supercomputers too or maybe another area of study? You can leave comments below as I would love to read about all of your plans and projects!

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6 comments on “Introducing a Vegan to Protein
  1. Collette says:

    Loving it! Keep it up Beckie ❤️

  2. Harry says:

    That all sounds amazing, Beckie! I look forward to reading about your final project soon. What’s been your favourite part so far?

    • Rebecca Lait says:

      Thank you so much Harry! I can’t wait to update you on it! I think my favourite part has been being able to use VMD (visual molecular dynamics) to be able to visualise the proteins in order to learn about their structure. I talk more about this in my next blog post too which should be up by the end of the week! In addition, I am so grateful for doing an internship that allows me to connect to the ARIS supercomputer here is Greece.

  3. Caroline lait says:

    This looks like a great project! You seem really motivated and look like you’re doing really well! What a great opportunity from PRACE!

    • Rebecca Lait says:

      Thank you! I have really loved learning about the biochemistry that governs the protein’s structure and learning about how to perform the molecular dynamics simulations. I am so grateful to PRACE for this opportunity and would recommend the summer internships to everyone!

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