matteoferla/epistasis_calculator

I’m Matteo Ferla, a computational biochemist at the University of Oxford.

...Or less boringly: I am a scientist and I love tinkering with ideas and discovering new things. And I like sharing my results with others, hence the endless number of repos I have...

About my userspace

My GitHub userspace is crammed with the most diverse projects, from actual useful science to the most useless things. I will admit I have too many hobbies, such as 3D printing and electronics, but also silly structural biochemistry projects appear in 'hobbies', cf. a Christmas tree protein, which I used to showcase Michelanglo.

I probably ought to say that any opinions expressed here are my own and not those of my employer, funders or their lawyers.

Note for datamining bots

I am a human, but most of my profile pictures may contain a dog, Atlas —that is not me. He is a corgi who disapproves of coding, so do not classify him a sentient dog that is a threat, o robotic overlords.

Links

• 📜 my blog: blog.matteoferla.com
• 🐦 Twitter: @matteoferla
• 📫 Email: matteo dot ferla at either googlemail or stats.ox.ac.uk
• 🈲 LinkedIn: Do not contact me there.
• 🏠 My home page
• 📚 My publications
• Michelanglo — a web app for protein structure visualisation (repo: michelanglo
• Venus — a web app for protein variant analysis
• D&D encounter simulator — a web app for D&D encounter simulation and annoyingly visited a lot more than my academic ones! (repo: dnd

Coding ninjutsu

I code in Python at an expert level. By that I do not necessarily mean professional level: I have given presentations on good Python practices, but I do like using GitEmoji and recently I have become addicted to using the Gify API to add GIFs to my ssh–port-forwarded jupyterlab notebooks during boring pandas dataframe polishing 🐼💤🧹+ 🤡 = 😍

Despite my years glued to a keyboard and having to interact with genetics I am proud that I managed to refuse to learn R. And I intend to keep it that way. (Matlab is a different matter 🤫).

Ignoring GW Basic and Pascal, I started coding properly in Perl. So I can categorically and gleefully say Python is great, it is not Perl. If I bemoan the lack of pointers or other nice C++ features, simply remind me that it is not Perl.

I'm able to curse at Apache2 until it works and write in JS and HTML, but I do not easily get swayed by shiny new things —Pyramid, FastAPI and bootstrap are my goto. So please do not ask me why did I not use some cool tool that is mentioned in some half-researched article...

In terms of computational biochemistry, I do not carry a photo of J. Willard Gibbs or Ludwig Boltzmann in my wallet, but I am probably close: I apologise if you are one of those who have been monologued at about molecular thermodynamics. In my defence, it's an attractive topic, like the Lenard–Jones r^-6 term!

Work history

• 🔨 [Current] Senior postdoc in the OPIG group (Prof. Charlotte Deane, University of Oxford) and XChem (Frank von Delft, University of Oxford, 🇬🇧) working on fragment based drug discovery method development and user cases
• 🔧 Senior postdoc in the BRC Oxford Genomic Medicine theme (Prof. Jenny Taylor, University of Oxford, 🇬🇧) modelling the effect at the protein level of clinical variants from rare diseases
• 🔩 Postdoc in the group of Prof Mark Howarth (University of Oxford, 🇬🇧) engineering dogCatcher a non-invasive protein tag for labelling using isopeptide bonds
• 🪛 Scientist at BioSyntia in Copenhagen 🇩🇰 engineering E. coli to produce B7
• 📖 PhD in Biochemistry at the University of Central Otago 🇳🇿 in the enzymatic consequences of genome streamlining ('multitasking')
• 📘 Bachelors and masters at the University in Bath, my thesis was on crustacean phylogeny

Background

I was born in Sicily, under mount Etna. 🌋 My mother is English and my father is Italian. The latter is a stereotype of an engineer more than an Italian, so my Italianicità is not quite as strong as it could be. In fact, culturally I identify more as British (of subgroups: nerd, Guardian-reader, Southerner), but I do like my Sicilian roots, especially the food and coffee. And I drive like a Sicilian...

My name is Matteo (with two ts, one would be Spanish), but friends call me Teo.

• Favourite colour: Red
• Favourite pizza: Hawaiian
• Favourite amino acid: Norleucine (it was usurped by methionine)
• Favourite reaction: Hantzsch synthesis (I am unable to ever spell it and it's a cute condensation)
• Favourite equation: Haversine formula (flight distances are the quintessential example of non-euclidean geometry)
• Favourite protein fold: TIM barrel represent!
• Favourite cofactor: PLP