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CECAM Macromolecular simulation software workshop

computing, meetings, molecular dynamics, software carpentry

I’m co-organiser of this slightly-different  in October 2023 at the Forschungszentrum Jülich, Germany. Rather than following the traditional format of 3-4 day populated by talks with the odd poster session, this is an extended workshop made up of six mini-workshops. Since it is focussed on python-based tools for biomolecular simulations, of which there are an increasing number, the first mini-workshop will be a bootcamp that I will be lead instructor on (helped by David Dotson from ASU). I’m also leading the next mini-workshop on analysing biomolecular simulation data.

Is Software a Method?

bps15, computing

Last month I went to the . As a   I was interested not only in my research area, but also in how my community viewed software. Were there talks and posters on how people had improved important pieces of community software? After all, there would be talks and posters on improving experimental methods. Turns out, not so much. Click to read the full post.

 

data-on-acid

HackDay: Data on Acid

computing, meetings, skills

Every year the (SSI) run a brilliant meeting called the , usually in Oxford. This is an lasting two days. At first glance it doesn’t look like it would be relevant to my research, but I always learn something new, meet interesting people and start, well, collaborations. The latest edition was last week and was the fourth I’ve attended. (Disclaimer: for the last year-and-a-bit I’ve been which has been very useful – this is how I managed to train up to be a Software Carpentry Instructor. Alas my tenure has now ended).

For the last two years the workshop has been followed by a hackday which I’ve attended. Now I’m not a software developer, I’m a research scientist who uses million-line community-developed codes (like GROMACS and NAMD), but I do write code, often python, to analyse my simulations and also to automate my workflows. A hackday therefore, where many of the participants are research software engineers, pushes me clear out of my comfort zone. I remember last year trying to write python to access GitHub using its and thinking “I’ve never done anything like this before and I’ve no idea what to do.�?. This year was no different, except I’d pitched the idea so felt responsible for the success of the project.

The name of the project, , was suggested by Boris Adryan and the team comprised myself, , , and . The input was data produced by a proof of principle project I’ve run to test if I can predict whether individual mutations to S.aureus DHFR cause resistance to trimethoprim. The idea was to then turn it into abstract forms, either visual or sound, so you can get an intuitive feel for the data. Or it could just be aesthetic.

To cut a long story short, we did it, it is up and we came third in the competition! In the long term I’d like to develop it further and incorporate it into my volunteer crowd-sourced project, , that aims to predict whether bacterial mutations cause antibiotic resistance or not (when it is funded that is).

lecture

BPS15: Yes! Yes! But why? But why?

bps15, meetings

As part of my series of guest blogs at the 59th Annual Meeting of the US Biophysical Society I wrote some thoughts on the National Lecture by Klaus Schulten that was last night. To find out what the quote refers to, you’ll have to follow …

Update: you can now .

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BPS15: Twitter and conferences: an ideal match or a nuisance?

bps15, meetings

I’m at the of the Meeting in Baltimore which is large (6,500 scientists) with multiple parallel sessions. You might have thought that Twitter would be the ideal platform for providing a feed for all the questions, reactions and suggestions but very few people are using it, although there is definitely more tweeting compared to last year. You can read my musings on it . This is part of my series of posts as one of their guest bloggers.

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BPS15: Where shall we have lunch?

bps15, meetings

The most useful and enjoyable part of coming to the Annual Meeting for me is not the talks, nor is it the poster session nor even the free T-shirts. It is meeting up and talking with fellow scientists. But one must first solve an important question that Douglas Adams describes better than I ever could in his book The Restaurant at the End of the Universe:

The History of every major Galactic Civilization tends to pass through three distinct and recognizable phases, those of Survival, Inquiry and Sophistication, otherwise known as the How, Why, and Where phases. For instance, the first phase is characterized by the question ‘How can we eat?’ the second by the question ‘Why do we eat?’ and the third by the question ‘Where shall we have lunch?’

My favourite place, recommended to me back in 2011 by two friends who were at the University of Maryland at the time, is a sandwich shop. I went today to the one a few blocks on W Pratt St west of the convention centre but I’ve heard there is one in the Inner Harbor too. It’s quick, tasty and you can while away a pleasant half an hour chatting before hitting the posters.