“Yes! Yes! But why? But why?”

This was what Klaus Schulten heard from an experimental colleague after he had told him what he’d found and it neatly highlights one the key advantages of molecular simulation; you can see in extraordinary detail what is happening or, as Klaus put it in his National Lecture last night,

It doesn’t only agree with the experiment, it tells you more.

Implicit in that statement is that the simulation must first agree with experiment, which is pretty obvious, but still worth saying! The best way of achieving this, in my experience, is that you work closely with experimentalists, preferably from the beginning of a project. Klaus did not explicitly spell this out it but it was clear from his lecture that this is what he always tries to do.

He also showed several very nice examples from ankyrin repeats to cadherins to aquaporins where simulations from his group have made predictions that were subsequently confirmed by experiment. Predictions of this kind are, I think, the possible the best demonstration of the utility and power of computer simulation in molecular biophysics. Another key theme was choosing the appropriate level of description for any simulation, or as Klaus put it,

Chemical detail is important.

This is true; we must resist the urge to discard detail to make our simulations simpler and faster at the expense of biological accuracy and instead chose the most appropriate description for the system at hand.

Given the audience was mostly experimentalists it was striking how long Klaus spent talking about the tools i.e. the software, or to be specific the molecular dynamics (NAMD) and visualisation (VMD) codes that his group have developed and now supported for around twenty years. But then again these are important and both NAMD and VMD are very widely used so why not talk about them?

What is unusual is that both codes have a full-time developer which allows them to make regular releases, have good documentation and also nurture a community of academic contributors. I think the question this raises should be why don’t more academic codes have this degree of support? And, in tandem with that, why don’t we as a community use more software engineering tools, as encouraged by Software Carpentry and institutes like the Software Sustainability Institute in the UK.

That Klaus ended with an advertisement for a training course is especially poignant for me; I attended the first NAMD summer school back in 2003 and this really kick-started my PhD (I was at the end of my first year). As an aside I enjoyed the anecdotes and stories during the lecture, like the one I started with, and so I thought I’d end with one of my own. During the summer school in 2003 I have a vivid memory of Klaus addressing us all and booming out “if you use molecular dynamics to calculate free energies you are braindead!”. So when I saw those free energy profiles last night I smiled. I’m glad that even distinguished scientists can change their minds.


A Twitter phase transition?

fowler imageThis is the biggest conference I ever go to; this morning there were two symposia and six platform sessions all running in parallel and, as often seems to be the case, the two I was interested in were about a five minute walk apart. In a, platform each speaker has just three minutes at the end of their talk where a fellow scientist may ask that question that saves six months work. Sometimes there are no questions from the floor.

Imagine a different, a more, dare I say it, 21st century approach. And yes, it involves Twitter. Imagine that, as you are speaking, members of the audience are posting questions or links to helpful papers on Twitter tagged with an appropriate hashtag. Maybe the feed is projected on a second screen so everyone, including the speaker and chairs, can follow it during the talk. In the question session the chair could simply pick out a few questions from the feed for the speaker to elaborate on. Or maybe the speaker tries to answer them as they go along. Either way you’d come away with having had a lot more interaction with your community, and almost as important, a permanent record of the questions and suggestions. (Can you remember word-for-word the questions you are asked after you’ve given a talk? I can’t.) This might sound like fantasy but it isn’t. I’ve been to smaller conferences, in computer or computational science, where this isn’t far off the norm. See here for an interesting article on scientific tweeting.

Or, imagine you are sitting in a session and you see in the feed that the talk in the other session you were interested in is actually exactly what you’ve come all this way to see so you swap. Or, you see that the other session down the hall is running five minutes late so you can grab a coffee. Or, that a room key card for the hotel you are staying in has been handed in and so you check your pocket…

So how are we doing? Well in the last week there have been 206 tweets using the #bps15 hashtag from 98 accounts. That is not many, it works out at about one per thirty people attending. To get a live updating feed let’s say you need about one per minute. That works out at over 3000 over the course of the conference (I think this is a lower limit). So we are about an order of magnitude below that simple estimate. Why? Well I think because most of us don’t use social media like Twitter and, if you do, you know this and so are aware that no-one will read your tweets. In which case, what is the point? In other words we are below the tipping point (or perhaps I should say phase transition?).

Are things getting better? Last year there were 518 tweets using the #bps14 hashtag during the whole conference. So, yes, it looks like the trajectory is upwards. Of course Twitter isn’t the only way of doing this. Maybe the social aspects to the new 360 app will take on the mantel, but I doubt it.

There have been five #bps15 tweets since I started writing this half an hour ago. Not bad, but not enough to change how this meeting works either.

Where shall we have lunch?

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 Pot Belly 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.lunchblog1 lunchblog2