Twitter at #ECCMID

A bit over two years ago I was a guest blogger at the US Biophysical Society Annual Meeting in Baltimore. I was disappointed by the lack of Tweeting at the conference – there were 208 tweets using the #bps15 hashtag when I wrote a blog post in which I speculated that, one day, there might be a tipping point and Twitter at large conventions would become genuinely useful.

Well, I’ve just returned from ECCMID, which is the European Congress of Clinical Microbiology and Infectious Diseases in Vienna, and it seems we are now there!. For example, on the morning of the last day, there were over 200 tweets per hour which is about 20x the level of Tweeting at BPS15. That is enough activity that it was really worth keeping an eye on the #ECCMID2017 hashtag using TweetDeck whilst sat in talks. It was especially useful when some of the talks were less relevant or interesting.

It isn’t a perfect comparison as ECCMID is a bit bigger than BPS (10,000 v 7,500) and the attendees have different backgrounds (clinical microbiologists v biophysicists), but the difference is so stark that I’d hope the increase applies across all or most large conventions.

Likewise, not everything that I wrote about in my previous post has come to pass. Yes, occasionally people did post links to papers that the speaker had just mentioned (and this is incredibly useful) and yes you got an idea of which sessions were “hot” and interesting in real-time. But the chairs were not, as far as I could see, monitoring twitter (you’d really need a session specific hashtag for that) for questions from the floor) or even tweeting themselves. Also there is a tendency, which I mostly follow as well, to be positive, upbeat and effusive on Twitter so there are lots of posts saying “Professor X is giving an amazing talk in Hall Y!”, rather than “I was a bit disappointed that Professor X just did the same talk as last year in Hall Y”. You’d be forgiven for thinking all the talks were interesting and engaging if you just followed the hashtag Twitter, but of course some talks were poorly delivered or aimed at the wrong audience or were a touch too sycophantic.

So Twitter is now a useful addition to large, international conventions. Jon Otter gave a presentation at ECCMID (which, alas, I missed) on social media use by healthcare professionals and has surveyed that cohort. He found that a bit over 70% of respondents used some form of social media platform, with about 35% using Twitter. To read more, please visit his blog post. By the way, I’ve never met him in person, I only know of this work because … you guessed it, he followed me on Twitter during ECCMID and then I retweeted him during the conference.

That’s what happens.

Diagnosing antibiotic resistance: future trends?

It is Sunday, I’m in Vienna at the European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) congress. As is traditional at all large conventions, I’m sitting on the floor outside one of the halls because the organisers have put one of the most popular sessions (Gram-negative resistance) in one of the smallest rooms. A good time to record some thoughts.

I see a coming paradigm shift away from species to plasmid and, perhaps, resistance genes. Several talks this morning discussed “plasmid outbreaks” in Gram-negatives, where although you see multiple species, what is actually happening is a plasmid is hopping between species. Or worse, resistance genes embedded in a transposon are hopping between plasmids which are themselves hopping between species. The growth and transfer of such beta-lactamase (bla) genes (and probably also mcr-1) will contribute significantly to the growth of antibiotic resistance in the coming years.

This will drive the adoption of using genetics to follow and understand these outbreaks, since culture-based microbiology is species-based and so struggles to sort out what is happening in this sort of situation. Since there are many different genes involved, PCR-based methods will probably not be much help either. Second-generation sequencing (e.g. Illumina), with its relatively short reads will also struggle since it is difficult to tell where a read originates from, although it can tell you if a gene is present or not. That leaves long-read sequencing which is either expensive (e.g. PacBio) or still in development (ONT MinION). So there isn’t yet a cheap, off-the-shelf genetic approach that allows you to sequence bacterial DNA and determine how many and which plasmids are present.

Much of the current whole-genome sequencing effort is focussed on Tuberculosis with good reason: you don’t have to worry about detecting plasmids since there is little horizontal transfer and there is a huge clinical gain to be made in reducing the time to producing an antibiogram. But ultimately, the skills and knowledge here will have to be transferred to Gram-negatives.

So who is going to do it?

The answer to this is, I think, not obvious since there are commercial issues. Basically, any solution will require a sequencing method that produces long reads. The key questions are: (i) will company A who own a long-read sequencing method license it to company B for a “reasonable” amount, if not (ii) will company A develop such a clinical microbiology workflow itself? I worry this will retard the development of a genetics-based microbiology that can follow a resistance-gene or plasmid-mediated outbreak.

You get a very clear illustration of the importance of commercial considerations walking around the Exhibition Hall here at ECCMID; the vast majority of the stands are for diagnostic solutions and there are very few stands marketing antibiotics, even to the point where companies, whose name you would historically associate with antibiotics, appear to only be marketing diagnostics.

Analysing Simulation Data CECAM Workshop, Jülich, 14-15 October 2015

IMG_0987 (1)

This two day workshop on Analysing Simulation Data was part of the larger CECAM Macromolecular Simulation Software Workshop at the Forschnungzentrum, Jülich that I co-organised. It was the second workshop and immediately followed an introductory Software Carpentry workshop.

Prior to a few years ago I analysed all my simulation data using either VMD, often by writing Tcl scripts, or using a GROMACS g_tools, if one was available. Then I started using MDAnalysis, a python module. This enabled me to do two things: first MDAnalysis has its own analysis routines and therefore you could often do all the analysis you needed to in a simple python script. More powerfully, since it can read many different simulation formats, it can also act as a gatekeeper to the huge range of powerful python modules. The net result is I have been able to analyse my data in ways that previously would not have been possible (i.e. I would have had to write C code.)

For example we presented a paper (open access) at a Faraday Discussion meeting where we used the image-processing tools in scikt-image to analyse whether the presence of a small cell-signalling protein retarded the rate at which a three-component lipid bilayer phase separated. I posted some example code on GitHub. In other work, not all published, I have used scipy and numpy to, for example, calculate the power spectra of fluctuations in lipid bilayers (using fast fourier transforms).


The workshop brought together researchers, especially PhD students and postdoctoral researchers, and academic software developers.

The hope was that the researchers would come out of it feeling not only more confident about developing their own software and maybe even start contributing to an academic open source project but also that they could use the python ecosystem to analyse their data in new and interesting ways.

For the developers the hope was they would get to talk to a range of current and prospective users and gain a better understanding of how people are using their code (and maybe pick up some contributors along the way)



I felt that a traditional didactic approach wouldn’t work; so no sessions of talks + questions. In the end I stole shamelessly from the excellent series of Collaborations Workshops run by the Software Sustainability Institute in the UK. The workshop worked towards and cumulated in a HackDay. I now believe HackDays are great ways of not only teaching but also as a way of building teams — I am writing a post of this for the SSI and will link to it here when it is up.

IMG_0988 (1)I invited developers from two biomolecular python projects: MDAnalysis and pmx. Given more budget I would have loved to invite other developers, e.g. from mdtraj. On the first day each project gave a short talk followed by around two hours of guided tutorial. Then at the end of day one, I invited participants to present analysis problems drawn from their own research that they would like to solve. Teams were allowed to form around six ideas. On day two these teams had around six hours to solve their problem, before presenting their solution to the rest of the workshop. The winning project, MDARTINI, aimed to make MDAnalysis more aware of the coarse-grained forcefield, MARTINI.



  • 94% of participants enjoyed the workshop,
  • 100% learnt something useful that will help their research
  • 100% would recommend a workshop like this one to other researchers.
  • 88% feel confident enough to contribute to an academic open source project.

“I now understand enough to try using the following tools”

I then asked “I now understand enough to try using the following tools”. Given most participants had heard of MDAnalysis, but only a few had used it – and very few had heard of pmx – this is an encouraging shift. This was then followed up by: “I intend using the tools and methods to help my research”. Usually, the answers are a bit more pessimistic as people might understand a tool, but not have any intention of using it. Here, though it goes the other way.


“I intend using the tools and methods to help my research.”

To try and understand which parts of the workshop went well: “I enjoyed the following components of the workshop”. So, talks were ok, then the HackDay but the tutorials and meeting other researchers were most highly rated.


“I enjoyed the following components of the workshop.”

Finally, to find out if there were any practical problems I asked “The following elements contributed to making the workshop a success”.


“The following elements contributed to making the workshop a success.”

The big problem here was the network; we had better connectivity in the small hotel in Jülich. It turned out there was a problem with the wireless router in the room and this was fixed a few days after this workshop. Nor did many people like the location in Jülich, however the various coffee breaks – which we were grateful to the Software Sustainability Institute for sponsoring – and the general social atmosphere were appreciated.



Lessons for next time

This type of workshop is very complicated and plenty can go wrong. Always have a Plan B. For example, assume that not everyone will be able to install all the necessary software on their laptops so come prepared with a (linux) virtual machine image that will work in all the tutorials. And don’t assume that the network will “just work”.

Software Carpentry Workshop, Jülich, 12-13 October 2015

IMG_0944 (1)Last week, myself and David Dotson from
ASU, ran a 2 day Software Carpentry workshop to kick off the CECAM Macromolecular Simulation Software Workshop at the Forschnungzentrum, Jülich. The idea was to give participants who were less well versed in python and working collaboratively with e.g. git a crash course to bring them up to speed for the following five mini-workshops. As you can imagine, coffee and tea are essential for running an intensive bootcamp and we owe thanks to The Software Sustainability Institute for sponsoring our coffee breaks.

As we were a self-organised workshop, there was no centrally coordinated surveying of the participants to gauge their level of experience. So instead I sent out a questionnaire very similar to one I’d previously sent before the first workshop I organised back in 2012. As is often the case, the learners were more comfortable with bash and simple python, but hadn’t heard or used testing or version control. Interestingly, compared to this previous workshop a higher proportion of learners were experienced in bash and python. Both groups were drawn from the bimolecular simulation community so this may reflect an increasing level of expertise.

fig-pre-expertiseThe workshop itself was the smoothest I’ve been involved in; I think it helped that both myself and David have taught several now. Also, devoting three hours for each of bash and version control and then six hours for python (including coffee breaks) meant it wasn’t quite as rushed. The last workshop I taught was in January 2015 and the course materials have been overhauled and updated and separated from the workshop GitHub repository. The latest version of the materials seemed to work well.
It also meant I was unfamiliar with the evolution of ipython notebooks into jupyter notebooks which David used to teach. Interestingly, although there was only one helper, Charlie Laughton, we were never overwhelmed. At each workshop I have taught or organised the ratio of helpers to learners decreased, which may reflect improvements in installation and the course materials.
Finally, I was live coding on my Mac laptop and using the new Split View in Mac OS 10.11 worked really well.

That is what I thought: what about the learners? I had fifteen
responfig-post-understand-enoughses to the questionnaire which was about a two-thirds response rate. All of them agreed with the statements “I enjoyed the Software Carpentry workshop” and “I feel I learnt something useful that will help my research”, but as we know, enjoyment does not necessarily translate into learning! As before I asked two key questions. First “I now understand enough to try using the following tools/approaches.”. As you can see there is a big shift in attitude compared to before the workshop with the majority of people feeling that they understood the tools covered during the workshop.

fig-post-intend-usingBut will this translate into a change in behaviour? To try and test this I also asked
“I intend using the tools listed below to help my research”. The results are pretty similar but interestingly peoples intentions were stronger than their understanding, i.e. there was a slightly stronger response to the intention question than the understanding question. Compared to the workshop I ran in Oxford in January 2015, the shift in behaviour was more dramatic, although the two groups were drawn from different research areas so can’t be directly compared.

CECAM Macromolecular simulation software workshop

I’m co-organiser of this slightly-different CECAM workshop in October 2015 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 Software Carpentry 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?

Last month I went to the Annual Meeting of the US Biophysical Society. As a Software Sustainability Institute fellow 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 here to read the full post.


HackDay: Data on Acid

Every year the Software Sustainability Institute (SSI) run a brilliant meeting called the Collaborations Workshop, usually in Oxford. This is an unconference 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 an SSI fellow 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 API 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, Data on Acid, was suggested by Boris Adryan and the team comprised myself, Robert Haines, Alys Brett, Joe Parker and Ian Emsley. 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 on GitHub 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, bashthebug, that aims to predict whether bacterial mutations cause antibiotic resistance or not (when it is funded that is).

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

I’m at the Annual Meeting of the US Biophysical Society 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 here. This is part of my series of posts as one of their guest bloggers.

BPS15: 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.