Reflections on the 2019 Festival of Genomics conference in London

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For the third year in a row, I attended the Festival of Genomics conference in London. This year saw the conference change venue, moving from the ExCel Arena to the Business Design Centre in Islington.

The new venue was notably smaller leading to many sessions being heavily overcrowded. There were also fewer 'fun' activities compared to previous years. No graffiti wall and no recharging stations (massage stands and power points for phones).

The opening keynote was given by Professor Mark Caulfield (Chief Scientist at Genomics England

From 100K to 500K

Reflecting on the completion of the 100,000 Genomes Project, Professor Caulfield revealed that the 100,000th genome was completed at 2:40 am on the 2nd December.

He also shared details that at the peak, the project was completing 6,000 genomes a month and it has now reached 103,311 genomes.

The next phase will see 500,000 genomes completed within the NHS over the next five years, with an 'ambition' to go on to sequence five million genomes.

Looking at the global picture of human genome sequencing, Professor Caulfield projected that there will be 60 million completed genomes by 2023.

I wrote more about the conference in a blog post for The Institute of Cancer Research:

Fun at the Festival: a mini-report of the 2018 Festival of Genomics in London

Graffiti wall at the Festival of Genomics

Graffiti wall at the Festival of Genomics

Last week I once again attended the excellent Festival of Genomics conference in London. As before, I was attending in order to produce some coverage for The Institute of Cancer Research (where I work).

I really enjoy the mixture of talks at this conference which always has a strong leaning towards medicine in general and the rapid integration of genomics in the NHS in particular. This was a topic I explored in more detail in a blog post last year for the ICR.

I like how the conference organisers, Front Line Genomics, make an effort to ensure the conference is fun and engaging. It is easy to dismiss things like a 'grafitti walls' and 'recharge stations' (where you can power up your mobile phone and get a massage) as gimmicks, but I think they add to a feeling that this is a modern and vibrant conference.

NHS meets NGS

Opening the conference was a presentation from Sir Malcolm Grant, the Chairman of NHS England. He presented an update on Genomics England's 100,000 Genomes Project.

Sir Malcolm noted that consent is such an important part of this project as participants are consenting to provide information that may affect others, e.g. their children and heirs. He stressed the importance of ensuring public trust and support as the project moves forwards.

Although initial progress towards achieving those 100,000 genomes may have been slower than some would have liked, work has been accelerating. The project has taken almost five years to reach the halfway point but is now on course to reach the 100K milestone within the next 12 months.

The following day saw Genomics England's Chairman, Sir John Chisholm, take to the stage for a chat with Carl Smith (Managing Editor of Front Line Genomics). He stressed that people should think of the 100,000 genomes project as a "pilot for the main game", i.e. the routine sequencing of patients within the NHS.

Rigged for silent running

The conference has four 'stages' but as the whole area at the ExCel Area is just one big open space, they make use of wireless headphones to have conference areas which are effectively silent to people walking past.

In addition to headphones being left on each seat, there are also many additional headsets that can be given out to people who are just standing by the sides of the 'stages' to more casually listen in to each session.

When genomics meets radiotherapy

This year the ICR was honoured with our own conference session in which four early-career researchers talked about how they used genomics data in their own areas of cancer research.

I have writen a Science Talk blog post for the ICR that focuses on a presentation at the conference by Dr James Campbell, who is a Lead Bioinformatican at the ICR. He is using genome data from almost 2,000 patients that have undergone radiotherapy treatment for prostate cancer, in order to develop a model which predicts how well a new patient — given their particular set of genotypes and clinical factors — will respond to radiotherapy.

You can read the blog post here:

What did I learn at the Festival of Genomics conference? →

Last week I attended the excellent Festival of Genomics conference in London, organised by Front Line Genomics. This was the first time I had been to a conference as a communications person rather than as a scientist…something that felt quite strange.

In addition to live-tweeting many talks for The Institute of Cancer Research where I work, I also recorded some videos of ICR scientists on the conference floor. All were asked to respond to the same simple question: Why is genomics important for cancer research?. You can see the video responses on the ICR's YouTube channel.

I also made a very short video to highlight one unusual aspect of the conference…the talks were pretty much silent. Wireless headphones worn by all audience members meant that there was no need to amplify the speakers…and therefore no need for the four different 'lecture theatres' to actually have any walls!

 

My first ICR blog post!

My final task was to write a blog post about some aspect of the conference. Before the conference started, I thought I might write something that was more focused on genomics technologies. However, I was surprised by how much of the conference covered genomics as part of healthcare.

In particular, I was left with the sense that genomics is finally delivering on some of the promises made back in 2003 when the human genome sequence was published. One of the target areas that was mentioned in this 2003 NIH press release was 'New methods for the early detection of disease'.

This is something that is now possible with whole genome sequencing being deployed as part of the 100,000 genomes project (undertaken by Genomics England). The ability to screen a patient for all known genetic diseases leads to many concerns and challenges — you should see Gattaca if you haven't already done so — but it was heartening to see how much groundwork has been put in to stay on top of some of these issues.

This is my first proper blog post for the ICR, and if you are interested in finding out more, please read my post on the ICR's Science Talk blog:

Concerning the gender ratio of speakers at the 2015 Genome Science Meeting

The Genome Science 2015 meeting has announced their speaker line-up. At the time of writing, not all of the speaker positions are finalized, but currently the published agenda reveals:

  • 13 men
  • 9 women

So currently 41% of the speakers are women which is excellent. Hoping that the remaining 15 slots keep this conference free from notable gender bias.

About my idea of a 33% target for women speakers at genomics conferences…

Last week I wrote a post on the subject of gender bias at genomics/bioinformatics conferences. I suggested a figure of 33% might make for a minimum target for the proportion of women (and men) who give talks at such conferences. I also went so far as to end that post by saying:

I don't attend many conferences, but from now on I won't be attending any if at least 33% of the talks are not by women.

At the time that I wrote this, I knew that I was going to be speaking at a genomics conference myself later this year. What I didn't know at the time, was the gender ratio of speakers at this conference. That information only came to light this week. So what is the proportion of talks by women at this conference?

28.2%

If you're quick on the uptake, you will notice that 28 < 33 So what did I do? Well, I wrote to the conference organizers and explained my position and told them that I would like to withdraw my speaking role. I also suggested that they find a woman to take my place (and offered a suggestion of a female co-worker who has worked on the very project that I was intending to talk about).

The conference in question is the new Festival of Genomics that will take place in California in November. This is the second Festival of Genomics conference organized by Front Line Genomics and you may have read about the first conference in this series that recently took place in Boston. This conference was very well received (e.g. see this, this, or this) and so I was very much looking forward to speaking in November (especially as this was the first time that I have been asked to speak at a conference).

The current list of speakers shows 66 men and 26 women. It's possible that these numbers might change slightly; adding just 7 more women speakers, or replacing only 5 male speakers with women would be enough to reach my suggested 33% target.

I have had several productive exchanges with Front Line Genomics about this issue. They acknowledge the problem and seem to genuinely want to do something about it to reduce gender bias in this field. I'm confident that subsequent conferences that they organize will do an even better job at representing women in speaking roles. It also must be said that they are doing much better than most genomics conferences and 28% is higher than the current proportion of women in senior roles at most genome institutes. Once again, I want to reiterate that I have found Front Line Genomics to be extremely open about this issue, and I genuinely believe that they are receptive to suggestions that might improve the situation in future.

What can be done?

If you are a male scientist who is concerned by the current level of gender bias at genomics conferences, and if you are ever invited to give a talk at such a conference, then you do have the power to help change the situation. If you learn that women speakers are going to be underrepresented, you can withdraw your speaking position and instead make some suggestions of female scientists to take your place. You can also raise this issue when first invited to speak. If conference organizers received responses from all potential speakers saying 'I will only talk if your conference has an unbiased gender ratio of speakers', then this could change the situation dramatically.

Time to conclude this post by saying (once again): I don't attend many conferences, but from now on I won't be attending any if at least 33% of the talks are not by women.

The problem with posters at academic conferences

I recently attended the Genome Science: Biology, Technology, and Bioinformatics meeting in the UK, where I presented a poster. As I was walking around, looking at other people's posters, I was reminded of the common problem that occurs with many academic posters. Here are some pseudo-anonomous examples to show what I mean (click images to enlarge):

The problem here is not with the total amount of text — though that can sometimes be an issue — but with the width of the text. These posters are 84 cm (33 inches) wide, and it is not ideal to create text blocks that span the entire width of the poster. The reasons behind this are the same reasons why you never see newspapers display text like this…we are not very good at reading information in this manner.

To quote from Lynch & Horton's Web Style Guide; specifically the section on Page Width and Line Length:

The ideal line length for text layout is based on the physiology of the human eye. The area of the retina used for tasks requiring high visual acuity is called the macula. The macula is small, typically less than 15 percent of the area of the retina. At normal reading distances the arc of the visual field covered by the macula is only a few inches wide—about the width of a well-designed column of text, or about twelve words per line. Research shows that reading slows as line lengths begin to exceed the ideal width, because the reader then needs to use the muscles of the eye or neck to track from the end of one line to the beginning of the next line. If the eye must traverse great distances on a page, the reader must hunt for the beginning of the next line.

In contrast to the above examples, there were a couple of posters at the #UKGS2014 meeting that I thought were beautifully displayed. Bright, colorful, clearly laid out, not too much text, and good use of big fonts. Congratulations to Warry Owen et al. and Karim Gharbi et al. for your poster presentation prowess!

Thoughts on the supply of bioinformatics services and training in the UK

I am currently at the 2014 UK Genome Sciences meeting (hashtag #UKGS2014). It has been a long time since I have been at a UK science conference and it has been good to meet old colleagues and acquaintances who I have known from various stages of my career.

From informal chats with various people, it seems that UK universities are tackling their bioinformatics needs in different ways. Some have specialized facilities that try to meet the bioinformatics need from local users (and potentially from those further afield). E.g. the University of Surrey has a Bioinformatics Core Facility, Newcastle University has a Bioinformatics Support Unit, and here at Oxford there is the Computational Biology Research Group.

These examples represent core facilities with dedicated staff. An alternative approach is to bring together — physically or virtually — existing bioinformatics talent, with a view that they will be able to help others. This is the strategy taken by the new Bioinformatics Hub at the University of Sheffield, which brings together six talented folk who are based in different departments. The success of strategies like this may heavily depend on having enough skilled bioinformatics faculty who also have enough time to help others.

Other universities seem to lack any central pooling of bioinformatics expertise, and instead rely on people doing bioinformatics themselves or outsourcing it to places like TGAC. The former approach (doing it yourself) will be fine for some people, particularly those who are comfortable learning new computational skills themselves, but this will not be a good fit for everyone. 

If you are not outsourcing your bioinformatics and you don't have the necessary skills yourself, then the other approach is to attend one or more training courses. Three places that seem to be leading the field for bioinformatics training are TGAC, CGAT, and Edinburgh Genomics…and all three have a heavy presence at this conference.

Depending on your definition, bioinformatics has been around — as either a recognized skill set, or a field of study — since the early 1990s. The number of people who might consider themselves a bioinformatician has probably grown exponentially since then. Likewise, the demand for skilled bioinformaticians, or for facilities that offer bioinformatics services and training, continues to grow. Clearly, there are different ways of meeting this demand.

The current diversity of approaches to bioinformatics services and training presumably is a reflection on the local supply of, and demand for, such services. If you are about to join a new university, and if you plan on needing some bioinformatics help at some point, it may be useful to first find out more about that university's bioinformatics strategy.

My poster for the UK Genome Sciences meeting is about a new version of our IMEter software

One of the many projects I am involved with looks at Intron-mediated enhancement (IME) of gene expression. Our collaboration with Alan Rose at UC Davis has been a fruitful one, and has led to the development of computational tools that can predict how much an intron might enhance expression.

The initial version of what we called 'the IMEter' was published in 2008 and an improved v2.0 version was published in 2011. The online version of this software only lets you test Arabidopsis introns…not so useful when there are now so many different sequenced plant genomes.

We addressed this limitation in a new — as yet unpublished — v2.1 version which is available online. IMEter v2.1 can now test the expression enhancing ability of introns from 34 different plant species.

The new IMEter is the subject of my poster at the forthcoming UK Genome Sciences meeting in Oxford. The poster, available below via Figshare, explains a little more about how the new version of the IMEter came about. It also discusses some of the problems that arise in trying to adapt a software tool from working with one, very well annotated, genome, to working with many different genomes of varying quality.