Happy to announce that our Unix & Perl book is finally on sale!

Unix and Perl to the RESCUE! A field-guide for life scientists (and other data-rich pursuits)

At least in the UK. It will take a few weeks for US warehouses to receive stock, and we have still not received our own copies, but at least the book is out there (somewhere). Amazon is discounting the book which puts it into a more affordable price range.

It will be very strange the first time I spot it 'in the wild' by chance. If I spot someone reading it on a bus/train/plane, I wonder whether I will be tempted to say anything.

Genome sequencing projects…it’s all about the numbers

G10K-Teal-c-101209.png.scaled1000.png

So there is this project called Genome 10K. They aim to sequence the genomes of — wait for it — 10,000 vertebrate species. Impressive projects like this need impressive names, which increasingly means inserting [big number of your choice] into the project name. Don’t believe me? Well let's see what other big 'omics' sequencing projects are out there?

I wonder if there has been any confusion between the '1000 Genomes' and 1001 Genomes' projects, or the '100,000 Genomes Project' and '100K Pathogen Genome Project' ("these human genomes seem awfully small").

So where do we go after 100,000? A million of course. Although there isn’t a dedicated collaborative project for this, there is already an aim by the company Complete Genomics to sequence a million human genomes by (the end of?) 2014

So if you want to make a big splash in genomics, then you ideally need to be thinking of at least a '10M' project to begin with. Otherwise, I guess you need to look for some other 'novelty' numbers like the '959 nematode genomes' project. How about the '42 Genomes Project — dedicated to finding the ultimate answer to life, the universe, and everything.

 

Updates:

  1. 2014-10-27: now includes mention of 1KP project
  2. 2014-10-28: now includes mention of 100,000 genomes project (h/t @NazeemaFatima), which also gave me a reason to reorganize a lot of the information in this post.
  3. 2014-10-30: added 3K RGP project

 

The slow death of bioinformatics and the eternal popularity of shoes

Some time ago I was playing around with Google Trends (formerly Google Insights for Search) and I randomly decided to see how the search term bioinformatics has fared since 2004 (this is as far back as you can search for a trend). This is what I found:

Initially I was quite surprised by this and so I then performed a search for genomics, only to see the same sort of trend:

According to Google the Y-axis of these graphs reflect "how many searches have been done for a particular term, relative to the total number of searches done on Google over time" (emphasis on the word 'relative' is mine). This could just mean that the absolute number of search terms for 'bioinformatics' and 'genomics' is the same, or has even grown, but has been swamped by an increase in the frequency of all other search terms. To a lesser degree, there seems to be fewer searches occurring for many different biologically-related terms, e.g. here is the graph for the word biology.

On top of the overall declining trend, I noticed that you can clearly see a dip in the middle of each year. Possibly, this corresponds to when millions of high-school kids take their long summer vacation and are therefore not searching about anything to do with school work. You can see similar annual 'wobbles' if you also search for chemistry or physics. So does this mean that all science-related searches are declining? Well, you might expect there to be growing interest in the newer fields of biology (and bioinformatics in particular) and related technologies. This does seem to be the case. Here is the graph for the search term next generation sequencing (note, I do not advocate using this phrase):

Clearly this term has exploded in popularity as everybody moved to using many of the newer sequencing technologies as opposed to the traditional Sanger method.

So clearly, some topics are becoming more popular, and more searched for. However I still feel that the decline for the term bioinformatics might indeed represent a real decline in the whole field of bioinformatics. That is not to say that I think less bioinformatics is being done these days, or that it is less 'worthy' as a field. Rather, I think bioinformatics has moved from being a specialist field that was carried out somewhat separately from 'traditional' wet-lab research, to something which is much more integrated with many other fields of research. There are still many dedicated bioinformatics group (the lab where I work is one such group), but I think that it is increasingly common that biologists need to — and want to — undertake some bioinformatics as part of their wider research. To me, bioinformatics has become part of mainstream biological research and that means that it no longer makes sense to think of it as a separate field as such.

Anyway, regardless of whether any particular biological term is rising or falling in popularity, I think it is more interesting to see what search terms remain eternally popular. Despite changing governments, economic turmoil, and global uncertainty what is it that we search for with any degree of constancy? My first guess seemed to be a good one. So let me end by presenting the Google Insights graph for the search term shoes:


Adding polish to presentations: 10 tips to make your talk shine

One of my greatest frustrations in life is sitting through bad presentations. Sadly, this is all too common in academia. We all know the signs:

  • Sparse, or nonexistent, background material
  • Too many slides full of bullet-point text (often read verbatim by the speaker)
  • Too many figures crammed on to a single slide
  • Speaker faces the screen while talking
  • Speaker has no passion, doesn’t seem to care much about their subject matter
  • No conclusion or summary to the talk, just data
  • Slides continuously vary in design, font choices etc.
  • Speaker overruns because they haven’t practiced

I could go on. I’ve been to so many talks where you can see audience members switch off after the first 5 minutes (and then usually reach for their smart phones to check their email). Bad talks become a waste of time for both the speaker and the audience. It doesn’t have to be this way. Indeed, it really shouldn’t be this way. You might be the greatest scientist the world has ever seen, but if you can’t communicate your research to others then there really is no point being in science. And by ‘communicate’ I mean making sure that people a) understand your talk and b) remember it.

Here are some slides (with notes) that list some relatively simple tips that I think could help many people who are new to giving presentations. These are tips that I have learned from many years of giving scientific talks in academia, but I think they could be useful to anybody who has to present their work to others.

10 tips for adding polish to presentations