Off to Melbourne tomorrow for perhaps my favourite annual work event: the Bioinformatics FOAM (Focus on Analytical Methods) meeting, organised by CSIRO.
Unfortunately, but for good reasons, it’s an internal event this year, but I’m putting my presentations online. I’ll be speaking twice; the first for Thursday is called “Online bioinformatics forums: why do we keep asking the same questions?” It’s an informal, subjective survey of the questions that come up again and again at bioinformatics Q&A forums such as Biostars and my attempt to understand why this is the case. Of course one simple answer might be selection bias – we don’t observe the users who came, found that their question already had an answer and so did not ask it again. I’ll also try to articulate my concern that many people view bioinformatics as a collection of recipe-style solutions to specific tasks, rather than a philosophy of how to do biological data analysis.
My second talk on Friday is called “Should I be dead? a very personal genomics.” It’s a more practical talk, outlining how I converted my own 23andMe raw data to VCF format, for use with the Ensembl Variant Effect Predictor. The question for the end – which I’ve left open – is this: as personal genomics becomes commonplace, we’re going to need simple but effective reporting tools that patients and their clinicians can use. What are those tools going to look like?
Looking forward to spending some time in Melbourne and hopefully catching up with this awesome lady.
In 2015, I’d like to write, think and do more about things that I care about. One of those things happens to be the koala. Now, this being a blog about bioinformatics and computational biology, I can’t just start writing about any old thing that takes my fancy…I guess. So in this post I’m going to stretch the definition to include ecological informatics and tell you the story of how I achieved a long-held ambition using one of my favourite online resources, The Atlas of Living Australia. And then we’ll wrap up with a quick survey of the (sorry) state of marsupial genomics.
I’ve never attended a hackathon (hack day, hackfest or codefest). My impression of them is that there is, generally, a strong element of “working for the public good”: seeking to use code and data in new ways that maximise benefit and build communities.
Which is why I’m somewhat mystified by the projects on offer at the Sydney HealthHack. They read like tenders for consultants. Unpaid consultants.
The projects – a pedigree drawing tool, a workflow to process microscopy images, a statistical calculator and a mutation discovery pipeline – all describe problems that competent bioinformaticians could solve using existing tools in a relatively short time. For example, off the top of my head, ImageJ or CSIRO’s Workspace might be worth looking at for problem (2). The steps described in problem (4) – copy and paste between spreadsheets, manual inspection and manipulation of sequence data – should be depressingly familiar examples to many bioinformaticians. This project can be summarised simply as “you’re doing it wrong because you don’t know any better.”
The overall tone is “my research group requires this tool, but we’re unable to employ anyone to do it.” There is no sense of anything wider than the immediate needs of individual researchers. This does not seem, to me, what hackfest philosophy is all about.
This raises an issue that I think about a lot: how do we (the science community) best get the people with the expertise (in this case, bioinformaticians) to the people with the problems? In an ideal world the answer would be “everyone should employ at least one.” I wonder about the market (Australian or more generally) for paid consulting “biological data scientists”? We complain that we’re under-valued; well, perhaps it is we who are doing the valuation when we offer our skills for free.
Last week, I attended the annual Computational and Simulation Sciences and eResearch Conference, hosted by CSIRO in Melbourne. The meeting includes a workshop that we call Bioinformatics FOAM (Focus On Analytical Methods). This year it was run over 2.5 days (up from the previous 1.5 by popular request); one day for internal CSIRO stuff and the rest open to external participants.
I had the pleasure of giving a brief presentation on the use of Git in bioinformatics. Nothing startling; aimed squarely at bioinformaticians who may have heard of version control in general and Git in particular but who are yet to employ either. I’m excited because for once I am free to share, resulting in my first upload to Slideshare in almost 4.5 years. You can view it here, or at the Australian Bioinformatics Network Slideshare, or in the embed below.
See the slides…
January/February are exciting months for open [data|research|science|access] proponents in our region – by which I mean Australia and New Zealand.
First, we’ve enjoyed a speaking tour by Sir Tim Berners-Lee, during which he discussed the benefits of open data several times. I was able to attend two events in Sydney in person and a third, linux.conf.au, by video stream. The events were the work of many people but in particular, Pia Waugh. Go follow her on Twitter, now.
Next – I wish I had been able to get to this one – the Open Research Conference on February 6-7, University of Auckland. I’m enjoying the high-quality live stream right now. Flying the flag for Sydney are Mat and Alex.
Not strictly under the “open” umbrella but worth a mention anyway: software carpentry is in town, February 7-8, just up the road from me at Macquarie University. Looking forward to hearing some reports from that.
We can debate the economics, complexities, details, implementation… of open access publishing for as long as we like. However, the basic principle: that publicly-funded research should be publicly-accessible seems to me at least, very obviously correct and “the right thing to do”.
So this, from April 2012, was very depressing.
Open access not as simple as it sounds: outgoing ARC boss
For those outside Australia, the ARC is the Australian Research Council. Much debate ensued in which one contributor to the comment thread wrote:
…it is particularly galling that Sheil is projecting her own simplistic understanding of open access onto its advocates. Hopefully she will be replaced at the Australian Research Council by someone who understands and supports open access.
The ARC has introduced a new open access policy for ARC funded research which takes effect from 1 January 2013. According to this new policy the ARC requires that any publications arising from an ARC supported research project must be deposited into an open access institutional repository within a twelve (12) month period from the date of publication.
I did giggle at the assumption that the author’s version of their article is by default a Word document, but then I guess that’s true for > 90% of authors.
Outcomes like this come dangerously close to restoring hope.
What’s a “Friday fun project”? It’s a small computing project, perfect for a Friday afternoon, which serves the dual purpose of (1) keeping your programming/data analysis skills sharp and (2) providing a mental break from the grind of your day job. Ideally, the skills learned on the project are useful and transferable to your work projects.
This post describes one of my Friday fun projects: how good is the Sydney weather forecast? There’ll be some Ruby, some R and some MongoDB. Bioinformatics? No, but some thoughts on that at the end.
Read the rest…
Are you looking for a postdoctoral position in structural bioinformatics? Preferably at a highly-regarded university, on an attractive campus in a lovely city with a great climate? Did I mention great colleagues?
I highly recommend my old job – details here.
Every day, I’m amazed by the information ecosystem that we call the WWW and how it has changed forever the way we educate ourselves.
Today’s illustration. I spent part of last weekend strolling through the beautiful rainforest of Brisbane Forest Park, a mere hour’s drive from the city. On the track at Maiala I heard a very bizarre noise, high in the misty canopy. The sound was a blend of fighting cats and crying children, yet strangely musical. It was a new sound to me but the cat-like aspect was a give-away, since I was aware of a species called the green catbird.
Back at home, I consulted the trusty Simpson and Day’s Birds of Australia. It described a sound similar to what I had heard but of course, bird sounds don’t translate to written English very well. So I headed off to the appropriate Wikipedia entry. It’s not one of the more compehensive pages but in the external links includes:
Green Catbird audio recording at Freesound
I played the sound – it was exactly what I had heard. What’s more the page is tagged, geotagged and part of a wonderful resource called the Freesound project – a collaborative database of Creative Commons licensed sounds.
So in the space of a few hours I lifted my spirits in the great outdoors, heard something new, tracked it down on the Web and discovered a bunch of new, interesting related information. That’s the Web at its best; integrating seamlessly with your daily life to enhance what you see around you. When it works, it’s an almost Zen-like experience.
Who isn’t fascinated by the strangest of mammals, the platypus? It has fur and lactates, like a mammal. It has a bill and webbed feet, like a bird. It lays eggs and produces venom, like a reptile. It finds prey using electroreception, like sharks. The platypus is so weird that when first described, many scientists assumed that it was a hoax.
To celebrate the publication of the draft platypus genome, here’s a brief guide to this wondrous creature.
Read the rest…