Presentations online for Bioinformatics FOAM 2015

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.

New publication: A panel of genes methylated with high frequency in colorectal cancer

I’m pleased to announce an open-access publication with my name on it:

Mitchell, S.M., Ross, J.P., Drew, H.R., Ho, T., Brown, G.S., Saunders, N.F.W., Duesing, K.R., Buckley, M.J., Dunne, R., Beetson, I., Rand, K.N., McEvoy, A., Thomas, M.L., Baker, R.T., Wattchow, D.A., Young, G.P., Lockett, T.J., Pedersen, S.K., LaPointe L.C. and Molloy, P.L. (2014). A panel of genes methylated with high frequency in colorectal cancer. BMC Cancer 14:54.

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Git for bioinformaticians at the Bioinformatics FOAM meeting

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…