Tuesday, 5 January 2016

Hooray for rain radar!

With all the doom and gloom of climate change, over-population and the stresses of "the rat race", it's easy to forget how amazing the modern world is thanks to advances in science and technology. On Sunday, we were in the city for a spot of sales shopping and a visit to the Australian Museum. When we went to leave the shopping centre for the bus, we looked outside to see it tipping down. I'd brought umbrellas but it was a bit windy. Should we risk a soaking, or wait and see if it would blow over?

In the past, this would have been a bit of a gamble, possibly combined with some kind of superstitious activity to try and alter the outcome. Thanks to the wonders of modern technology, I just had a quick look at the Sydney Rain Radar, saw it was blowing over: and we went and got a (very nice) coffee instead. After coffee, another quick check of the radar confirmed that the rain had moved on. Home and dry!

Of course, the rain radar doesn't always tell you what you want...

It’s going to be a wet one!

Monday, 4 January 2016

Earthworks 2014 Barossa Valley Shiraz

Today's You-app task was to "think positive" and make a note of something positive. This was actually my chosen "keep-it-up" habit-forming activity, so I had to do it twice. Fortunately, living in Australia gives you many positive things to think about, even on a rainy day like today. One of them is the wine - and one of the wines to be positive about is Earthworks 2014 Barossa Valley Shiraz, which is rich and velvety without being too in-your-face like some Aussie wines can be. (Not that I have a problem with that!)

It’s on offer at Vintage Cellars at the moment, so that’s two things to be positive about in itself!

Sunday, 3 January 2016

Making it a positive 2016

One of my Christmas presents this year was Jamie Oliver’s new book, Everyday Super Food. As well as having some delicious-looking recipes, it also contains some advice for healthy living. One of the things recommended was the YOU-app for small steps in mindfulness, food and movement for health and happiness.

The basic idea is to make a positive change to your life through “micro-actions”, which are quick and simple to perform, rather than setting big goals that are hard to meet. The actions come in four flavours: mind, food, move and love. So far, I like it, and it’s inspiring me to make 2016 a year of making positive blog posts wherever possible. The first is this: check out the You app. It’s free!

Saturday, 21 November 2015

Is this the shortest abstract ever?

I’m currently writing a new program as part of a comparative genome analysis, which has the working title of “Snapper”. Unusually (but not uniquely) for me, this is not an acronym, but is instead a simple contraction of “SNP Mapper”.

Before doing too much, it is always wise to check for existing tools with the same name, especially if they might do similar things. A quick Google search for “Snapper bioinformatics” threw up this paper:

  • Kolesov G, Mewes HW & Frishman D (2002). SNAPper: gene order predicts gene function. Bioinformatics 18(7):1017-9.

The abstract:

SNAPper is a network service for predicting gene function based on the conservation of gene order.

The SNAPper server is available at http://pedant.gsf.de/snapper. SNAPper-based functional predictions will soon be offered as part of the PEDANT genome analysis server http://pedant.gsf.de.

I know that Bioinformatics application notes are pretty concise - the idea is that the described software has the documentation you need - but that has to be one of the shortest abstracts that I have ever seen!

SNAPper itself is not an acronym, although the SNAP part is: Similarity Neighbourhood APproach. For such a common acronym as “SNAP”, that one needs some work, I think.

PEDANT, on the other hand, is a full ORCA-worthy acronym: Protein Extraction, Description and ANalysis Tool. It reminds me a bit of a defunct classic of my own, PIRATE: Protein Identification, References, Annotation and Tissue Extraction (or something like that, lost in the mists of time) that was basically just a parser for Uniprot entries that tabulated certain data, after I discovered that a PhD student in the department had spent several days copying and pasting data from Uniprot into Excel. Happy days!

Tuesday, 17 November 2015

Creamy mustardy lentils with bacon and squash

This is another repeat favourite, based on a Waitrose recipe, Rosemary-roasted squash with ham hock and lentils. Aussies are more into cow than pig products, so it’s not so easy to get decent ham/bacon etc. However, this recipe does just fine with some fried bacon chunks rather than the (cooked) ham hock in the original. The original also used frozen squash.

You can pre-roast the squash for this recipe.


  • ~1kg Butternut Squash
  • 2 sprigs fresh rosemary, chopped
  • 250g puy Lentils
  • 1 tsp olive oil
  • 1 small onion, finely chopped
  • 1 tbsp Dijon mustard
  • 100ml Single Cream
  • 180g pulled ham hock or cubed bacon
  • 25g sunflower seeds
  • 20g pack flat leaf parsley, chopped
  • 100g frozen peas


  1. Preheat the oven to 200C, gas mark 6. Cut the butternut squash into large chunks (e.g. quarters) and spread in a single layer on an oiled baking sheet. Sprinkle with the chopped rosemary. Bake for around 45 minutes until tender and lightly browned, tossing in the oil about halfway through. Cut into something resembling even cubes. Bitesize chunks, if you will. (Don't obsess too much - there's a chance the squash will, well, squash to mush anyway.)

  2. Cook the lentils in a pan of boiling water for 15–18 minutes until tender. Drain.

  3. If using bacon, fry the bacon cubes in a bit of oil until cooked.

  4. Heat the oil in a large non-stick frying pan and cook for 5–10 minutes until good and soft.

  5. Stir in the mustard, cream and some seasoning and bring to simmering point.

  6. Stir the cubed squash, drained lentils, bacon/ham hock, sunflower seeds, parsley and peas into into the cream sauce.

  7. Heat through gently until everything is hot.

  8. Check seasoning and serve.

Tastier than it looks (with my food photography skills, at least) and makes good leftovers too.

Sunday, 15 November 2015

Humpbacks ahoy! Whale watching off Sydney

We’ve been meaning to go whale watching since we moved to Sydney and today we finally got round to it. The weather was not the best - and the sea was a bit choppier than ideal - but it was a fantastic morning, well spent. Best of all, we got to see humpback whales!

It was only a small pod - a mother and calf, plus “escort” - but we got some reasonably close up views when one of them was having a play.

As well as a couple of breaches, this included a couple of good tail slaps.

Amazing animals. We saw some birds too - and, of course, some great views of the cliffs around Sydney harbour. All in all, a recommended half day trip.