Friday, 22 November 2013

Changing file extension associations on a Mac

One of the problems with making the switch from Windows to Mac is that you lose a lot of little tricks and tips that you have picked up over the years. Despite claims that Macs are much more intuitive than Windows machines (something that I have never found, personally), I quite often find myself frustrated at the lack of an obvious way to do something that I know how to do in Windows.

Yesterday, it was file extensions that briefly gave me angst. For historical (i.e. forgotten!) reasons, I have a lot of programs generating *.tdt files, which are tab delimited text. (The correct extension for such things actually seems to be *.tsv, or tab separated values.) Being a biologist, I generally like to open my delimited files to look at in Microsoft Excel - the number one bioinformatics tool in world! (By use, that is!) Naive Macs (and naive Windows machines) do not know what a *.tdt file is, though, so they will generally offer a text editor instead. Similarly, I have a lot of draft notes in Markdown, saved as *.md files, but Finder wants to open them in TextWrangler rather than Mou, my Markdown Editor of choice.

Happily, the internet has once again come to the rescue, in the form of a 2009 post on OSXDaily, Change File Associations in Mac OS X. Simply right-click (or ctrl+click) in Finder and select Get Info.

You can then change the program to open that file with and choose Change All to change the default action for all similar files (e.g. those with the same extension). This was so useful that I thought I would re-share here.

Thursday, 21 November 2013

RIP Fred Sanger (1918-2013)

I opened my email this morning to the news that Fred Sanger had died. This was not entirely surprising, given that he was 95, but still sad. Although I have never met him, I think it is fair to say that I am one of many scientists whose careers have been shaped and influenced by the work of this great scientist.

I still remember sitting in lectures as an undergraduate and discovering how “Sanger” sequencing worked - like many of the ideas that change the world, it was gloriously simple and yet spectacularly clever. And, I think it is fair to say, it changed the face of biology forever.

Indeed, that was back in 1977, and Sanger sequencing is still used all over the world today, even in the face of stiff competition from “Next Generation” methods. It was the sequencing method (albeit in a much tweaked and automated version) that got us the Human Genome and one of the world’s leading sequencing centres - the Wellcome Trust Sanger Institute at Hinxton, outside Cambridge - still bears his name.

The centre has a press release about the “remarkable man”, which has been written by greater wordsmiths than I:

“Fred Sanger, who died on Tuesday 19 November 2013, aged 95, was the quiet giant of genomics, the father of an area of science that we will explore for decades to come.

His achievements rank alongside those of Francis Crick, James Watson and Rosalind Franklin in discovering the structure of DNA. We are proud that he graciously agreed to allow our Institute to be named after him.

In research marked by two Nobel Prizes, he developed methods that allow us to determine the order of the building blocks of DNA and of proteins. This technique allowed the languages of life to be read.

Because of Fred’s work we have been able to interpret those languages and to use that knowledge for good.”

There is more, including quotes and links out to other resources about his work, at the site.

I remember thinking in those lectures back in Nottingham how I wished that one day I might have an idea as good as Sanger sequencing. I doubt that I ever will; instead, I will just have to settle for trying to do the best I can with all of the amazing sequence data that now exists as a result.

Monday, 18 November 2013

More rain than Dublin!

One of the most surprising statistics about Sydney is that it has more annual rainfall (~1200 mm) than Dublin (~700 mm). It’s not really something that one tends to associate with Australia - particularly as we arrived to news of raging wild fires across New South Wales following a particularly dry winter.

The reason, of course, is that Sydney also has more daily sunshine hours on average too (mean 6.8 per day versus 4.0 for Dublin) - the difference is that when it rains in Sydney, it tends to rain hard. (The main difference, at least - Dublin has around 10 fewer rainy days on average, according to Wikipedia.) This past week or so has been testament to that - so much so that I felt the need to buy a new umbrella at the supermarket today for the 5-10 minute walk back to my office. (My previous umbrella finally died on the way to work this morning.)

If you are visiting Sydney, check the forecast - and, if in doubt, pack an umbrella!

Friday, 15 November 2013

Reunited at last!

One of the hardest thing about selling up and moving 17,000km away was putting our two cats through the trauma of being shipped off to a cattery then flown half-way round the world before spending another 30 days in quarantine at the other end - and, of course, being without them for all this time (barring a couple of visits). Today was the day that we picked them up from quarantine!

PlacematsWe had obviously done our best to prepare for the arrival of our furry friends - complete with comedy placemats from Ikea for their food and water bowls. (I am not sure whether they will appreciate them as much as we do!)

PetAir CratesThe whole process was also made much easier through the knowledge that they had been well looked-after throughout. This started with their cattery stay and relocation by PetAir, who have been great and clearly care for all the animals they relocate. We picked them up in the PetAir crate that they were shipped over in, and it made me smile to see the stenciled cats on top. The lady at the quarantine station also made us feel that they had received good care as, like the PetAir staff, she reported a bit on their personalities as well as simply their condition.

The most traumatic part of the process (today) was probably the journey out and back, which was largely due to a combined lack of familiarity with the car (a GoGet Hyundai i30 called Lorna), the route and our new Garmin sat nav. (I am not getting on with the latter but I’ll save that for (maybe) another day.) Given that it was only my second drive in Australia, though, it did not go too badly - thanks largely to some human navigation and Google maps on the iPhone.

Arthur exploring Arthur in hole

Arthur is not shaken by much and so, somewhat predictably, it was he that settled in quickest, giving the apartment a bit of a look over before settling down in the “cat condo” to survey things for a bit.

Mia in bath Mia, on the other hand, went and hid in the bath for a while. I can’t say that I blame her - if it had been me then I think I would have wanted a bit of alone-time. The introduction of a bowl of food was well received and she did not stay in there for long.

Mia bath timeMia tickles

Unfortunately, I had to go into work for the afternoon but was pleased to receive reports that tummy-tickles were being enjoyed - and a photo of Arthur doing what he does best: sprawled relaxation.

Arthur sprawled

Mia on kitty condoBy the time I got home again, it was almost like business as normal - I got a good greeting, Arthur was only interested in food and Mia was soon surveying her new realm from atop the cat condo. That was, at least, until I started showing an interest - this post has been slowed down at times by a purring Mia on my lap! :o)

Sunday, 3 November 2013

Saving the world, one glass at a time with Sydney Tap(TM)

In my recent post about brunch at One Six Nine Cafe, I mentioned Sydney Tap™ but I thought it deserved a post all of its own.

The website has a great animation to scroll through and discover what a difference can be made just by drinking tap water rather than bottled water but (spoiler alert!) I’ve also grabbed a screenshot of the summary data below. The data (based, admittedly, on a somewhat arbitrary 2l/day) speak for themselves, really:

Saturday, 2 November 2013

One Six Nine Cafe - setting the bar high for Sydney brunch

Australians are big into their brunch (I have been told) and today we had our first proper brunch in Sydney, at One Six Nine Cafe in Randwick, which we discovered thanks to Urban Spoon. (I neglected to take any pictures at the time, so I pinched the one to the left from their gallery.)

We shared the smoked salmon brunch - smoked salmon on sourdough toast with ricotta, avocado and a poached egg - and the day’s special: peanut butter pancakes with maple syrup, grilled banana and crispy bacon. Amazing. The portions were just right (for me) - large enough to feel that I was getting value for money (and full!) but not obscene - and the food was all top quality. The coffee was good too!

I suspect that this is the first of many brunches to come but it might be a hard one to beat! Fortunately, One Six Nine is within walking distance of where we'll be living but not too close. (The temptation might be too strong for our wallets!)

As an added bonus, they also served Tap™, which I had seen advertised outside a cafe before but did not really understand what it was. It turns out that it’s not a crazy gimmick/scam (along the lines of Dasani) but is instead an attempt to save resources by encouraging people to drink tap water, something that I can happily get behind!