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.

AVAILABILITY:
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!

My number one exam tip

Answer the question! (I’ve said it before but some things are worth repeating.)

Click here for more exam tips.

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.

Ingredients

• ~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

Instructions

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.

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.

ICBCSB 2015: Another scam conference comes to Australia

I am a bioinformatician working in Sydney, Australia. I recently helped to organise the ABACBS2015 conference in Sydney, where ABACBS stands for the Australian Bioinformatics And Computational Biology Society, of which I am a member. I am also part of the New South Wales Systems Biology Initiative. You may therefore find it surprising to know that I found it surprising to find out that in December, Sydney NSW will be host to "ICBCSB 2015 : 17th International Conference on Bioinformatics, Computational and Systems Biology".

This is not the only surprising thing about ICBCSB 2015. For Sydney is actually at least the 15th 17th International Conference on Bioinformatics, Computational and Systems Biology (ICBCSB 2015). Next week, the conference is being held in Madrid. Last month, there was the 17th International Conference on Bioinformatics, Computational and Systems Biology in Bali. And Prague. And Chicago. And Istanbul. The 17th International Conference on Bioinformatics, Computational and Systems Biology (ICBCSB 2015) has also been in Venice, London, New York, Berlin, and Geneva and will be held in Penang and Dubai. And that’s just in the first two pages of a Google Search - there are more (including Lisbon and Stockholm).

This makes OMIC Group Conferences look positively legit. Indeed, the organisers of all 15+ ICBCSB 2015 conferences - the World Academy of Science, Engineering and Technology (WASET) - seem to be basing their conference business model on that of OMICS. Or perhaps it was the other way round. Either way, if you replaced the WASET logo on the website with OMICS Group, nothing would seem out of place.

If you have ever attended a (real) scientific conference, pick one of those past conferences at random, for example Berlin, and click on the conference photos page, then tell me if you have ever seen anything so depressing in your life. And remember: these are the photos they chose to put up, so presumably show the conference in its best light. Given the number of group photos of (all?) the delegates, I wonder whether they had time for much else other than publicity shots. And in case you are thinking: “those are probably just the invited speakers”, I would bet good money that the delegates were all invited - and still had to pay top dollar to attend.

Finally, in case you have any doubt, just Google “WASET scam”. It does not make for happy reading.

If you are in bioinformatics or systems biology, please spread the word far and wide about these conferences and why they should be avoided at all costs. The sooner we starve the likes of OMICS Group and WASET of naïve unsuspecting scientists to prey on, the sooner these parasites will f#@k right off. There are plenty enough legit conferences to choose from. (Yes, it makes me angry.)

And if you have already signed up for Sydney ICBCSB 2015, do not despair. As luck would have it, there is a real bioinformatics event being held in Sydney that same week: BioInfoSummer 2015. It’s more of a workshop than a conference but there will be plenty of opportunities to discuss science with some excellent bioinformaticians and systems biologists. At least that way, you won’t waste the plane ticket and hotel costs, even if WASET won’t give you a refund for pulling out. (Not likely!)

A tale of two conferences - #ABACBS2015 and #AGTA15

Two weeks ago, I attended the awesome double-header of ABACBS2015 and AGTA15. In some ways they were chalk and cheese - ABACBS was cheap and cheerful, where as AGTA was expensive and (therefore) exclusive - but both were great and highlighted some of the very best features of successful academic conferences.

As part of the ABACBS2015 organising committee, I needed to collect my thoughts for a debrief, so I thought I’d got down some thoughts here. (Thanks to grant writing, the post itself got a little delayed!) As with biology itself, most decisions are trade offs and the following comparison is not to criticise - I just find it interesting. As with the awesome ABiC14 conference last year, I mainly want to document good practice for future reference. (Some of these will no doubt be repeats of my ABiC14 thoughts!)

Size. Both conferences were, for me, the perfect size - around 180-190 people. This is enough to give the conference a good buzz and ensure that there are sufficient interesting people to listen to and posters to visit. Critically, though, it was small enough that you could find and speak to the people you wanted to. (Even if I didn’t fully get the chance at ABACBS2015 because I was busy, and managed to miss some people at AGTA15 because time ran out!)

Venue. ABACBS2015 was run on a budget and we were very fortunate to have the Garvan Institute provide a free venue for the conference. The Garvan lecture theatre is lovely, with a great AV system and comfy seats. The only negative for a conference of that size - and we got close to our 200 person limit - is that the space outside the theatre for breaks and posters does get a bit cramped. In contrast, AGTA15 was held in the Crowne Plaza at Hunter Valley, which is a pretty luxury hotel in the wine region of New South Wales. It took me a while to warm to the main conference setup, with seats around tables in a large, wide room with a screen each side of (and a long way from) the podium. However, the “trade exhibition” space where the breaks, lunch and posters were, was excellent. I am big fan of having the posters up all the time and in the same place as the breaks.

Location. ABACBS was held in the city centre at a research institute. This kept the costs down and made it easy to get to. (We did not organise accommodation.) It also made it easy to escape from, which might have affected evening social numbers. AGTA was out in the sticks, which made it harder to get to and may have put some people off attending - it essentially added another day to the length of the conference. The plus side of this was that everything was on one site and it was not so easy to disappear or go home, and so most people were around most of the time, I think. (Although there was the temptation of wine tasting on the doorstep!)

Goodie bags. I’m pleased to say that both conferences went down the reusable shopping bag route (pick above). Being budget, we got UNSW to sponsor us with some canvas bags for ABACBS. (Complete with the scary statistic that plastic bags take 15-1000 years to break down.) AGTA was (a) a bit more upmarket and (b) in wine country, so they provided wine coolbags!

Trade exhibition. We binfies are a cheap lot - and I don’t mean tacky or miserly, I mean that we don’t need a lot of money to do great things. As a result, it is hard to attract trade sponsors: we just don’t spend (or often even have!) any money! Genomics is clearly a different matter, as you literally cannot do it without lots of expensive kit. The AGTA trade exhibit was therefore pretty big and bustling. Again, putting it with the food and posters made for some great…

…Breaks. Breaks really do make or break a conference. One of the few criticisms of ABACBS2015 was that the breaks were a bit too short - we were somewhat hemmed in for time because we needed to leave people enough time to get to AGTA in the afternoon of the second day. We also tended to over-run a little, because people would be enjoying the breaks and take a bit of time to filter back into the theatre for the talks. My advice for conference planners: (1) make all breaks 5-10 minutes longer than you think they should be (e.g. 40 minutes for coffee and over an hour for lunch); (2) build in some dummy time into the program to soak up delays; (3) Make sure you have a bell or something to signal that the next session is starting! Being a more leisurely multi-day conference, AGTA had nice long breaks, including a session off for posters etc. after lunch. Lots of opportunities for mingling and looking at posters.

Invited speakers. Both conferences had outstanding invited speakers that gave really interesting talks. I know some of the binfie crowd would have enjoyed a bit more about the methodology in ABACBS2015 - and we should perhaps brief our speakers a little better in future - but personally I was blown away by the quality of the science presented. Both fields are rapidly changing as technology opens up opportunities and there is some really cool stuff going on out there! AGTA in particular seemed to have a lot of invited speakers, talking about really cool stuff - possibly part of the reason it's so expensive. (It must be said: the quality of the selected abstracts was good too!)

Gender Equality. Both conferences did pretty well on the gender front, I think. ABACBS2015 in particular nailed it, with a 50% split of invited speakers and over 50% female speakers overall! (The latter wasn’t deliberate as such - there are just loads of good female bioinformaticians in Australia who submitted interesting abstracts!)

Twitter. (And #confBingo.) I have mixed feeling about live tweeting at conferences. This year, I decided to throw myself in a bit more and, on balance, I feel that I got more out of it than I missed. It is true that sometimes I missed something a speaker was saying because of a tangential Twitter conversation (such as #JediKelpie) - but I also learnt stuff and picked up on things that I had missed thanks to the Twitter feed. The #confBingo thread was also quite entertaining a fun, and helped networking and building community spirit, which is what a lot of a good conference is ultimately about.

Coffee. Unfortunately, we were unable to attract the barista sponsor from ABiC14 to sponsor ABACBS2015. AGTA did have a sponsored barista, though. Roche (I think) gave out three tickets with registration for the trade exhibit barista. Not quite as good as unlimited but it hit the spot. My other top conference coffee tip: bring a reusable cup! It' so much easier/safer if you want to take coffee into the talks and generally cuts down on spills - and refills! (Next year, I am hoping for ABACBS Keep Cups in the goodie bags!)

Overall, I had a lot of fun helping with the conference organisation - and would recommend it - and even more fun attending. Australia has some great science going on and a really strong/vibrant bioinformatics community, and I am proud to be part of it.

Quick and easy pasta with Italian sausage and kale

Coles magazine quite often delivers the goods in terms of convenient and tasty meals that I can actually be bothered to make - and are quite forgiving to deviations from the recipe. This is my variation on Curtis Stone’s “Penne with sausage and kale” from April 2015. I’ve made this a few times now, so it’s time to post it so that I don’t have to dig out the magazine. (Yes, I really am that forgetful!)

Ingredients

• Coles finest Italian sausages. (Any tasty quality sausage will do but these have fennel in, which adds an extra dimension.)
• Bunch of kale, stalks removed and sliced. (Recipe calls for half but I go for a whole bunch - it cooks down.)
• 2-3 cloves of garlic, crushed.
• Small/half glass of dry white wine.
• Jar of tomato pasta sauce. (The recipe calls for 1.5 cups of passata but then you are left with lots of passata.)
• 300g pasta. (Recipe says penne. I tend to use small spirals… for everything.)
• Parmesan, salt, pepper to serve.

Instructions

1. Get a large pan of salted boiling water going to cook the pasta. See below for the timing you’re aiming at. (Err on the side of too late, I think - the rest can simmer for a bit longer.)

2. Remove the sausages from their skins and fry them over a medium-high heat, breaking them up with a wooden spoon/spatula as you go.

3. Add the kale and garlic and cook until the kale is wilted. If you are using a whole bunch, like me, you may need to add it in a couple of batches - unless you have a very big pan. Don’t worry: it cooks down a lot.

4. Add the wine and the tomato sauce. This time, we used puttanseca sauce, which was quite olivey. If olives aren’t your thing, you might be happier with a simple tomato or tomato and basil sauce. (You can just use passata as in the original recipe, of course!) The sauce had a few cherry tomatoes in it, which was nice. This recipe would work well if you roasted some cherry tomatoes and chucked them in too.



5. Bring to a simmer and cook for a few minutes until at the desired consistency. Hopefully, your pasta should be done by now. Drain and toss with the sausagey tomato goodness.



6. Season to taste and serve. Sprinkle with grated parmesan and black pepper. This makes enough for four adults, or two good dinners and lunches.

And, of course, it passed the Arthur test. (No, he didn’t get any.)