“I’ve got this other idea, but I’m not sure if it’s really appropriate. It’s probably really boring. I want to show who gets NHMRC grants and who doesn’t. The NHMRC release all this data but it’s in spreadsheets and PDFs. I spent so many months last year pulling the data together. It looks like an upside down wine glass! Early to mid career scientists are mostly women, and the further you go up the chain, the more money gets given to men who should have retired but are still hanging around for 15 years.”

Meet Marguerite Evans-Galea. Maggie founded the Australian Academy of Science Early to Mid Career Researchers Forum. It gathers information about challenges of younger researchers and lobbies government for science policy reforms.

Everybody knows that the start of the pipeline in life sciences is full of women. Everybody knows the people who get grants are senior male researchers. It’s a lot easier to explain with pictures.

Big data it ain’t – the input was 1000 excel rows. But now, Maggie can show the too-many-old-men problem to man-in-charge-of-not-landing-the-government-on-front-page-of-The-Australian, in a format he can understand: the humble bar chart.

Amount of NHMRC funding awarded in 2013 broken down by sex and career stage

They’ve got heat maps too, but they’re not as telling for a minister’s adviser.

Aaron McAleese, Sean Fleming, Iulian Stefanica, Irith Williams, Marguerite Evans-Galea and Scott Ritchie, winning team of HealthHack Melbourne 2014

Maggie’s project idea won HealthHack in Melbourne. She is now in all kinds of interesting conversations with government departments that shall remain nameless.

The Sydney first prize winner is delighted. They extended an existing open source project to create a family pedigree drawing tool. The current tools for clinical geneticists include one that lets the user draw a family tree, and a different one that provides a list of family members and their genetic variants. It’s so frustrating for geneticists they usually end up drawing family trees on paper. The tool Andreas’s group created does both, and then some. “We’ll be using this on Monday!”

Phenotips extension family pedigree tool

Then there’s Clare Coleman, the Sydney researcher who learned to JavaScript over the weekend. Her team didn’t start writing code until late Saturday, by then they had a clear picture of what their Minimum Viable Product would be. Clare offered to work on the function that would do most of the calculations. “What language do I use? I only know Pascal. Well, Delphi.” Two hours later Clare came back and said “I’m done, I think”. After changing a few commas to semicolons and writing a unit test, the function was added to the website.

Their group didn’t win a prize, but they did make a nice tool for showing how various parameters affect life expectancy of Aboriginal people. You might want to watch their video.

Clare Coleman at HealthHack Sydney

Nobody used the cluster installed especially for the weekend (thank you V3 Alliance!), but one group in Melbourne worked to optimise a processing pipeline problem on the VLSCI (Victorian Life Sciences Computation Initiative) supercomputer. You can really feel for them, all they got was a special mention (and some good options for managing an evolutionary biologist’s python workflow). Nobody’s sure if Sydney’s equivalent of the ugly duckling did in fact have better results, or were just able to articulate them better – hard to argue with “What used to take 3 days now takes 3 minutes”, but they won second prize.

Back in Melbourne, Charles Galea came in with a problem that’s been plaguing the field of biosciences for some time. Once a protein is linked to a disease, the next question becomes: which mutations are important? A protein can have many point mutations, some can be fatal to the protein, others have little effect. Genomics can tell us where mutations occur, but establishing which are actually associated with disease is done via expensive, laborious, time consuming experimental work.

But wait! Structural biologists have the power to examine proteins and tell which mutation is most likely to have major repercussions on the protein, and therefore the human it floats in. Charles, a structural biologist, uses a selection of online tools to do that. Download sequences here, upload there, configure web app after web app. It’s tedious and it takes forever. Charles’s group created a tool that semi-automates this process and shows all results in the one place.

The Mutation Instability Filter helps structural biologists to determine which point mutations in proteins are most likely to cause disease

Charles can now do his analyses in a fraction of the time, an army of young postdocs can come into the lab on weekends knowing their efforts are effectively utilised, and the devs got to play with biology.

Know what they won? Charles Galea, scientist at the Murdoch Children’s Research Institute, won half a day shadowing scientist Maggie Evans-Galea at the Murdoch Children’s Research Institute.

(The prize went to the developers. They’re genuinely thrilled.)

There’s also the group that created two mobile apps over the weekend, for another first-of-its-kind: tracking gamblers’ addictive behaviour and mood out in the wild, realtime, not just in the psychologist’s office. It’s a survey-based ‘like fitbit for addiction’. It’s nothing revolutionary from a tech perspective, but it’s changed what the field of psychology can do. The research group Ben And George work in have a proof of concept they can use to get more funding for employing developers.

One of their devs left early on Saturday to his job at Crown Casino. He had some choice ideas for user testing.

Superpowers

HealthHack is all about solving problems that researchers face. It’s about demonstrating to scientists the value of investing in good software and design. If they can see why they need it, they’ll pay for it.

It’s also about getting software people into science. We often hear something to the effect of “It’s so good to work on something other than finance back end integration. I had no idea this was so interesting.”

Although the main output of HealthHack was open products to assist health researchers, there was a secondary output, which is just as important: networks built across communities. The participants on many teams promised to remain in contact, and even continued discussions with researchers on how to better the tools they created over the weekend.

We have a lot of lovely emails from participants with quotes like these:

Makes it all worthwhile.

Thanks to:

• Maia Sauren, overall HealthHack supreme organiser
• Kelvin Nicholson, Sydney HealthHack puller-together, sponsor wrangler extraordinaire and Open Knowledge Hackathon repeat offender
• Website and graphics: Nic Smythe, Nigel Fernandez, Amanda Wise, Svetlana Filimonova, Carol Mak
• Logistics and management: Dan Samson-Gower, ops hero, who juggled a family holiday with two kids under 5 with panicky messages about network wrangling; Olivia Leonard, marketing; Health Informatics Society of Australia; Andrew Chalmers, cluster guardian; Rose Elhage, whirlwind
• Melbourne volunteers: Andrew Scott, Matt Cenga, Jordan Wilson-Otto, Olivia Platek, Dejan Jotanovic, Martin Feckie, Luke McDonald, Nat Young, Mayase Jere
• Sydney volunteers: Shaheedha Hussainiah, Paul Manuel Joseph, Frederic Lemay, Venus Izadi, Esther Butcher, Marzieh Morovatpasand
• Judges: Steve Bennett, Matt Ritchie, Jarni Choi, Alison Stringer, Anthony Sceresini
• Our sponsors: ThoughtWorks Australia, RedHat, Walter & Eliza Hall Institute, The Garvan Institute, V3 Alliance, VLSCI, NeCTAR, Life Letters, GitHub and Fishburners HealthHack is proudly part of the ChangeMakers Festival.

Links:

• HealthHack site
• Twitter action on Storify

Glenn made icons – you know Glenn, he’s got those pants, and that guy with the beard – no, the other guy with the beard – he wrote down a heap of stuff on index cards which we converted to data points. Lots of people added locations.

Whaddaya mean, why can’t you see the roads? You can see the bike paths and train lines, can’t you? And the laneways? There’s like literally nothing on the main streets, haven’t you been to Melbourne? Look, fine – just zoom in, the roads will show up eventually. Why would you even want to do that, jeez. Besides, when you zoom in like that, all the OpenStreetMap cafes are shown, and they’re so mainstream. And see how we colour-coded suburbs according to density of free-range syntagmas? It’s a secondary indicator of pseudo-relevance.

Yeah, so, there are a couple of problems with this. We’re a bit worried this will become too kitsch – we risk schisms in the ideosphere. We experimented with being typeface agnostic but it was too much. I can’t even. We’re also not really sure about the ethical implications of sartorial gentrification. Like, how do we interact with readymade-free? It’s a bit twee, all that twitterigentsia clambering to understand our culture. On the other hand, we were concerned about the asymmetrical knowledge exchange so there’s a suggestion option. Yes, if you can think of something, let us know. Totally. Flexiterian, eh?

…

All right, that’s enough. I’m giving myself a headache.

The hipster map of Melbourne was created on the back of a frivolous idea by a bunch of volunteers. We wanted to see what we could achieve in an evening using nothing but open source technology and enthusiasm.

The underlying basemap is TileMill, an interactive open source mapping tool that uses OpenStreetMap data. The placemarkers are served from CartoDB, another open source interactive mapping resource. The whole lot sits on a web server hosted at hipstermelbourne.org that loads both the base map and the placemarkers.

Props to: Steve Bennett, Maia Sauren, Matt Cengia, Hamish, Mike Ebinum, Glenn Todd, Anthony Mockler, Nic Smythe, Peter Dudley, Fiona Tweedie, AJ, Tim Hordern.

Oh no, we hear you cry! Dirty hipsters are filthying my local with their fixietaches, I would like them to disappear to the even more obscure cafe down the road! Never fear. Let us know the name of your dinghy renovated sweatshop. Is it too cool to advertise its name? Even better. We’ll get to it as soon as we finish drinking out of these jars.

Here’s who we all declared ourselves to be:

We joined forces with Code For Australia so the room was nice and full. Wanna find more details about the person with the cool project you didn’t quite talk with last night? Try stalking them on the OKFN Melbourne Meetup page or the Code For Melbourne Meetup.

If you came to the March meetup, we’ll be playing the ‘Who are you and what are your interests” game again.

Drinks were so successful….We thought we might hold them again!

Thanks for coming along everyone! That was excellent. Can’t remember the last time I heard ‘You should talk to X!’ so many times.

Watch out for notices in March – we will be holding drinks in Melbourne every 2 months.

Come have a drink. Tell us what you’re doing. Find out what everyone else is into. Because why not.

Thurs 23rd Jan, 6pm, 1000 Pound Bend

See you there!

The full HealthHack site is up! Go look!

What is HealthHack?

HealthHack is a weekend datahack working on problems that medical researchers face. Medical researchers create vast amounts of data, but don’t always have good ways to analyse, visualise and communicate it. On the weekend we’ll have available for you real life medical researchers, their problems, their data.

HealthHack is part of ChangeMakers Festival

Latest news

We’ve got a few new problems for you! See down the bottom of the page…

Sadly, Pia Waugh, chair of the Australian arm of the Open Knowledge Foundation, can’t make it to Melbourne anymore. Pia will  be joining us live via Google Hangout on Friday 25th October.

Don’t forget you can now participate remotely if you’re not in Melbourne – register as normal, and get get in touch to organise details.

Where and when?

Fri 25 Oct – Sun 27 Oct, at ThoughtWorks office, 15/303 Collins St Melbourne.

Please arrive 6pm Friday night a 7pm start.

Register so we know you’re coming!

How will it work?

Before: Some suggested problems will be on the site beforehand so you can start thinking about what and how to tackle. There will also be pointers to the free datasets available online if you’d rather choose something freeform – and a bunch of scientists will be around on the weekend to help, guide and mentor.

Friday night, 6pm onwards: This is a must. You can’t take part in the hack if you miss out on Friday night! Form a team, choose a problem, have a drink if you fancy, get started. When you choose a problem, you will need to figure out what ‘done’ means, and how you will test it. Arrive at 6 for a 7pm start.

Saturday & Sunday, 9am onwards: All the wifi, coffee and food your heart desires. Plenty of developer tools and support. Experts in research and technology will be around to act as data custodians and problem owners, as well as facilitators to help teams focus and move through problems.

Saturday 3-4pmish : checkpoint. Stop for a break, tell everyone where you’re at, maybe find someone to exchange skills with.

Sunday 4pm: down tools! THE END! showcase! prizes! drinks!

Who is this for?

Health Hack is open to everyone and anyone. From data vis, designers and UX’ers, through to web developers and hard core application developers. Never participated in one of these things before? A bit of a newbie? Perfect; come along. Pull a team together to tackle some fascinating problems in medical research. Build your own mashups, data visualisations and apps. HealthHack is about having fun and learning, regardless of your level of expertise. From first year university students through to hardened developers, everyone who gets involved will come away from the weekend with something new, whether it be code, content, an idea or new contacts.

Can I participate remotely?

Yes you can! Form your own team where you are, or find a team in Melbourne to work with on Friday night. We’ll have video link facilities. If you know any scientists near you who would like to participate, all the better. If you’d like to be involved remotely, please get in touch with us ahead of time so we can organise All The Things.

Register

And it goes without saying, bullying and harassment have no place at HealthHack – play nice or go home

Our sponsors

ThoughtWorks Australia

Monash University, Faculty of IT

V3 Alliance

Unlockd

Walter & Eliza Hall Institute

VLSCI