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Coming to ResBaz? Please read our policies (recording, reporting and anti-harassment) and Code of Conduct. We’re really serious about making sure that everyone feels safe and has a good time at all our events!
Throughout these policies, we refers to the Research Bazaar team of staff and volunteers.
By accepting a place at the Research Bazaar, you agree to be bound by these policies and Code of Conduct.
This Code of Conduct draws inspiration from the Django Community Code of Conduct
The Research Bazaar is a learning environment where everyone is welcome. It’s a diverse community from a wide range of backgrounds and interests. To ensure that everyone has an enjoyable and enriching experience, please bring a spirit of respect and friendly inquiry to all your interactions at the Research Bazaar.
Be friendly and polite.
Be welcoming. The Research Bazaar strives to be a community that welcomes and supports people of all backgrounds and identities. People from all stages of their careers and fields of inquiry are welcome.
Be respectful. Participants come from a huge range of backgrounds and experience levels. Everyone should feel comfortable to ask for the help they need to understand the discussion. Listen and support others to learn. Remember that everyone here has their own field of expertise.
Be kind to others.Be careful in the words that you choose. Do not insult or put down other participants.
We will be taking photographs and video of sessions (training and social) at ResBaz. These images and recordings may be used to promote the conference and other activities by the Research Bazaar team.
If you do not wish to be photographed, please let the organisers know and obtain a `no photos’ sticker for your name badge.
If someone indicates that they do not wish to be photographed, respect their wishes and delete any photographs you have taken that include them. This includes group shots and photographs where they appear in the background.
We encourage all ResBaz attendees to join the conversation on Twitter before, during and after the conference. We also encourage attendees to discuss their experiences by blogging or writing pieces for their home institution blogs and newsletters if appropriate. We will be covering the conference by live-tweeting and blogging. Attendees are reminded that the Code of Conduct and Anti-Harassment policy extend to online interactions associated with the Research Bazaar.
Comments made on social media may be republished with attribution (for example retweeting or embedding of Tweets in blogs). If you wish to attribute an opinion or statement to an individual in a long-form piece, please verify with that individual that they feel you have written an accurate representation of their view, especially if it concerns their research.
Please remember that the Research Bazaar is a learning environment and don’t distract other attendees by photographing/ live tweeting excessively during training sessions.
This policy is based on the anti-harassment policy developed by the Ada Initiative and other volunteers for use by geek conferences.
The Research Bazaar is dedicated to providing a harassment-free experience for everyone at our events and in our forums. We do not tolerate harassment of attendees in any form. Attendees violating these rules may be sanctioned or expelled from the event and its forums at the discretion of the anti-harassment officers or the host.
Harassment includes:
Participants asked to stop any harassing behavior are expected to comply immediately. Any member of the Research Bazaar staff can issue a verbal warning to a participant that their behaviour violates the conference’s anti-harassment policy. A record of complaints received and warnings issued will be maintained to enable any repeat offenders to be identified.
If a participant engages in harassing behavior, the anti-harassment officers may take any action they deem appropriate, including warning the offender or expulsion from the event.
If you are being harassed, notice that someone else is being harassed, or have any other concerns, please contact the anti-harassment officers immediately. If you are being harassed by an anti-harassment officer or otherwise don’t feel safe reporting to them, please contact David Flanders.
Anti-harassment officers will be happy to help attendees contact police or crisis services, provide escorts, or otherwise assist those experiencing harassment to feel safe for the duration of the event.
We value your attendance. We expect participants to follow these rules at the Research Bazaar venue, any related social events, and online forums.
Mozilla Festival (or MozFest, to its friends) is a weekend-long extravaganza for the open web community. Taking over Ravensbourne Arts College in Greenwich, MozFest 2014 boasted 11 streams of activities, ranging from art and music of the web, open community building and data journalism, to building the open web and, of course, open science as practiced by the Mozilla Science Labs. I was privileged to attend MozFest as part of the Science and the Web stream, where I shared the work that we’ve been doing at the Research Bazaar to introduce the Python Natural Language Toolkit to researchers from the Humanities and Social Sciences. The notes from the session are here - big thanks to all the lovely participants!
As you’d know if you’ve been to our trainings using Python, we’re big fans of the iPython notebook here at the Research Bazaar and we’ve got a great cloud platform built by our own Tim Dettrick. I felt pretty proud to show off our DIT4C to iPython developer Kyle Kelley, who agreed it’s a great way to bypass installation hassles during a workshop. MozFest was also a great chance to meet Software Carpentry instructors from around the world, like Aron Ahmadia, and compare how we’re using the tools.
There’s more to Open Science than Software Carpentry, and the Science track had an amazing array of activities. I went to a workshop on Cleaning Messy Data run by the School of Data, discussed plans for the ideal open journal, and added some post-its to the Open Science Skills Map. In fact, the Science and the Web space, expertly wrangled by Kaitlin Thaney, Bill Mills and Abby Cabunoc, was an incredibly friendly and collaborative place to spend a couple of days.
I’d already had the benefit of a week in London talking Digital Humanities with a number of researchers and practitioners, and was formulating my thoughts about the sorts of digital skills and knowledge Humanities researchers are going to need, so I was really interested to attend the Hacking the Library session, where we started to map out a curriculum to give the librarians of the future the skills they’ll need. Again, I was happy to see that the work we’re doing here in Melbourne puts us in line with international thinking about data literacy and the need for everyone to learn a little code.
Over 1700 people came through MozFest over the weekend, which is a massive number and the experience could easily have been overwhelming. But the Mozilla team know how to put on a good show. There was excellent coffee available (yep, Australian baristas!) and enough space in the college that you could find a spot to chill out between sessions. I learned some new skills and saw some great tools in action, but perhaps the best part of MozFest was the community. Everyone I met was curious and enthusiastic and, even though I was worried about showing basic NLTK to a group of experienced Python users, seeing people light up as they realised that text can be interrogated like any other dataset was a real thrill.
Thank you to Mozilla and in particular the Mozilla Science crew for an amazing experience and see (some of) you in February!
All photos from the Mozilla Europe Flickr stream
We’re pleased to announce that we’ll be running a two-day Software Carpentry Workshop on December 8th & 9th.
We’ll be teaching the basic lab skills for scientific computing using the R statistical programming language, along with the unix shell for interacting with and pipelining scientific software, and Git/GitHub for tracking changes to your work and collaborating with other scientists.
The material will be novice level, so while it’s helpful if you’ve encountered R or another programming language before, we won’t expect you to have any level of detailed knowledge.
The workshop will be co-hosted by COMBINE, a national student group for postgraduate and early career researchers in the life sciences who do computational research.
The workshop is free, but space is limited, so make sure to register to secure a place!
Date and Time:
Monday December 8th, 9:00am – 5:00pm
Tuesday December 9th, 9:00am – 5:00pm
Location:
Alan Gilbert Theatre 2
Registration:
https://www.eventbrite.com.au/e/university-of-melbourne-software-carpentry-r-bootcamp-registration-14287794177
Cost:
FREE!
Contact:
Scott Ritchie is our lead instructor for R. He can be contacted at scottr [at] student.unimelb.edu.au
The research landscape is changing and research can now be more of an adventure than ever. Bringing new technology to research problems in the humanities and social sciences is making new areas of inquiry accessible and changing the scope and scale that’s possible for researchers. Whether it’s using the latest CT scanners to learn more about ancient Egyptian mummies or using text-mining techniques to analyse huge digitised archives, there are whole worlds becoming available to bold explorers. So what do the adventurous new digital humanists look like and what’s in their toolkit?
While the digital tools are exciting, it’s critical that researchers are still experts in their domains and understand the background of their field and its problems. Only someone with deep knowledge of their field is going to know which are the compelling research questions to ask and how to begin looking for the answers. It’s no good going looking for treasure if you won’t recognise it when you see it!
At a fundamental level, the digital humanist gets data. Humanities researchers have always been collecting data, but we haven’t always thought about it like that. Digital tools, however, demand that researchers think much more explicitly about how we collect, manage and structure information. Whatever the object of study, the data itself must be set up correctly to enable the dataset to be interrogated. This means basics like having files in the right formats for the tools and the information structured so that it can be analysed. Want to analyse the dates of letters in an archive? Make sure that the date is in a consistent format in your database. Getting these basics right is essential to being able to work effectively with data.
Going further, the digital humanist needs to know how to process and combine data to get the most out of it. She also needs to understand the limitations of the data she’s using, which sometimes means recognising the challenges and limits of digitisation itself. To be really sure that she’s not going astray, our digital explorer must also understand the tools she uses and their strengths and weaknesses. Like any research methodology, digital tools will return a result but the researcher needs to be critical when interpreting it. Knowing the field, knowing the data and understanding the tools mean that our explorer is less likely to mistake a crocodile for a safe bridge across a river.
It sounds like a lot to ask. And it is. Researchers are already under pressure to know and do a huge amount. But digital humanists need to be prepared to strike out into the unknown. Most importantly, the digital humanist is unafraid of technology. She’s willing to try new techniques and lines of inquiry and is excited to collaborate with experts from other fields who bring fresh learning and perspectives to their projects. With a fearless attitude and the right tools and companions, the digital humanist is equipped to go exploring in uncharted territories and bring back new discoveries!
I was recently fortunate to go to London for Mozilla Festival and meet with a number of digital humanities practitioners. This post grew out of my conversations with them. Special thanks to Ben O’Steen, James Baker, Daniel Pett, Jane Winters, Simon Mahony, Ben Showers, and Mark Hedges for being so generous with their time and thoughts.
By Dejan Jotanovic & Scott Ritchie
point of #healthhack: a) solutions for scientists c) hackers doing science d) scientists see what software can do http://t.co/HpBeeGjqF5
— MSF Australia (@WePublicHealth)
October 24, 2014
This year’s #HealthHack had two sites, rainy Melbourne & (brand new) sunny Sydney, and was on the operation table for three days: October 24th - 26th. But let’s give a quick diagnosis - what IS #HealthHack? As explained on their website:
HealthHack is a weekend data hack dedicated to problems that medical researchers face. Scientists often create vast amounts of data, but don’t always have good ways to analyse, visualise and communicate it. This weekend will bring together software developers, user experience designers, data analysts and visualisers working directly with researchers to create new, better tools.
Basically a bunch of smart people are kept in a big room (cheers, ThoughtWorks) with a load of dumplings, sticky-notes and coffee coupons. Teams are formed, questions are asked, data is tugged, pulled, sculpted. Two sunsets later and the answers are presented in the form of apps, videos, visualisations and speeches. What you can do with the right people in the span of two and a half days is truly outstanding. The event was brought to life by the Open Knowledge Foundation.
Here’s a quick recap of the different Melbourne teams and their collective projects.
Epilepsy Visualisation Tool
And now we have team, Epilepsy Visualisation Tool! #healthhack pic.twitter.com/IYMNM4jabA
— OKFN Australia (@OKFNau)
October 26, 2014
Kate Birch and Anne Mcintosh, two researchers from the University of Melbourne, wanted a tool that could be used by clinicians to visualise patient data, so that they can more easily find correlations between seizure frequency, medication, quality of life, and any potential surgery.
Why? Because epilepsy is a very complicated disorder: seizures frequency and severity vary from person to person, having different impacts on each individual. Understanding how patients are impacted by epilepsy is further complicated by the messy way in which patient history information is stored.
A team of four created a tool allowing the researchers to visualise patients’ seizure history. This could help clinicians make better, more informed decisions. And it was mobile friendly!
Data visualisation.at #healthhack for Epilepsy, from @Esther_Lim and team. Love seeing responsive design! pic.twitter.com/CvYLfSlqvV
— Jason Cormier (@jadacormier)
October 26, 2014
You can read more about this team here.
Same problem. Another solution!
Epilepsy Case Management team highlights their visualisation tool at #healthhack pic.twitter.com/aynaEbyef7
— Marguerite Galea (@MVEG001)
October 26, 2014
This team created visualisations which would help clinicians quickly and easily see their patients seizure, surgery and medication history! It’ll also how any medication frequency changes or how severe the seizure experiences were.
“gives clinicians ability to quickly & easily visualise patient’s longitudinal seizure, surgery and medication history” - great! #healthhack
— OKFN Australia (@OKFNau)
October 26, 2014
This is not a pipe: VLSCI Bioinformatics Pipeline
Now we have the very cleverly named, “This is not a pipe”: @vlsci Bioinformatics Pipeline #healthhack pic.twitter.com/3ZURrIrTUT
— OKFN Australia (@OKFNau)
October 26, 2014
Let’s all be honest here, sequencing and processing genomes can be tough. Outputs, inputs, the creation of pipelines. Often very complicated pipelines! Dr Bernie Pope and Dr Phillipa Griffin from VLSCI wanted to improve Rubra, a pipeline management tool used at VLSCI, to make it more user friendly for the biologists doing the sequencing, since they often don’t have a lot of computational experience!
“work we have completed so far could be used as seed for developing a more complete pipeline control solution” - Woohoo! @vlsci #healthhack
— OKFN Australia (@OKFNau)
October 26, 2014
The team made some serious progress into improving Rubra - and here’s hoping they continue!
Whole genome sequencing experiments involve complicated workflows: Challenging @vlsci protect for #HealthHack https://t.co/dbTDUvWphN
— BioMelbourne Network (@biomelb)
October 26, 2014
Mutation Instability Filter (MIF)
You know how it goes: you’re trying to identify genetic mutations responsible for a disease within a family, so you sequence their DNA, and after a series of analysis and filtering steps you’re left with a couple of hundred potential genes. Identifying the correct one is usually expensive and time consuming, requiring many experiments in the lab. But what if we could speed up this process AND reduce the cost? Enter, MIF.
“This project with decimate the time and cost associated with identifying harmful genetic mutations” 👍 #healthhack pic.twitter.com/GbMGSO7eVa
— OKFN Australia (@OKFNau)
October 26, 2014
Dr Charles Galea wanted to create an automated pipeline to query protein databases, automatically matching genes to their proteins, and measuring whether the mutations identified significantly disrupt the protein structure. This would hopefully allow researchers to massively narrow down the list of candidate genes from a few hundred to just a handful to follow up on.
A team of developers, scientists, and user experience designers were able to successfully build this pipeline over the weekend, creating a filter that dramatically decreases the cost and time required to identify the genes underlying familial diseases! This is the bit where someone in the audience would typically shout “That’s so awesome”.
Wolf whistles from the audience at #healthhack for sexy #dataviz on gene mutations pic.twitter.com/pcVn2qx8So
— Louise Schaper (@louise_schaper)
October 26, 2014
And that they did. MIF then went on to win the coveted “Spirit of #HealthHack” award, for being so damn awesome.
Check out all the awesome details here.
GIRROR: Tracking your emotions and gambling behaviour
How do environmental and emotional factors impact addictive behaviours like gambling? That’s the question Ben Fulcher and George Youssef from Monash University wanted help answering. To do this, they wanted to create a smartphone app, to allow gambling addicts to report on the factors that might influence their decision making.
Girror’s beautiful app - using standardised gambling addiction questions #healthhack pic.twitter.com/3hJ6j7NlUv
— OKFN Australia (@OKFNau)
October 26, 2014
They cleverly created an app (available for both iOS & Android - score!) which used pop-up messages asking patients to complete questions about their emotional state and environmental context. A short reaction time game was also included.
Nice looking Happiness Meter #healthhack https://t.co/jmDG6QjIR4 pic.twitter.com/GyzNOi6NUJ
— Louise Schaper (@louise_schaper)
October 26, 2014
Sounding cool? Well, it was! The future of this project lies in the ability for practitioners to develop personalised treatment plans, targeting the special things about patients - their wide ranging emotions and environmental contexts!
It’s therefore no surprise that team GIRROR came second at the #HealthHack awards! Read all about the project here.
VizMyGrant
Every year medical researchers across Australia eagerly await the results of the NHMRC funding, which are announced in late October. It’s an exciting and terrifying time for everyone: will they receive funding this year to pursue their research questions? Or will they have to join someone else’s lab? Or even contemplate moving overseas? Although the NHMRC makes their data publicly available, you have to pore through spreadsheets, pdfs, and word documents if you want to go any deeper than the summary statistics the NHMRC provides. Dr Marguerite (Maggie) Evans-Galea wanted to solve this problem by creating a tool to generate user-friendly graphics to clearly explain where the funding goes each year. Maggie was particularly interested in visualising the gender balance in funding outcomes at different career stages, having spent many hours trawling through the documents several years ago to visualise those imbalances.
But what if we could take it a step further? What if we could create an interactive tool that dynamically creates user-friendly graphics to view the NHMRC funding landscape in any way an interested individual could think of? What trends might that reveal? Our very own Scott Ritchie joined team VizMyGrant with the aim of creating an interactive web-based tool for visualising the relationships in the NHMRC funding outcome data.
Welcome to @VizMyGrant: an interactive online tool to visualise @nhmrc funding. https://t.co/M9sYsZhNY2 #VIZmyGRANT
— VizMyGrant (@VizMyGrant)
October 26, 2014
Scott, along with the rest of team VizMyGrant spent the weekend cleaning up the NHMRC funding outcome data and creating a suite of tools and visualisations, all of which were deployed online live at Health Hack! VizMyGrant proceeded to make waves on twitterverse with their visualisations of the gender imbalances in funding outcomes:
Well look at that. Senior male researchers get most science grants https://t.co/rgPDqCjoFJ #healthhack pic.twitter.com/armlju4OnW
— OKFN Australia (@OKFNau)
October 25, 2014
With the potential impacts on policy, and broad utility for early career researchers, its no surprise that Team VizMyGrant went on to win the Melbourne #HealthHack awards.
And the first prize goes to the phenomenal @VizMyGrant! Woohoo! Go out and expose those career structures (& inequalities) #healthhack
— OKFN Australia (@OKFNau)
October 26, 2014
You can find out more about Team VizMyGrant by watching their video, visiting their team page, or following them on twitter @VizMyGrant. All of the interactive visualisations created by the team can be viewed online, and Scott Ritchie’s tool can be found at https://viz-my-grant.shinyapps.io/view.
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Want to learn more about #HealthHack? Read organiser Maia’s musing here, and Tim Hildred’s (from Open Source) here. And check out the official storify.
Want to plan an event like #HealthHack and join the Open Science movement? Get into contact with the Open Knowledge Foundation. Ping them on Twitter or check their website.
Our very own Damien Irving (Research Community Coordinator for the Physical Sciences) has written a great post to demystify software installation for researchers. Enjoy!