eResearch and Bioinformatics Cross Paths at CUB

(Written by Anelda van der Walt)

This week we decided to reach out to the local eResearch initiative at the University of Cape Town to find out how eResearch is impacting the world of Bioinformaticians locally (and internationally).

Anthony Beitz, previously general manager at Monash eResearch Centre in Melbourne now interim director of UCT eResearch, treated us to a whirlwind tour of computational solutions for data analysis, visualisation, and even collaboration.

UCT eResearch was the brainchild of Sakkie Janse van Rensburg, executive director at UCT ICTS and was formed in 2014.  The initiatives partners with researchers at UCT to accelerate and transform research discovery through the application of advanced ICT technology such as high performance computing, visualisation, data management, and communication technologies.  In the past 12 months eResearch have collaborated with a diverse set of researchers on high-impact projects such as the Human, Hereditry, and Health project and specifically the H3ABionet subproject, African Mining Legislation Atlas, building computational infrastructure for the Olympus Virtual Microscope, and collaborated to establish one of the few first-in-human clinical trial sites on the African continent amongst others.

Training forms an integral part of the eResearch philosophy and for this reason they’ve recently launched a HPC training programme at beginners and advanced levels.  In 2014 eResearch co-organised a double-room Software Carpentry workshop as part of the eResearch Africa conference and this year they will be running several more Software Carpentry workshops.  The next workshop will run on 16 and 17 July on UCT Upper Campus.

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The eResearch team consists of researchers, IT and HPC experts, and software developers.

After Anthony’s presentation there was ample opportunity for the bioinformaticians representing Stellenbosch University, University of the Western Cape, and University of Cape Town, to informally discuss the opportunities around eResearch.


CUB#8: eResearch

Hi All,

The next CUB will take place on Thursday, 21 May 2015, from 17h00.  For this event, Anthony Beitz, interim director at UCT eResearch will provide insights about why eResearch came about, and how it is applied at research institutes across the world.

If you’re interested, please sign up!

CUB #7: The Cape R User Group

New Beginnings for the Cape R Community

(Written by Anelda van der Walt)

 The first official Cape R User Group event were hosted last night at “The Lab” on UCT Upper Campus and what a turnout! Thanks to the sponsors – Revolution Analytics – there were free beers for the first 20 people and two beautiful R t-shirts up for grabs during a lucky draw (run in R!).

The speakers did a great job of convincing R novices of the usefulness of R for their research, whilst the more experienced R folks had an opportunity to share advice and ideas and discuss best practices.

Jean-Baka Domelevo Entfellner, originally from Rennes (France) but now a postdoctoral research fellow at the South African National Bioinformatics Institute, currently works on an NIH funded project known as H3Africa – specifically H3ABionet.  During his talk, Jean-Baka gave a comprehensive overview of rworldmap and showed how they are plotting bioinformatics capacity at H3A nodes in Africa with this function.

Jean-Baka talking about rworldmap used in the H3ABionet project

Jean-Baka talking about rworldmap used in the H3ABionet project

Maia Lesosky, senior lecturer and biostatistician at UCT Department of Medicine, took us for a whirlwind tour of the Hadleyverse and couldn’t hide her love for R.

Hands up - who uses R regularly?

Hands up – who uses R regularly?

There were a total of 37 participants!  Really a fun event to be part of and gauging from the happy faces and the excited buzz throughout the evening, definitely an event that I would highly recommend for CUB-ers interested in meeting others working in R.  See you at the next event in Stellenbosch!

[Co-authored by Natasha Wood, Marike Visser, Anelda van der Walt, Gustavo Salazar. Photos by David Matten and Anelda van der Walt.]

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Networking can be tough, but it can also be surprisingly easy!  

What do you get if you use technology to introduce different groups of people from three geographically remote locations for an unseminar in Bioinformatics?  Three rooms filled with computers and strangers and very little choice on whom to approach and what to say as you introduce yourself…

The instruction from the organiser: “Talk to the person standing in front of you – you have 90 seconds. Go!”

Within this scenario, awkwardness is allowed and often expected but disappears as the clock starts ticking because you soon realise that everyone else is faced with the same predicament.  The fleeting encounter is over before you can think of what you should have said instead, and you leave contented having met a new peer.

This was exactly our experience at CUB#6.

After a quick meet-and-greet, between CUBers in Cape Town and GrUBers in Grahamstown, we were ready to mingle with the HUBers in Heidelberg, Germany. The initial social conversation evolved into enthusiastic planning around a collaborative project. And, almost like an exciting children’s party, ended too early as ideas were still being bounced around when goodbyes had to be said.

During this week’s session we were once again introduced to several great tools for inter-institutional, or rather, intercontinental, collaboration. We started the meet-and-greet using, a video chat room tool that allows up to 8 people joining for free. It’s as simple as

  1. Navigate to the website
  2. Create a room by entering a room name
  3. Share the link with your colleagues and start chatting

We also used PiratePad (an implementation of Etherpad) a collaborative, real time editor, which allowed us to take notes of discussions and ideas as they were happening.  The end result was that everyone had access to the notes in real time and everyone could contribute to the note taking.  No longer does a single person have to be nominated for taking minutes, and no longer do we have to wait for days or weeks before minutes are circulated after laboriously re-typing handwritten notes in a word processor.  And one of the greatest benefits of using this web-based editor?  Every person, even the one who never gets a chance to talk, can contribute by adding their thoughts to the PiratePad.

We decided to work on a common software project where any member can contribute according to their preferences and skills. The project is to create a user friendly version of a program that divides a group into pairs, prioritising the preferences of each person wanting to talk to someone in particular. The algorithm was presented in a paper in 1985 by Irving and we will use an existing implementation in Perl as our reference. The final notes of the event organised by each of the focus groups are available in the links below:

Of course these tech-type link-ups don’t always run smoothly right from the start, but after the initial disarray we managed to achieve our overall goals for the evening. And with each event there is progress towards that sense of community where a group of scientists with a keen interest in bioinformatics can meet and discuss topics and philosophies related to their field.

We’re looking forward to our next CUB-HUB-GrUB meetup! *

We are extremely grateful to UCT ICTS for the use of their facilities. aneldaDSC_0465

CUB#5: On visualisation, gamification, and science communication.

  • Co-authored by Anelda van der Walt, Natasha Wood and David Matten.

17 March 2015

“We don’t just want to develop games, we want to change the world” is what Glenn Gillis, managing director of Sea Monster, had to say about their company’s vision when he welcomed a group of bioinformaticians and computational biologists on Monday evening.

These words resonate well with the researchers and postgraduate students who visited the Sea Monster offices in Gardens, Cape Town, to discuss innovative ideas for science communication, education, and visualisation.  The event forms part of the Cape Unseminars in Bioinformatics initiative that was recently established by Dr Natasha Wood and Gustavo Salazar in order to provide opportunities to explore new ways of communicating and developing bioinformatics amongst students, researchers, and non-scientists.

Effective communication is key, both within and outside of academia. Wynand (Munki) Groenewald, Gillis’ partner and creative director at Sea Monster, provided a number of tips for good storytelling, an artform that is not often associated with scientists.  One of the most important tips, in his eyes, is to really understand who your audience is and to engage each listener individually. Other examples included trying to think of five words to describe what you do, or to practice an “elevator pitch” to both peers and non-scientists alike.

The informal event was attended by bioinformaticians from various institutes across South Africa, including WITS, University of Pretoria, University of Stellenbosch, University of the Western Cape, University of Cape Town, the Centre for Proteomics and Genomics Research as well as Talarify, a local bioinformatics startup company. Some of the latest products developed by Sea Monster were showcased, which transpired into stimulating discussions on the underlying premise and purpose for each application.  These conversations prompted further debates on the use of augmented reality in scientific poster presentations and infographics, as well as the use of gamification in tackling complex research questions.  The concept of using both intrinsic as well as extrinsic reward and gratification in learning and development was another topic where the hosts and participants shared the same vision and enthusiasm.

Although it might be hard to imagine what an animation studio and a bunch of researchers could possibly have in common, it was clear that the same passion was shared and that there are many touching points that remain to be explored.  Interlacing the commonalities between two seemingly disparate disciplines opens such a vast world of interesting ideas that we truly do feel like we will change the world.

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Planning meeting + coffee

Let’s have Coffee

Hey guys, for those interested in taking part of the planning of the next Cub Hub, please join us for coffee this Wednesday (12th of November 2014) at the IDM cafe in UCT – medical school.
Sorry about the short notice, but hope to see you there!

Novartis Internship Opportunities: The Next Generation Scientist Program 2015

Applications are now open for the Novartis Next Generation Scientist Program – see the attached flyer for more information (closing date: 31 October).

The Next Generation Scientist Program is an intensive internship program for talented and motivated research scientists from emerging countries. The 3 month program (1 June to 31 August), hosted at our research site in Basel, Switzerland, is designed to foster both their scientific and professional development. Guided by Novartis mentors, the interns work on a jointly-agreed upon, pre-competitive scientific or clinical project and also participate in a leadership development program designed to enhance their decision-making and communication skills.