Ebola Crisis Hackathon

The Ebola Virus has killed almost 6000 people in West Africa since Dec 2013

Ebola has infected over 15000 people in West Africa since the start of the current outbreak in December 2013. The disease has an estimated case fatality rate of about 71%, and efforts to control the outbreak have been hampered by the political and economic situations in the countries affected (so far almost all cases have occurred in Liberia, Sierra Leone and Guinea). Problems have included, but are certainly not limited to, the extreme poverty in the region (including very limited infrastructure), a lack of trust in government officials, traditional death customs (e.g. physical contact with the dead) and the propensity of health workers to become infected with Ebola.

It was with these obstacles in mind that the Said Business School's Oxford Launchpad (which aims to support entrepreneurial endeavour in Oxford) organised and hosted the Ebola Crisis Hackathon, which aimed to "explore and solve 'pinch-points' in the response, care and management of the global response against Ebola". The hackathon (an exciting name for a workshop or study group, which has the consequence of labelling its participants as hackers, in this case making me sound much cooler and edgier than I am) was held on the weekend of the 8th-9th of November and brought together life-scientists, MBAs, software developers, physicians and charity workers.

Participants were encouraged to gather ideas over the week or so before the workshop and the event started on the Friday evening with brainstorming sessions. We worked in groups to generate and evaluate different ideas for solutions. The most popular ideas were then pitched to all participants, with groups forming around a few ideas.

While researching the problems around the diagnosis and treatment of Ebola, before the hackathon, I read about the potential for Ebola to be diagnosed using mobile apps. However I soon discovered that internet access was severely limited in West Africa (1.5% in Guinea, 1.3% in Sierra Leone and 3.8% in Liberia) which reduced the scope for using apps. However, mobile phone use is reasonably high (47% in Guinea, 52% in Liberia and 48% in Sierra Leone), and this encouraged me to think about developing similar systems using SMS text messages. I found that an open-source Django based package for writing SMS based systems had been developed and had been deployed in similar medical applications around Africa (RapidSMS).

Mobile phones are a primary communication method in West Africa

At the Hackathon, I teamed up with others who had had similar ideas. Given the severe lack of health workers in the affected region, we decided that a risk assessment tool would be particularly useful. Concerned individuals would text a number, and would receive a series of five questions on their symptoms and recent travel history. They would then  be categorised into several risk categories and would be given automated advice by the system and, in some cases, have their details passed onto agencies who would be able to help. We worked in three subgroups: one looking at the risk assessment questions, another looking at the obstacles to deployment and one implementing the system in RapidSMS.

We called our product SymptomSMS and were mentioned in an article on the Hackathon in last week's New Scientist.

Maths in the city

Outreach is an incredibly important part of a researcher's job. Many mathematicians are funded through research councils that rely on tax payer money, so we really should be able to justify the work that we do. One project set up to do just that is Maths in the City. WCMB members, Dr Thomas Woolley and Paul Taylor, were recently filmed demonstrating the tour. Here, Paul recounts the experience.

On tweetcasting

After a travel- and conference-induced silence over the past months, we're back from the ECMTB in Gothenburg with some fresh thoughts for new posts. To start, Alex Fletcher, Linus Schumacher and Jacob Scott discuss a newly fashionable conference activity: tweetcasting.

James D Murray, Reflections of a life in Academia, in conversation with Phillip Maini

Founder of the WCMB, James Murray, visited Oxford last month to give the inaugural Hooke lecture, "Why there are no three-headed monsters, resolving some problems with brain tumours, divorce prediction and how to save marriages". While he was here, he was interviewed by his former student and our current director Prof. Philip Maini, featuring questions from various members of the WCMB. You can watch the interview here as part of the podcast series The Secrets of Mathematics.

Discrete and continuous models for tissue growth and shrinkage

In this post Dr. Christian Yates summarises his recent paper “Discrete and continuous models for tissue growth and shrinkage”, on modelling tissue growth and shrinkage using mathematical models that explicitly incorporate randomness in the tissue deformation process.

Understanding the host-virus interaction in chronic HTLV-I infection with the help of mathematical modelling

In this post Aaron Lim, a DPhil student at the WCMB and the EEID, discusses his work on within-host mathematical modelling of host-virus interactions.

Taking randomness into account

In this post Dr. Ulrich Dobramysl, a Postdoctoral Research Assistant working at the WCMB, discusses stochastic modelling and randomness in biological systems.

Silver at SET for Britain

In this post Dr. Christian Yates , a Junior Research Fellow working at the WCMB, gives us a description of his poster on locust migration which scoped the Silver Award in the Mathematics section of SET for Britain, a national poster competition held in the Houses of Parliament.

Chemical reactions, spatial information processing, and model invalidation, oh my!

In this post Dr Heather Harrington, Hooke Research Fellow and EPSRC Postdoctoral Fellow at the WCMB, discusses her research interests.

Interdisciplinary communication: stuck in the middle?

In this post D.Phil. student Linus Schumacher sums up recent thoughts on interdisciplinary communication and science career paths.

Ten simple rules for effective computational research

With the increasing use of computational techniques in the life sciences, a wide range of scientists are finding that software development plays an increasing role in their day-to-day research. In this post Dr Alexander Fletcher discusses a forthcoming article on best practice when developing and using software for scientific research.

Mid-term update

We're halfway through term here in Oxford, and at the WCMB we've had a busy week with excellent talks by Zhuoyi Song and Luca Cardelli. Next week Frits Veerman and Adam McLean are speaking at Monday's group meeting, while Friday's research seminar will be given by David Smith.

Our blog admins have been hit by scheduling delays this week, so there's no new post from us. But why not check out some of our group's very successful individual blogs, The Laughing Mathematician and Cancer Connector.

We've got some exciting posts in the pipeline for the rest of this and next month, and will be back for you all next Sunday.

Hamilton’s haplodiploidy hypothesis and the females who do all the work

In this post Nick Davies, who is doing his DPhil between the WCMB and the Foster lab in Zoology, provides some history on the long-standing question of why worker castes in social colonies of wasps, bees, and ants are exclusively female.

Blabbing about blebbing: Oxford University’s Mathematical Institute conference on membrane dynamics and blebbing, September, 2013.

In this post Dr Thomas Woolley reviews a recent conference he organised in Oxford. Bringing together experimentalists and theoreticians from around the world they had one focus: blebbing cells!  

Poster: Investigating bacterial ecology and evolution in complex environments

Another recent poster from Katharine Coyte, who is doing her DPhil between the WCMB and the Foster lab in Zoology. This poster wan an award at the id2 conference.

21st Century Turing

In this post Dr Thomas Woolley describes one of the original, biggest and most outrageous ideas of mathematical biology. Thomas achieved his doctorate working on mathematical pattern formation within the WCMB in 2012, under the supervision of Prof. Philip Maini, Dr Ruth Baker and Dr Eamonn Gaffney. He is currently a Junior Research Fellow for St John’s College, Oxford and works on the solid mechanics behind cellular motion. However, he still likes to keep an eye on pattern formation. He runs his own mathematical outreach website as well as working as a mathematical consultant on the TV show “Dara O’Briain’s School of Hard Sums”. 

Poster: The fractured bacterium: how horizontal gene transfer and selection divide the genome

Another poster from the DTC 4th year conference, by Rene Niehus who is co-supervised between the WCMB and the Foster lab in the Department of Zoology.

Workshop on "Mechanics and growth of tissues: from development to cancer"

In this post Dr Alexander Fletcher, Research Fellow in Computational Science at the WCMB, discusses the workshop "Mechanics and growth of tissues: from development to cancer", which took place at the Institut Curie in Paris on 13-16 January 2014, and describes the content of his poster contribution.

Poster: A simple model of wound healing in normal and diabetic mice

We will try and upload most posters that members of the WCMB present at conferences. The DTC 4th year conference is coming up, for which Lucie Bowden has prepared the poster below.

Mathematical modelling of oxygen transport in cardiac and skeletal muscle tissues

In this post Abdullah Al-Shammari describes the DPhil project he worked on at the WCMB during the last 4 years. This project was supervised by Dr Eamonn Gaffney in close collaboration with Prof Stuart Egginton, whose labs in Birmingham and Leeds kindly provided us with biological datasets and interpretation of our modelling results.

Mathematical modelling and analysis of bacterial motility

In this post Gabriel Rosser, who completed his D.Phil. at the WCMB in early 2013, describes his research in bacterial motility.