LABORATORY INFORMATICS


today, and it is even possible to detect patterns of vaccine compliance in the smallpox maps”


response on the ground. This current epidemic is much more serious: by May 2019 the known death toll had passed 1,000 and charities were urging the UN to ramp its response level up to ‘level three’: the highest possible, reserved for the most serious global crises.


This epidemic has,


their code, so it could be re-used more easily in future similar epidemics.


An open-source approach Thibaut Jombart, who is now based between LSHTM, the UK Public Health Rapid Support Team and Imperial College, was a member of the WHO’s analysis team during that epidemic, developing the team’s analysis infrastructure using the R programming language.


During a ‘hackathon’ on


software for outbreak analysis that he organised in Berkeley, California, in 2017, he and a group of colleagues decided to form a network of like-minded people that could decide on the most important priorities and needs for outbreak analysis tools. He is now the president, and Cori the methodology coordinator, of the international R Epidemics Consortium (Recon), which was incorporated as an NGO in France in September


2018. 'We chose to focus the network only on R, because it has the largest number of statistical libraries of any open-source programming language', Jombart said. 'We were determined to make all our code completely publicly available free of charge, and we didn’t want to have to reinvent the wheel.' Recon has produced, and maintains, a wide variety of tools for outbreak analysis, including – thanks to a diverse membership including statisticians, field epidemiologists and software developers – extensive documentation and open access training resources. Members of Recon and


others were able to test some of their computational tools during a relatively small and well-contained Ebola epidemic in the Democratic Republic of the Congo (DRC) in 2017. When the disease returned the following year, so did the epidemiologists, with software from Recon informing the


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however, provided a second opportunity to test candidate vaccines using a technique called ‘ring vaccination’. This involves vaccinating each contact of each person infected, and each contact of those contacts, to form two ‘rings of vaccination’ around each case. 'Consortia developing Ebola vaccines rely on epidemiologists and mathematical modellers to predict which areas the disease will be most active at a given time, and how many cases there will be, so they can estimate the number of vaccine doses required and get them to the right places', explains Cori. Clearly, software developed during one epidemic, or even for monitoring one disease, will be of limited benefit unless it can be re-used in many situations. Any code that is developed or even adapted ‘on the fly’ in response to an emergency is highly unlikely to fit these requirements. Adapting such software to make it robust and generic enough for rapid and effective re-use is the role of research software engineers such as Richard Fitzjohn, a senior R developer at Imperial College London.


'My background is in


software development, not epidemiology' he explains. 'My work is to make the


epidemiologists’ lives easier, so they can focus on research questions without worrying about whether the programs will fall over or how long they take to run. Crucially, this also includes improving the interface, so it is user- friendly enough to be used by scientists who may be inexperienced and are bound to be under stress.' Much of the software his group produces is designed to be used in to endemic, as well as epidemic, situations, and to monitor bacterial, as well as viral, disease.


Epidemiologists studying


outbreaks of infectious disease have another powerful tool available to them in genomics. It is less than a quarter-century since the genomes of the first pathogenic bacteria were released, often via publication in the most respected journals and to worldwide acclaim. Now, in contrast, a complete bacterial genome can be sequenced very rapidly using relatively cheap equipment. This data has multiple uses, from clinical decision-making ‘on the ground’ to worldwide surveillance programmes for mapping, and thus combating, the spread of antimicrobial resistance.


Epidemic outbreaks The Centre for Genomic Pathogen Surveillance, based at both the Wellcome Trust Sanger Institute, near Cambridge, and the Big Data Institute at Oxford University, was set up four to five years ago with the ambitious aim of translating microbial genomics into a public health context. Its director, David Aanensen, also leads research programmes


August/September 2019 Scientific Computing World 21


”Resistance to vaccination against smallpox was as strong then as the so-called ‘anti-vax’ movement is


g


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