On 14th-16th December 2017, Prof. Sam Sheppard and Dr. Sion Bayliss from the Sheppard Lab (University of Bath) presented the MRC CLIMB project at the SMBE satellite meeting – “Evolution of microbes in natural and experimental populations”. The meeting was hosted by Dr. Siddartha Satapathy and Prof. Suvendra Ray (Tezpur University, Assam, India) in Kaziranga National Park, Assam, India.
During the MRC CLIMB session, Sam Sheppard and Sion Bayliss introduced the CLIMB project, described the infrastructure and detailed the VM provisioning model. Sion Bayliss gave an introduction to methodologies used in the analysis of whole genome sequence data for microbial genomics. Dr. Harry Thorpe (University of Bath) provided a video walk-through of a data analysis project, from raw data to phylogenetic tree, by way of a user testimonial for CLIMB.
Finally, a limited-over cricket game between India and the Rest of the World unsurprisingly resulted in a smashing win from our Indian hosts (by 6 wickets)!
Upcoming meeting about microbial evolution held next December 2017 in the Kaziranga National Park, Assam, India. For more information, click on the image below:
Ben Pascoe, Sion Bayliss and Radoslaw Poplawski have returned from a successful MRC CLIMB workshop in Vietnam. The two-day workshop introduced attendees to CLIMB and working with their own virtual machine. Participants used EDGE to assemble bacterial genomes, asses the quality of sequence reads and assemblies, identify contamination, define isolate phylogeny compared to selected reference genomes and identify common virulence and antimicrobial resistance genes. Many thanks to our hosts Guy Thwaits, Stephen Baker, Phil Ashton and Cate Anscome for inviting us to OUCRU and we hope to visit again soon.
Today, our good friend and collaborator Koji Yahara (National Institute of Infectious Diseases, Tokyo, Japan) came to visit on his May 2017 UK tour. Good times catching up!
From left to right, Harry Thorpe, Ben Pascoe, Guillaume Méric, Evangelos Mourkas, Diego Flores Cuadrado, Koji Yahara, Sam Sheppard.
We are glad to welcome Diana Espadinha (ITQB NOVA, Oeiras, Portugal) and Diego Flórez Cuadrado (Complutense University of Madrid, Spain) to our lab for a research stay with us as part of their PhD studies. Diana will stay 3 weeks, working on Staphylococcus genomics while Diego, for his second stay with us, will spend 3 months working on Campylobacter genomics and antimicrobial resistance. #goodtimes!
Top picture: Diana and Diego, on St. Patrik’s day at the Parade (Uni. of Bath); bottom picture, at the Raven of Bath, from left to right: Ben Pascoe, Evangelos Mourkas, Jean van Elsen, Diego Florez Cuadrado, Diana Espadinha, Jess Calland, Sam Sheppard, Guillaume Méric.
MRC CLIMB fellow, Daniel Falush hosted a well-attended meeting on development of pipelines for bacterial evolutionary genomics at the University of Bath. With attendees from all over the UK, Europe and even Asia (via Skype) the latest techniques for analysis of populations of bacterial genomes were discussed.
Ben Pascoe from the Sheppard Lab has returned from a successful workshop in the Gambia organised with collaborators from MRC CLIMB. The two-day workshop introduced attendees to CLIMB and working with their own VM participants assembled a test set of bacterial genomes, which they analysed to asses quality, type, call MLST sequence types, identify antimicrobial resistance genes and define core and accessory genomes. The visit was enjoyable and with the inauguration of President Adama Barrow tomorrow (18th Feb) these are very exciting times in the Gambia and hopefully the beginning of a fruitful collaboration.