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6th EBAME Workshop on Computational

Microbial Ecogenomics

October 25 - November 5 , 2021 in Brest - France
(application deadline July 1 , 2021)

Microbial Ecology is undergoing rapid evolution and dramatic progresses thanks to the combined advances in next-generation DNA sequencing technologies and computational approaches for data analysis and visualization. As a result,"microbial ecogenomics" has become an essential part of investigations of marine or terrestrial habitats, or host-microbe interactions. The aim of the EBAME workshop is to bring together researchers who generate complex 'omics datasets to investigate biologically significant questions with researchers who develop new ways to analyze complex datasets.

The workshop will have lectures on new methods
and their applications on real-world datasets, and  tutorials for hands-on experience.

The workshop will focus on various state-of-the-art data analysis practices targeting genome-resolved metagenomics including recovery of population genomes from metagenomes, analysis of micro-diversity through single-nucleotide variants, strain deconvolution, comparative genomics, application of network theory to complex metagenomic data, and data visualization.
Check EBAME 5 program and faculty


The workshop will be held exclusively in English and hosted by the European Institute for Marine Sciences at Western Brittany University, from  October 25 to  November 4, 2021. The institute is located on the wonderful setting of the Bay of Brest, at the heart of the largest French marine science campus, with easy access from Brest Bretagne international airport and train station. Funds and help for on-site child care will be made available on request

Attendance Fee
Fee of 700 euros per attendee for the 2 weeks workshop participation. It includes lunch meals, snacks, coffee breaks
and housing in small houses on the waterfront.

The workshop organization is made possible thanks to the sponsor of the ISBLUE graduate school, the IUEM Marine Science Institute, the region Bretagne, the Brest University research council, the  Brest Metropole BMO and the FACE / Thomas Jefforson fund.

The Institut Francais de Bioinformatique will provide computational infrastructure during the workshop 

Who should apply
The workshop will be most useful for researchers and graduate students who study microbes via shotgun genomics, metagenomic or metatranscriptomic datasets, and are interested in genome-resolved metagenomics and pangenome analysis. Applicants from different backgrounds are most welcome (such as computer scientists or biostatisticians). Hands-on tutorials will require familiarity with the UNIX terminal environment.

How to apply
An e-mail titled "EBAME 2021 Application" with application material as PDF attachments should be sent to lois.maignien@univ-brest.fr. Please make sure your application includes a short statement with your scientific background, current interests, the kinds of datasets you are currently working with, and expectations from the workshop (ideally in a single page). Feel free to add your CV as a separate PDF file to your application. We will consider applications until July 1, 2021.
Applicants will be notified shortly after regarding participation.

Thank you for your interest and we are looking forward to meeting you in Brest!

On behalf of the workshop faculty,

The organizing committee

EBAME5 alumni words....

"EBAME5 was the best workshop I ever attended. First of all, the program covers almost everything one needs to know about metagenomics to start/continue exploring this field competently. Secondly, EBAME gives an opportunity to communicate questions and ideas about novel approaches in NGS and microbial ecology with inspiring scientists. Finally, organizers of EBAME manage to create a unique atmosphere throughout the whole event: this atmosphere encourages attendees to discuss and look for solutions and input for their own research and to build connections among young scientists. EBAME is a unique event that was created by the collective effort of scientists [...] making sure that every attendee of the course is following all the difficult concepts of the lectures. "

"EBAME = 2 intense weeks in beautiful surroundings that will blow your mind about what you can do with 'omics data and additionally lets you meet many great people!"

"Really nice workshop. Well organised and the housing was awesome. The anvi'o part was amazing. Well explained, well prepared and really easy to follow. 650 euros is really cheap for a 2 weeks workshop with logistic. I admit it's the best workshop I have seen. We were really close to the speakers and it allowed us to discuss with them about our own projects."

"I have thoroughly enjoyed my experience at the EBAME workshop. As a novice in metagenomics, I did not feel left out at any point over the entire duration of the course! I learned about a broad range of information, ranging from the basics to the relevant cutting edge tools useful for microbial ecologists. The atmosphere was extremely friendly and educational. I would absolutely recommend EBAME to anyone daunted by the prospect of metagenomics, or to those more advanced wishing to learn about the evolution of the field."

"The workshop gives a thorough overview of the field of ecological and evolutionary meta-omics that attendees can build upon to confidently shape their research project and analyse their data accordingly. Also... great place and great people. A very pleasant environment to spend two enjoyable weeks."

"EBAME5 was a great opportunity for me as a Postdoc researcher. It helped me to deepen my knowledge for some parts which I knew about before and get new views on them. Not only that but also it provided a chance of learning new concepts, for example, Machine learning approach for Microbial 'omics. I highly recommend this workshop for postdoc researchers and PhD students"

"EBAME not only gave me insights into the latest software and tools for metagenomic processing but also provide a network of researchers with similar problems with their data. The very diverse topics of the course provide you with new tools in your own pipeline and also give you new ideas what you can do with your data. I liked the interaction betwen faculty and other participants and would recommend the workshop to any other scientist working with environmental metagenomics. "

"EBAME is a great workshop. Whether you are experienced or new to bioinformatics, within 2 weeks; time you will be upgraded to a new level of understanding of microbial research. I highly recommend it and consider coming again next year."

"EBAME gathers top-notch teachers to deliver an up-to-date overview of metagenomic research and its wide array of applications. I went back home with plenty of new ideas and a full contact book. A must go !!!"

"Computational Microbial Ecogenomics is relatively new and emerging field. With the decrease in sequencing costs more and more researchers are generating large and complicated datasets from a variety of microbiomes and are thus faced with the somewhat daunting task of analysis and interpretations. The EBAME course provides an incredibly strong foundation and training program to allow participants to learn about the latest analysis and new approaches to their own datasets. Participants are actively encouraged to take part in discussions, think outside the box and challenge themselves. All training material is provided so there is no need to attend with their own datasets, BUT it is important to have at least a good understanding of the field - this course is intense and rewarding but also high paced so pre-course reading and perhaps some experience is highly recommended. Aside from the high quality teaching and schedule , EBAME was also a wonderful experience for socialising and meeting other participants and teachers - the variety of backgrounds, nationalities and academic expertise created a lovely working environment and many good times both during and after classes. As such EBAME # 5 provided many stimulating conversations, and I feel confident to tackle some of my datasets; inspired to try some new things and excited to meet EBAMErs in future conferences and meet-ups. Do not miss the opportunity to take part in this course! "

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