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8th EBAME Workshop on Computational

Microbial Ecogenomics

October 21 - November 4 , 2023 in Brest - France
(application deadline July 1 , 2023)

Microbial Ecology is undergoing rapid evolution and dramatic progresses thanks to the combined advances of 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  workshop on Emerging Bioinformatics Approaches for Microbial Ecogenomics is to bring together researchers who generate complex 'omics datasets to investigate biological, ecological and evolutionnary questions with researchers who develop new concepts and computational methods to analyze such datasets.

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

Focus
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 previous EBAME program and faculty 


Venue

The workshop will be held exclusively in English and hosted by the European Institute for Marine Sciences at Best University, from October 21 to  November 4, 2023. 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 and family accomodation will be available.


Attendance Fee
Fee of 850 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.








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


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 8 Application" with application material as PDF attachments should be sent to lois.maignien@univ-brest.fr. Your application can  include 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, 2023.
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
.

EBAME7 alumni words....


    As a first/second year PhD student, EBAME was a fantastic experience. I could not recommend it highly enough for my peers. I learned a lot, and there were many useful perspectives to incorporate into my PhD project. The workshop was very well-organised, and I thank everyone involved for providing this workshop and keeping the value affordable. Suggestions/comments I have are: EBAME was great but also very exhaustive. Saturday could maybe be a morning-only day at the workshop. It would also be great to have a session dedicated exclusively to questions for the experts, that participants could submit different questions prior to the session and have a more free-flowing discussion.

 

    After these two weeks, I came home with a new way of thinking about my data. Some days of course were harder to follow, or maybe less related to what I do, but still very interesting. I would have loved to go on with anvio a bit more, maybe another few days!

 

    This course is an opportunity to develop new bioinformatics knowledge that will surely be useful for the research of any PhD, PI, master or technician. Even if bioinformatics is one of your strong points, this course is useful for deepening your knowledge and expanding your range of vision in research.

 

    Amazingly friendly learning atmosphere with highly knowledgeable lecturers. Beginners and advanced users both benefit from the broad spectrum of topics covered and the teacher's expertise.

 

    Super nice experience to learn about -omic technologies.

 

    This is a fantastic workshop, which can be attended by everyone (from beginners to advanced users) and which addresses various facets of microbial ecogenomics. It combines high quality lectures on cutting edge topics with practical applications on real datasets, under the supervision of multiple technical assistants, all in a relaxed and friendly atmosphere. I learned a lot and this workshop gave me a lot of ideas. Highly recommended!!!

 

    The EBAME7 workshop has been mind-opening and inspiring for my research. The organizers gathered top-level researchers and developers in several aspects of microbial ecogenomics. The bioinformatics challenges of short-read sequencing were organized in blocks and presented in separate lectures with associated lab practical sessions. Introductions to long-read approaches were also presented. The organizing team are passionate about what they do and this workshop. The faculty were highly experienced and recognized in the field. They were mostly currently collaborating or had collaborated in the past for several projects, which enabled a really cross-disciplinary setup (same bioinformatics approaches used to answer very different scientific questions, which is promising for future applications). Moreover, the ambiance was really friendly and fun. Highly recommended!

 

    This workshop, through its theoretical and practical teaching, allows participants to learn the fundamental concepts of metagenomics and to explore the different applications of this tool. The high quality of the lecturers, and the personalised assistance during the lectures, allow participants to follow the course independently of their starting level.

 

    EBAME7 workshop was an amazing experience. Two weeks of interesting lectures and a lot enthusiastic researchers to meet. The thing I appreciate more was the efforts of the organizers in following us in every request and necessity. In addition, all the speakers were fully available to talk and discuss strategies to analyze your own data. These two weeks gave me a lot of ideas on how to improve my analysis and get better results. I completely suggest this workshop to everyone want to start this journey in the metagenomic analysis.

 

    I got a feeling for what was happening around the world in my field by talking with other researchers and having the people who make the tools I use, present them personally

EBAME more than met my expectations with both the content and quality of the intense 2-week workshop! As a beginner in meta-omics, I was glad how well the fundamental theories were covered to build a proper foundation on all topics ecological metagenomics. And with so many topics and tutorials in them given by experts of their fields, even more advanced bioinformaticians were never bored but learned a lot! In addition, I met many amazing people, exhanged ideas and experiences and truly enjoyed my time in the beautiful location on the coast of Brittany! Would highly recommend this workshop to anyone learning ecological metagenomics!

 

    The quality of the course is very high and I learned a lot that will help me in my current and future projects. It was great to meet others working on similar data. We had good scientific exchange during the two weeks and there is really no other course like it! Would highly recommend if you work on metagenomics.

 

    EBAME was a great workshop in a great location. It was also a chance to meet and connect with people at all career stages across a diversity of disciplines.

 

    The EBAME workshop is a really nice experience, many different bioinformatic tools and inspiring studies are presented. You can also observe diverse ways of working from different research groups. More than that, it is a great opportunity to meet other people working in the same field and who face the same issues as you do in a great environment. Additionally, is in an amazing place, so peaceful and quiet, away from the hustle and bustle of the city!

 

    This training was very well organised and very enriching with a lot of information and practice on how to use anvio but also on other very interesting topics (ancient DNA, viromics, metabolism...). Thanks also to the many TAs who helped us out when we were stuck with our lines of code!

 

    The workshop is great for getting an overview of the field and the techniques used. The instructors put in a lot of effort to teach the theory and then show you the methods during the practicals. It s great for getting an overview of what you can do with your data, getting some inspiration for your own work, and for getting to discuss current research. I highly recommend attending EBAME, I learned so much and had a really fun time with all the participants and lecturers!

 

    The course offers a great opportunity to dig into bioinformatics tools and concepts. I suggest interested people to subscribe for it because is highly complete and clear, but just if you already have bioinformatics skills and expertise, because is also quite advanced and it can be challenging if you are beginners. The workshop covered most of the hot topics concerning microorganisms' world (concerning bacteria, virus and eukaryotes).

 

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