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.
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).