Micro B3 Bioinformatics I Training: Background

Rationale & Target Audience

Within WP9 (Outreach & Dissemination), the Micro B3 project offers dedicated bioinformatics training for developing multiple capacities and bioinformatics skills of PhD students, postdocs, and senior scientists.

The rational of this initial five days bioinformartics training is to bring the Micro B3 scientists to the same level of bioinformatics understanding, including the first steps in (meta)genome annotation using the the web-based training platform Annotathon. This introductory theoretical+practical workshop will be supplemented by advanced and hands-on course formats later in the project (to be announced) which will allow the trainees to also work on their own data during the workshops, together with experts from the Micro B3 consortium. The idea of the training is to offer a number of courses to incorporate the specific requirements of the trainees (to be explored in detail during the first course) and to merge students and professionals in a self-training community based on web-tools such as Annotathon.

Course Outline

The Bioinformatics I workshop is a pure computer-based training course. On the first three days, the trainees will be introduced to the basics of DNA sequence analysis in lectures, demonstrations, and hands-on sessions.  They will learn how to deal with the corresponding software tools and how to interpret their results. In the practical parts, the course will focus on resources like sequence databases, Linux and the command line as a toolbox for daily bioinformatics work, and common software tools for sequence similarity searches, alignments, etc. The aim of this course module is to provide basic bioinformatics and computational skills and understanding for the handling and later annotation of biological sequence data generated by today’s sequencing technologies. On the last two days, the course will focus on aspects of the in silico annotation of (meta)genomic sequence data, including initial open reading frame prediction, functional predictions, and taxonomic assignment through phylogenetic tree inference. This course module will be based on the e-learning portal Annotathon.


The course will be held at the Max Planck Institute (MPI) for Marine Microbiology in Bremen, Germany and is taught by the Micro B3 partners RIBOCON and CNRS with contribution of expertise from the Microbial Genomics and Bioinformatics Research Group at MPI Bremen.

Selection Criteria

Participants will be selected to cover a range of research fields and institutions in marine sciences. Major criteria will be that the knowledge gained in the course is of immediate use for the participant and that the participant is prepared to disseminate the knowledge to his colleagues and/or students in his home institution. Both must be made transparent in the application. Furthermore we intend equal gender distribution.

Application & Timeline

Deadline for submission of applications is Monday, July 16,  2012. Applications will only be taken into account if they are submitted via the electronic application form.

Notification of participants: July 23, 2012

Participants have to confirm their participation by July 27, 2012. In case of cancellations the next one in the waiting list will be notified.


The training course is free of charge. For members of the Micro B3 consortium, also accommodation for 5 nights (we will book a hotel for you) and the social event are included (guided city tour of Bremen plus joint dinner on day 4). All participants have to cover travel costs and extra nights by their own. Besides some drinks and snacks during the day there is no dedicated catering included. We will have lunch together in the canteen of the University of Bremen (if you like) but on own expenses. Dinner is within your free time and there are plenty of options in Bremen to have good food ...

We are looking forward to meeting you in Bremen!