Micro B3 Summer School, Crete: Background

Rationale & Target Audience

Within WP9 (Outreach & Dissemination), the Micro B3 project offers a training pipeline with several courses, partially building on each other.

We are now happy to announce our two-week summer school “from sampling to analysing microbial diversity & function”. This multi-disciplinary summer school is focussing on standardized sampling and analysis of integrated environmental and genomic marine data. It aims at developing the analysis and integration skills of PhD students, postdocs, and senior scientists with marine ecological, bioinformatics and biotechnological backgrounds, with a focus on OSD participants in need of such training. Trainees will actively apply the protocols and standards from the Micro B3 Ocean Sampling Day, the OSD handbook, to familiarize themselves with the overall procedures.

This two-week training course aims to provide participants with a broad understanding of the concepts and tools currently being used in marine bioinformatics and marine biodiversity research. Every day a high-level lecturer will share expertise with the students, focusing on standards & methods, with theory (lectures) in the morning and interactive practical work in the afternoon. These hands-on exercises and demonstrations will focus on diverse oceanographic and molecular methods available at HCMR. Highlights will be an enrichment experiment using mesocosms and a short boat trip to Cretan coastal waters, both focussing on OSD protocols.

By the end of the course, participants should have acquired enough conceptual and practical skills to lead the OSD sampling at their home institution, including analysis and integration of key data into the Micro B3 Information System, Pangaea for oceanographic and environmental parameters, and EBI for genomic data.

Half an hour per day will be reserved for volunteer trainees to present their own projects based on a poster (first week) or to give a short slide presentation on one chapter of the OSD handbook (second week).

Course Outline

The summer school focuses on preparing and planning integrated sampling work and data flows, taking into account some legal aspects, with a focus on bioinformatic and oceanographic tools. The group will perform data and sample management based on a mesocosm experiment with inorganic nutrient enrichments for diverse analyses during the course, on existing (OSD) data sets. Trainees will learn how to decide on using methods and standards to address their research questions in the fields of plankton diversity, ecology and function, including biotechnological applications.

A small boat trip will be planned, log sheets & standardized sampling methods tested on board and in the lab, and samples prepared for sequencing. Also the group will learn about Access and Benefit Sharing (ABS) and IPR (intellectual property rights) aspects when sampling marine waters. It is expected that some sequencing and analysis can be done of the mesocosm data, to be compared to results from former pilot OSDs, with a focus on the Mediterranean, in the second week. Finally, the use of selected datasets for ecological modelling will be explored.

Selection Criteria

Participants will be selected to cover a range of research fields and institutions in marine sciences with a main focus - for this summer school - on Micro B3 members and registered participants of the June 2014 Ocean Sampling Day.

Major criteria will be that the knowledge gained in the course is of immediate use for the participant and the institution sending him/her, i.e. in the context of standardizing genomic sampling, archiving and documentation. Another aspect is that the participant is prepared to disseminate the knowledge to his colleagues and/or students in his home institution. This must be made transparent in the application. Furthermore we intend equal gender distribution.

Application & Timeline

Deadline for submission of applications is March 15, 2014

Applications will only be taken into account if they are submitted via the

electronic application form.

Notification of participants: April 03, 2014

Participants have to confirm their participation by April 09, 2014. In case of cancellations the next one on the waiting list will be notified.


The training course is free of charge. Coffee breaks and lunches during the week are included, as is one social event, planned on Saturday evening. A group reservation has been made in Astir Beach Hotel (from Sunday 25 May until Friday 6 June), which is within walking distance from the HCMR. All participants have to cover travel costs and hotel nights (40 Euro p.p., incl. breakfast buffet, for more info please see logistics) as well as dinners on their own.

We are looking forward to meeting you in Crete this summer!