Trainbiodiverse ITN Summer School courses and Annual Network workshop.

Two new events are added to the Trainbiodiverse Calendar. Time is short so make sure to sign up as soon as possible. Also please forward this to any relevant new members of the consortium that may have just joined, in case it may be of interest to them.

Annual Network workshop

Trainbiodiverse is pleased to announce the first annual network workshop to be held in 18-08-2012 in Copenhagen.

The preliminary program will include presentations representing different aspects, challenges and experience of using molecular indicators of microorganisms as providers of soil ecosystem services.


Presentations will be held by:


Professor Michael Schloter. Pros and cons of using 16S rDNA as a molecular indicator of microorganisms as providers of ecosystem services 

Professor Jan Dirk van Elsas, Rijksuniversiteit Groningen, NL. Functional gene diversity as molecular indicators

Professor Paolo Nanipieri, University of Firenze, I. Contrasting molecular and enzymatic activity indicators of microbial diversity

Dr. Anders Primé, University of Copenhagen, DK: Experience with molecular diversity as indicators of climate change (16s)


Suggested discussion points for topics included in the workshop include

  • What is the need of molecular indicators of microorganisms as providers of ecosystem services?
  • Which are the potential molecular indicators and what are they indicating that is relevant for soil ecosystem services?
  • How can we validate the molecular indicators?
  • Can they be standardized and used by many laboratories?
  • Experience of using molecular indicators
  • What is holding back the implementation of the molecular indicators?

Emphasis will be made on highlighting network collaborations


A final agenda will be presented 14 days prior to the workshop.


Trainbiodivese Somme school Specialising in UNIX & Bioinformatics 13-17 August 2012


In conjunction with the summer school and timed for participation in the ISME conference Trainbiodiverse will hold the first summer school for the ITN


Who is it for?

This workshop is for biologists with little or no experience in UNIX/Linux and who wants to be able to analyze sequence data using state of the art command line tools including Unix and Biopieces for day-to-day bioinformatic analysis and QIIME for microbial amplicon data.

What is this?

This is a hands-on bioinformatics workshop. All participants should bring their own laptop which will be used as a terminal during the workshop. The first day will cover working with UNIX with a focus on how to navigate and manipulate files and folders and the concept of piping data between useful UNIX tools. After familiarizing ourselves with UNIX we will move on to Biopieces which are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. We will use Biopieces to manipulate tabular data and sequence data including sequence cleaning and searching along with gene finding and phylogeny. Finally, we will learn QIIME for the purpose of characterizing microbial communities.

How many participants?

We have a maximum of 16 participants.

How to apply?

Send a half page letter of motivation. E-mail to course organizer -> see below.

The deadline for submission of letter of motivation is 16.07.2012

ETCS points? 5

Fee 1000 DKK

Lunch Included



University of Copenhagen

Room 4-0-02

Biocenteret, Ole Maaløes Vej 5, 2200 København N


<Google Map>



Hardware/Software requirements

Bring a laptop. This will be used as a terminal, and thus it doesn’t need a lot of muscle. Windows users should install an SSH client such as SSH secure shell as well as Xming for X11 tunneling.

SSH Secure Shell:



Tutorial 1-3

Unix intro videos


Introduction and HowTo


Overview Tutorial