Workshop:Agenda

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First MOD-CO Workshop for Domain Experts

with invited experts from the fields of microbiology, microbial ecology, and bioinformatics

Background information

Objectives:

  • During the last nine months, the MOD-CO team developed the basic structure, the terminology, and the definitions of a standard for meta-omic material and data management. The aim of this first external workshop with invited experts from the fields of microbiology, microbial ecology, and bioinformatics will be to discuss the current state of the MOD-CO schema. Together with these experts, who did not have any influence in the development of the schema until now, the concept and the structure of the MOD-CO schema should be evaluated.

Background:

  • MOD-CO, which stands for 'Meta-omics Data of Collection Objects', should be the foundation for developments in the fields of data management of meta-omics material and data about meta-omics material. Currently, assignment of meta-omics data to reference samples in natural history and living culture collections is lacking, despite the fact that there are a number of standards for the deposition of molecular data.
  • The aim of this project is to select and categorize relevant descriptors from a wide range of procedural analysis protocols, and to set up a standard that avoids structural redundancy. Furthermore, descriptors belonging to related data domains will be evaluated and – if relevant – allocated to the new conceptual schema. Based on existing concepts and standards, integrative controlled vocabularies will be compiled, in order to describe the full spectrum of observation and measurement elements, as well as the procedural steps in the frame of meta-omics characterization of environmental collection samples. The name space schema with vocabularies will be exemplarily implemented in the Diversity Workbench and SILVA/megx.net management systems and published in collaboration with the standardization committees of TDWG and GSC.

Intention:

  • The MOD-CO schema, with its product oriented focus, will be demonstrated and discussed. MOD-CO will present the possibility to answer essential questions about the provenance and any processing of each object in a collection or in a workflow
  • Three different use cases will be presented to explain the structure of the MOD-CO schema, focusing on its completeness, exclusiveness, hierarchy, and precision. These use cases show various complexities.

The use cases that will be discussed are:

  1. Genomics: Sampling of lichen specimens for phylogenetic analysis and DNA barcoding
  2. Meta-genomics: Structural community compositions and shifting of endofoliar fungi of Picea
  3. Meta-transcriptomics: Functional fungal community analyses of endophytic ascomycetes associated with Viscum album ssp. austriacum (see doi:10.1016/j.funbio.2010.04.009).


Date:

  • Thursday July 16th and Friday July 17th, 2015

Time:

  • Thursday: from 13:00 to 17:30
  • Friday: from 9:30 to 15:00


Organisers:

  • MOD-CO team (event organisers) with local support by Ingrid Sebek (email: office[at]bsm.mwn.de)


Location:

Botanische Staatssammlung München with SNSB IT-Zentrum
Menzinger Str. 67
80638 München, Germany
Second Floor, Room 139
Tel. +49 89 17861 265

Agenda

Thursday, the 16th

  • 13:00 – 13:15: Welcome of participants
  • 13:00 – 14:00: Introduction; presentation of the MOD-CO project, the concept of the schema, its structure, terminology, hierarchy and function; discussions
15:00 – 15:30: Coffee break
  • 15:30 – 17:30: Presentation of work- and dataflow schema with the 1st and 2nd use case Genomics: Sampling of lichen specimens for phylogenetic analysis and DNA barcoding and Meta-genomics: Structural community compositions and shifting of endofoliar fungi of Picea on the background of the MOD-CO schema terminology, hierarchy and function
  • 19:00 – Dinner at Greek restaurant “Poseidon”, Maria-Ward-Str. 24 (5 min walk from the Botanische Staatssammlung) – at the charge of participants


Friday, the 17th

  • 09:30 – 11:00: Presentation of work- and dataflow schema with the 3rd use case Meta-transcriptomics: Functional fungal community analyses of endophytic ascomycetes associated with Viscum album ssp. austriacum on the background of the MOD-CO schema terminology, hierarchy and function; Demonstration of the MOD-CO schema in DiversityDescriptions
11:00 – 11:30: Coffee break
  • 11:30 – 13:00: Concluding discussion and validation of MOD-CO (part 1)
13:00 – 14:00 Lunch break
  • 14:00 – 15:00: Concluding discussion and validation of MOD-CO (part 2)

Lectures for download

Travel costs

  • Travel costs for invited workshop participants will be reimbursed by the SNSB administration. The participant has to use the template for "Reisekostenabrechnung" of his/ her own organisation and will get the money from it. After that the administration of the participant´s organisation should contact the Generaldirektion der Staatlichen Naturwissenschaftlichen Sammlungen Bayerns, z. H. Dr. Jörg Spelda, Menzinger Str. 71, 80638 München, Tel. 089/179 99 24-4, E-mail: mittelbewirtschaftung@snsb.de; Stichwort: MOD-CO, TR 290/8-1 for reimbursement of the money.

Participants

Name Institution Field of science Email address
Dr. Andreas Brachmann Ludwig-Maximilians-Universität München, Genetics Mycology; microbial functional genomics brachmann@lmu.de
Prof. Dr. Frank Oliver Glöckner Jacobs Univeristy Bremen, MPI für Marine Mikrobiologie, Bremen Microbial community structure (metagenomics) fgloeckn@mpi-bremen.de
Sabrina Klaster University of Bayreuth DNA Analytics and Ecoinformatics, mycology sabrina.klaster@uni-bayreuth.de
Anton Link Staatliche Naturwissenschaftliche Sammlungen Bayerns, SNSB IT Center Informatics link@bsm.mwn.de
Dr. Derek Peršoh Universität Bochum, Geobotanik Mycology; microbial community structure (metagenomics) derek.persoh@rub.de
Prof. Dr. Gerhard Rambold University Bayreuth DNA Analytics and Ecoinformatics, mycology gerhard.rambold@uni-bayreuth.de
Veronica Sanz Staatliche Naturwissenschaftliche Sammlungen Bayerns, SNSB IT Center Biodiversity informatics sanz@bsm.mwn.de
Dr. Carola Söhngen Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig (Information Techniques) Microbial community structure (metagenomics) carola.soehngen@dsmz.de
Prof. Dr. Thorsten Stoeck Universität Kaiserslautern (Microbiology) Microbial community structure (metagenomics) stoeck@rhrk.uni-kl.de
Prof. Dr. Christoph Tebbe Johann Heinrich von Thünen Institut, Braunschweig (Microbiology) Microbial community structure (metagenomics) christoph.tebbe@ti.bund.de
Dr. Dagmar Triebel Staatliche Naturwissenschaftliche Sammlungen Bayerns,SNSB IT Center Mycology, biodiversity informatics triebel@bsm.mwn.de
Dr. Pelin Yilmaz Jacobs Univeristy Bremen, MPI für Marine Mikrobiologie, Bremen Microbial community structure (metagenomics) pyilmaz@mpi-bremen.de

Logistics


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Botanische Staatssammlung München, Menzinger Straße 67.



  • ACCOMMODATION
  • Accommodation München provides a list of hotels in the vicinity of the Botanische Staatssammlung München SNSB IT Center


  • GETTING THERE

From the Munich airport (duration ca. 60 min) take the “S-Bahn”, which departs directly below the terminal, with line S 1 direction “Hauptbahnhof (Main Train Station)”. Get out after 30 min at the station “Moosach”. Trains depart every 20 min. The MOST DIFFICULT thing is getting a train ticket. These cannot be bought on the train and not on the platform either. Instead, you get them at the airport level above the trains, either from a vending machine or an actual person (there are 3 people selling them at a “Bundesbahn” booth just opposite the stairs leading down to the train platform.

Once at “Moosach”, exit the station and take the bus number 51 direction “Aidenbachstraße”. The 51 departs every 10 minutes. Get off after 10 min at “Maria-Ward-Straße”. Starting from there turn right and walk around 400 meters along the “Menzinger Straße” (alternatively take tram number 17, direction “Amalienburgstraße” for one stop. Get out at the station “Botanischer Garten”. For details see map above.

From Munich train main station (duration 20 min) take the tram number 17 direction “Amalienburgstraße”. The tram departs every 10 min. Get out after 20 min at the station “Botanischer Garten”.

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