Introduction
The German Network for Bioinformatics Infrastructure - de.NBI and Helmholtz-Centre for Environmental Research – UFZ invites you to participate to the 3rd International Metaproteome Symposium with the topic “Microbiome Research and Integrating Metaproteomics into a Multi-Omics Pipeline”.

The symposium is the leading event in the field of metaproteomics with an average of around 60 attending international scientists.

Research examining microbiomes are currently exploding and results are providing new perspectives. Multi-omics analysis is accepted as the gold standard to assess the microbiome samples but a variety of analytical and bioinformatics approaches are available. Therefore, we think the symposium will be a great opportunity to broaden the discussion on the integration of different datasets in different areas of microbial ecology and maybe learn from other people's experience on different systems. Apart from description of biological samples using Multi-Omics, we are interested in developing ideas how to integrate metaproteome data.

Lennart Martens (Ghent), Sergio Uzzau (Porto Conte Ricerche), Dirk Benndorf (Magdeburg) and Paul Wilmes (Luxembourg) are in the scientific committee.

We hope to welcome you from 03.-05.12.2018 in Leipzig at the UFZ!
Please use the links for more information, our competition, keynote speakers, on how to submit an abstract (oral or poster), important dates, or just send us an e-mail if you want to know more.

General Information
Contest: Multi-Omics study of microbiome samples
The success of protein identification in metaproteomics relies on whole genome sequencing. Therefore, multi-omics analysis is accepted as the gold standard to assess the microbiome samples in-depth. Thus, a variety of analytical and bioinformatics approaches are available.

Therefore, the scientific committee decided to announce a cooperate study of two microbiome samples. The results will be discussed in a workshop during the 3rd Metaproteomics Symposium. A final collaborate publication is anticipated. All labs working in the fields of Meta-Omics are invited to participate unless they are working only in Metagenomics, Metatranscriptomics, Metaproteomics, or Bioinformatics.

The combined study should target the following issues

- sample preparation (Multi-Omics protocols versus specialized protocols)
- impact of sequencing methods and sequencing depth on metaproteomics
- impact of processing methods and processing state of metagenome and metatrancriptome sequences (reads, contigs, gene prediction, binning) on metaproteomics
- impact of mass spectrometers types and measurement strategies (data-dependent versus data-independent, non-targeted versus targeted) on protein identification
- bioinformatics workflow for protein identification, inference and annotation
- suitability of metaproteome data to assist processing and annotation of sequencing data (proteogenomics)
- bioinformatics tools for visualization and comparison of multi-omics data

Samples

Sample 1 (provided by UFZ): defined mixed culture from a lab-scale bioreactors consisting of 8 sequenced microbes (SIHUMI)
Sample 2 (provided by de.NB/BIGI/OVGU): fecal sample from human gut, a minimal metagenome (reads, contigs) is provided

Conditions

- participants send a request to Dirk Benndorf (This email address is being protected from spambots. You need JavaScript enabled to view it.) or Nico Jehmlich (This email address is being protected from spambots. You need JavaScript enabled to view it.)
- after registration the samples and access to a platform for data exchange will be provided
- raw data has to be submitted to the data exchange platform until September 30th, processed data until Nov 30th (this allows other participants to apply the data in bioinformatics workflows)
- all participants with submitted data are invited to present the highlights of their results in a workshop (short presentation, 5-10 min)

Publication of results in a Special Issue of Microorganisms

- only participants with submitted data are accepted
- all participants are invited to submit a dataset brief
- for each sample a full paper merging the data will be prepared
- finally a review discussing major outcomes will be prepared

For more information: https://www.ufz.de/index.php?en=44235

Mon 15 October 2018, 11:00 to Tue 16 October 2018, 13:00 GMT - Frankfurt, Germany

This free ELIXIR Innovation and SME Forum on Data Driven Innovation in Industrial Biotechnology in Frankfurt is open to both large and small companies and aims to inform about ELIXIR resources and create a space to network for industry and academia.

In this lunch-to-lunch event, attendees will be immersed in a world of data-driven innovation, illustrated through talks. With a mix of high-level keynote speakers and interactive sessions, this event will allow you to discuss and interact with other companies and ELIXIR partners. A specific session with Flash Talks, will give new companies the chance to introduce their work to a broad audience.

This event programme is organised in cooperation with de.NBI, ELIXIR Europe, and DECHEMA and is free and open to all companies in Germany and beyond.

What is on the programme? Sessions include:

- Big Data Challenges and Opportunities
- Data driven Biotechnology in Germany and Europe
- Services offered by de.NBI and ELIXIR
- Flash Talks from companies showcasing their products

Complete programme here

Speakers included but not limited to:

- Alf Puehler, Head of de.NBI
- Bertram Weiss, Head of Bioinformatics Bayer AG
- Elizabeth Reynolds, Founder & Director General Bioinformatics
- Klaus Mauch, Board member of DECHEMA/CEO of Insilico Biotechnology AG
- Catherine Sirven, Scientist, Bayer Crop Science France
- Martin Eisenacher,  Medical Bioinformatics, Ruhr University Bochum
- Uwe Scholz, Institute for Plant Genetics and Crop Plant Research Gatersleben 

For whom? This event is aimed at companies active in industrial biotechnology, bio-data, software companies working with data and tools in life sciences and all research institutes active in the field of data science in all life science domains.

Meet and greet: In addition to coffee breaks and lunches, you are invited to attend the dedicated networking buffet dinner on the 15th of October.

Registration here

More than 120 participants joined us for the first Galaxy User Conference in Freiburg. 
 
It started with a tribute from Björn to Stephen Hawkings.
Followed by several talks across diverse topics:
- “de.NBI & RBC” by Andreas Tauch (Bielefeld, DE) and Rolf Backofen (Freiburg, DE)
- “Galaxy HiCExplorer” by Joachim Wolff (Freiburg, DE)
- “Analysis of the cardiac myocyte epigenome using Galaxy” by Ralf Gilsbach (Freiburg, DE)
- “Using direct reprogramming to find the master regulators of renal tubulogenesis and factors leading to congenital kidney defects” by Sören Lienkamp (Freiburg, DE)
- “Galaxy tools and workflows for metabolomics: A community effort to make data processing and analysis accessible, reproducible, and transparent” by Ralf Weber (Birmingham, UK)
- “Workflow4Metabolomics - Towards an international computing infrastructure and a tools showcase for Metabolomics” by Christophe Caron (Rennes, FR)
- “Deployment of genome databases for insects using Galaxy Genome Annotation” by Anthony Bretaudeau (Rennes, FR)
- “Galaxy-E: A french initiative dedicated to Macro-Ecological data analysis” by Yvan Le Bras (Paris, FR)
- “The ELIXIR Communities usegalaxy.eu/au launch” by John Hancock (ELIXIR, UK) and Frederik Coppens (Gent, BE)
 
At the end of the first day, Simon Gladman (from Australia) and Björn officially launched the useGalaxy.eu/.org.au!
 
After a nice dinner at Martin’s Bräu, the second (and last) day started. We had 13 talks, ranging from Beer and Proteomics to Imaging:
- “The Beerome – Science for the Mind and the Stomach” by Teresa Müller (Freiburg, DE)
- “Gene discovery with KnetMiner” by Ajit Singh (Hertfordshire, UK)
- “Fruit Fly reproduction” by Ihor Yurkevych (Ivano-Frankivsk, UA)
- “Proteomic analyses of mass spectrometry data using OpenMS in Galaxy” by Matthias Fahrner (Freiburg, DE)
- “Quality control and analysis of large scale MALDI imaging data of peptides from formalin-fixed paraffin-embedded tissues within the Galaxy environment” by Melanie Föll (Freiburg, DE)
- “Galaxy for microscopy image analysis workflows and systematic phenotyping” by Thomas Wollmann (Heidelberg, DE)
- “RNA Workbench” by F. Eggenhofer – Freiburg, DE
- “Integrated analysis of miRNA-mRNA regulatory networks in chordoma tumors using Galaxy” by Beata Scholz (Debrecen, HU)
- “Extracting biological sense from RNA-seq time series in dynamic biological systems” by Daria Onichtchouk (Freiburg, DE)
- “Microbiota analysis using Galaxy” by Saskia Hiltemann (Rotterdam, NE)
- “Galaxy Australia/USA communities” by Simon Gladman (Melbourne, AU) and Anton Nekrutenko (PSU, USA)
- “The Galaxy Training Network” by Bérénice Batut (Freiburg, DE)
 
We are discussing with the different speakers and we hope to add links to the slides soon. We will keep in touch!
Thanks a lot to all the speakers and participant! See you all in Freiburg in 2019 for GCC!
 
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