Applied Metaproteomics Workshop 2020
23 - 27 November 2020
Magdeburg, GermanyApplied Metaproteomics Workshop 2020 https://www.denbi.de/training/979-applied-metaproteomics-workshop-magdeburg-2020 https://tess.elixir-europe.org/events/applied-metaproteomics-workshop-2020 Educators: Dirk Benndorf, Stephan Fuchs, Robert Heyer, Kay Schallert (BiGi/MetaProtServ) Date: 23.11.2020 – 27.11.2020 Location: Magdeburg, Germany (Universitätsplatz 2, Building 28.205) Contents: Microbiome research is rapidly increasing. Meta-Omics data provide insights into microbial community influencing human health and biochemical cycle. Metaproteomics focusses on proteins representing the expressed genes and functions. In contrast to metagenomics or metatranscriptomics, the extraction and the analysis of proteins from human or environmental samples is challenging. The de.NBI course on Applied Metaproteomics trains the participants to apply a complete workflow starting from design of experiments via sample preparation to measurement and bioinformatics analysis of high-resolution MS data. Maximum 10 participants are strongly encouraged to analyze their own samples to start their own metaproteomics project. The workshop takes place at chair of bioprocess engineering at Otto-von-Guericke University Magdeburg. The team of microbial communities head by Dr. Dirk Benndorf is well experienced in metaproteomics. The samples will be measured on newly purchased timsTOF Pro MS. His group devellopes the MetaProteomAnalyzer service facilitating the analysis of of metaproteomic data. The provision of service is supported by the German Network for Bioinformatics Infrastructure - de.NBI. Monday 09:00-10:00 Arrival 10:00-11:00 Introduction to metaproteomics (lecture: Dirk Benndorf) 11:00-12:00 Design of experiments and sample preparation (lecture: Robert Heyer) 12:00-13:00 Lunch 13:00-18:00 Sample preparation I (protein extraction, protein quantification: Robert Heyer) during the afternoon short presentations of participant´s about their samples (each participant max. 10 min) Tuesday 08:00-11:00 Sample preparation II (FASP digest, SDS-PAGE: Robert Heyer) 11:00-13:00 Introduction to high resolution mass spectrometry (lecture: Dirk Benndorf) 13:00-14:00 Lunch 13:00-14:00 Sample preparation II (peptide extraction: Robert Heyer) 14:00-16:00 Introduction to the MPA 2.0 (lecture: Kay Schallert) non-stop: measurement of participant’s samples I Wednesday non-stop: measurement of participant’s samples I: Dirk Benndorf, Patrick Hellwig 09:00-11:00 MPA 2.0 exercise I (working with a small reference dataset, db searching, metaprotein concept: Kay Schallert, Robert Heyer) 11:00-13:00 MPA 2.0 exercise II (loading user db, BLAST search of unknown hits, quantitative comparison of datasets, visualization and data export: Kay Schallert, Robert Heyer) 13:00-14:00 Lunch 14:00-17:00 Prophane workflow (lecture and training: Stefan Fuchs, external speaker) Thursday 09:00-13:00 MPA 2.0 exercise III (analyzing own data: Kay Schallert, Robert Heyer) 13:00-14:00 Lunch 14:00-17:00 Training at MS (calibration, setup of LC-MS methods, solvent exchange, trouble shooting, Patrick Hellwig) Friday 08:00-10:00 MPA 2.0 exercise IV (visualization of data: Robert Heyer) 10:00-12:00 Individual discussion of results and preparation of presentations (Dirk Benndorf, Robert Heyer, Kay Schallert) 12:00-13:00 Short presentations of participant‘s results and conclusion 13:00 Lunch and departure Learning goals: To apply a complete workflow starting from design of experiments via sample preparation to measurement and bioinformatics analysis of high-resolution MS data. Prerequisites: Fee: 30 € Keywords: Microbiome, MPA, Metaproteomics, MetaProteomeAnalyzer, Tools: MetaproteomeAnalyzer 2020-11-23 09:00:00 UTC 2020-11-27 17:00:00 UTC de.NBI Magdeburg, Magdeburg, Germany Magdeburg Magdeburg Germany    workshops_and_courses  
de.NBI - CeBiTec Nanopore Workshop 2020 - Best Practice and SARS-CoV-2 applications
30 November - 4 December 2020de.NBI - CeBiTec Nanopore Workshop 2020 - Best Practice and SARS-CoV-2 applications https://www.denbi.de/training/978-de-nbi-cebitec-nanopore-workshop-2020-best-practice-and-sars-cov-2-applications https://tess.elixir-europe.org/events/de-nbi-cebitec-nanopore-workshop-2020-best-practice-and-sars-cov-2-applications Educators: Stefan Albaum, Jan-Simon Baasner, Sebastian Jünemann, Nils Kleinbölting, Alexander Sczyrba, Alex Walender (BiGi), Daniel Wibberg (CAU), David Brandt, Christian Rückert, Jörn Kalinowski (CeBiTec) Date: 30 November – 4 December 2020 Location: Online Content: Aim of this workshop is to familiarize the participants with the Nanopore sequencing technology, its applications, the "Best Practice" bioinformatics workflows and the analysis of SARS-CoV-2 genomes. The Nanopore technology has greatly facilitated the assembly of prokaryotic, viral and eukaryotic genomes. Therefore, the workshop is focused on the establishment of finalized genome sequences, ranging from basecalling, quality assessment over assembly to sequence polishing and finally assembly evaluation. A focus in this years workshop is on the analysis of Nanopore sequenced SARS-CoV-2 genomes and a suitable workflow for resequencing based on the ARTIC bioinformatics protocol. The course will start with a one day webinar on best practices for the lab work on sequencing SARS-CoV2 and a “guided tour” showing the necessary bioinformatics steps. This part of the workshop is open to a large number of applicants. The following 4 days will be a mixture of talks and practical sessions in the de.NBI cloud introducing, in more detail, the Nanopore sequencing technology and bioinformatics processing tools, as, for instance, base calling, assembly and polishing.This part of the workshop is, however, limited to a smaller number of applicants. Learning goals: This workshop aims to teach basic skills and best practices to researchers working with Nanopore data, e.g. SARS-CoV-2. The full course will include all necessary steps from raw sequencing data to finalized genomes (1) with a de novo assembly and (2) with re-sequencing and mapping to a reference. Prerequisites: This workshop is intended for PhD students and postdocs with molecular biology background in genomics or SARS-CoV2 background. Good understanding of command line tools is a plus, but not required. Tools: minimap2, canu, pilon, guppy, porechop, medaka, poretools, nextstrain, quast, ARTIC pipeline Keywords: Nanopore sequencing, genome assembly, genomics, SARS-CoV2, 2020-11-30 09:00:00 UTC 2020-12-04 17:00:00 UTC de.NBI    workshops_and_courses  
Data visualization using R
7 December 2020Data visualization using R https://www.denbi.de/training/965-data-visualization-using-r https://tess.elixir-europe.org/events/data-visualization-using-r Educators: Markus Stepath, Karin Schork, Nils Hoffmann (BioInfra.Prot / LIFS) Date: Monday, 7th Dec 2020 Location: Online training Contents: In this course you will learn how to use the ggplot2 package in R to create informative and beautiful figures to communicate your omics data and analysis results. We will cover the following topics: - Usage of the tidyverse for data preprocessing - Usage of the ggplot2 R package - Presentation of different types of graphics and when to use them - Customization of graphics Please be aware that basic knowledge of R is taught in our course “Differential analysis of quantitative proteomics data” on Monday, 2nd Nov 2020 (http://goo.gl/forms/mpKHnbT1Um). Learning goals: - Using the ggplot2 R package to create graphics for omics data - Decide which type of graph is appropriate for the given data - Ability to costumize the graphics using ggplot2 Prerequisites: - Basic understanding of high-dimensional data sets from quantitative proteomics or other life sciences; - Basic knowledge of R (e.g. data import, basic plots. This can for example be gained from our course “Differential analysis of quantitative proteomics data” (Monday, 2nd Nov 2020, http://goo.gl/forms/mpKHnbT1Um). - Computer with stable internet connection, headset and camera Keywords: R; tidyverse; ggplot2; high-throughput data; omics; proteomics; data analysis, graphics, data preprocessing Tools: Download and more information on R here: https://cran.r-project.org/ We recommend using an editor such as RStudio, see www.rstudio.com 2020-12-07 09:00:00 UTC 2020-12-07 17:00:00 UTC de.NBI    workshops_and_courses  
8 - 9 December 2020
Gent, BelgiumTranslational Immunology https://www.vibconferences.be/events/translational-immunology?utm_source=Event%20website&utm_medium=Event%20post&utm_campaign=TransImmu20&utm_term=Immunology&utm_content=Elixir%20Tess https://tess.elixir-europe.org/events/translational-immunology-fe17b83a-fab1-413f-94c3-9c6a1ecac893 Translational Immunology 8-9 DECEMBER 2020, GHENT, BELGIUM Due to the Coronavirus, Translational Immunology and the satellite BIS meeting were postponed from 26-27 March 2020 to the end of the year. We are happy to confirm the new date: 8-9 December 2020. The aim of this conference is to bridge the translational gap in immunopathology, bringing together clinicians, research scientists and industry partners to discuss prominent advances from the bench to the clinic. The different sessions will have a particular focus on precision medicine in general, starting from disease-oriented cases and lessons learned. Innovative and alternative therapeutic strategies in immune-mediated disorders will be presented, besides the regulatory challenges that companies and researchers are dealing with. Deadlines: - Abstract submission: 5 October 2020 - Early Bird deadline: 27 October 2020 - Late Registration deadline: 24 November 2020 Speakers: Rosa Bacchetta Stanford Medicine, US Dirk Elewaut VIB-UGent Center for Inflammation Research, BE Alain Fischer Assistance publique – Hôpitaux de Paris, FR Martin Guilliams VIB-UGent Center for Inflammation Research, BE Pleun Hombrink Sanquin, NL Bengt Hoepken Clinical Program Director, UCB Pharma, DE Isabelle Huys KU Leuven, BE Christophe Lahorte National Innovation Office & Scientific-Technical Advice Unit - (Famhp), BE Bart Lambrecht VIB-UGent Center for Inflammation Research, BE Antonio Lanzavecchia Institute for Research in Biomedicine, CH Sophie Lucas de Duve Institute, UCLouvain, BE Bénédicte Machiels FARAH Center, ULiège, BE Melanie Matheu CEO, Founder at Prellis Biologics, Inc., US Massimiliano Mazzone VIB-KU Leuven Center for Cancer Biology, BE Kathy McCoy University of Calgary, CA Eoin McKinney University of Cambridge, UK Fiona Powrie Kennedy Institute of Rheumatology, University of Oxford, UK Federica Sallusto Institute for Research in Biomedicine, CH Georg Schett Friedrich-Alexander University Erlangen-Nürnberg, DE Marvin van Luijn Erasmus MC, University Medical Center Rotterdam MS Center ErasMS, NL Location: De Bijloke, Jozef Kluyskensstraat 2, 9000 Gent Hashtag: #TransImmu20 2020-12-08 09:00:00 UTC 2020-12-09 17:00:00 UTC VIB Conferences Music Center De Bijloke, 2, Jozef Kluyskensstraat, Gent, Belgium Music Center De Bijloke, 2, Jozef Kluyskensstraat Gent Oost-Vlaanderen Belgium 9000 Immunoprecipitation experiment Immunology Immunoproteins, genes and antigens   PhDPhD studentsAcademicsindustry 600 meetings_and_conferences  ImmunologyImmunogenicityImmunogenomicsMetabolism of Immune Cellsantibodiestherapeutic antibodies
Plant Science for Climate Emergency
7 - 8 June 2021
Gent, BelgiumPlant Science for Climate Emergency https://www.vibconferences.be/events/plant-science-for-climate-emergency?utm_source=Google&utm_medium=Conference%20website%20post&utm_campaign=Event%20posting&utm_content=Elixir https://tess.elixir-europe.org/events/plant-science-for-climate-emergency Climate change is one of the most serious threats humanity has ever faced. Developing crops that are more resilient to rapidly changing and harsher environments will be crucial for tomorrow’s food production. Green biotechnology offers solutions to maintain high food productivity while preserving the earth’s valuable ecosystems. In addition, plants may also play an important role in mitigating the rising levels of greenhouse gases. This VIB conference ‘Plant Science for Climate Emergency’ aims at reviewing current research on adapting plants to climate change as well as on using plants for mitigating the accumulation of greenhouse gasses. Twenty leaders in plant biotechnology will present the latest developments in sessions focused on drought tolerance, tolerance to high temperatures, salt and flooding tolerance, the effects of climate change on defense systems against insects and pathogens, carbon capturing plants, crop engineering and improvement, nitrogen use efficiency, and much more. Besides an inspiring scientific program, conference participants will have ample networking opportunities during the poster sessions, the reception, and the conference dinner. Deadlines: • Grant submission deadline: 15/03/2021 • Abstract submission deadline: 29/03/2021 • Early Bird deadline: 26/04/2021 • Late registration deadline: 24/05/2021 Speakers: • Tom Beeckman - VIB-UGent Center for Plant Systems Biology, BE • Wout Boerjan - VIB-UGent Center for Plant Systems Biology, BE • Hidde Boersma - freelance science journalist, essayist and documentary film maker, NL • Wolfgang Busch - Salk Institute for Biological Studies, US • Jorge Casal - Leloir Institute Foundation, AR • Ana Caño Delgado - Centre For Research In Agricultural Genomics, ES • Laura Dixon - University of Leeds, UK • Tobias Erb - Max Planck Institute for Terrestrial Microbiology, DE • Matthew Gilliham - The University of Adelaide, AU • Cara Haney - The University of British Columbia, CA • Sheng-Yang He - Michigan State University, USA • Gabriel Krouk - French National Centre for Scientific Research, FR • Mark Lynas - British author, journalist & environmental activist with a focus on climate change • Wenbo Ma - University of California Riverside, USA • Donald Richard Ort - University of Illinois, USA • Pierdomenico Perata - Sant'Anna School of Advanced Studies Pisa, IT • Rashmi Sasidharan - Utrecht University, NL • Motokai Seki - RIKEN Center for Sustainable Resource Science, JP • Mechthild Tegeder - Washington State University, USA • Christa Testerink - Wageningen University, NL Information for poster submissions: The format for your poster should be: A0 (841 x 1189 mm / 33.1 x 46.8 in), portrait orientation. The best three abstracts were given a short talk slot in the plenary program. Travel grants: We offer 5 travel grants to international attendees, which will reimburse travel costs up to 400 Euros. Are you interested in attending PlantResearch21 and want to have a chance on a travel grant? Submit your motivation below by clicking on the 'Apply for a grant' button before 15 March 2021. The organizing committee will notify you of your travel grant acceptance by the end of March. No registration is needed before submitting a travel grant proposal. When you’re awarded with a travel grant you will receive a practical email containing the next steps. Note that being awarded a travel grant does not mean being registered for the conference. Scroll down to apply for your grant. 2021-06-07 09:00:00 UTC 2021-06-08 17:00:00 UTC VIB Conferences Music Center De Bijloke, 2, Jozef Kluyskensstraat, Gent, Belgium Music Center De Bijloke, 2, Jozef Kluyskensstraat Gent Oost-Vlaanderen Belgium 9000  firstname.lastname@example.org  PhD StudentsAcademicsIndustry  first_come_first_served 
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