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  • Applied Metaproteomics Workshop 2020

    23 - 27 November 2020

    Magdeburg, Germany

    Applied Metaproteomics Workshop 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 [] []
  • First steps with R in Life Sciences

    17 - 18 February 2021

    Basel, Switzerland

    Elixir node event
    First steps with R in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-r-in-life-sciences-df5cbd10-aefe-4795-949b-166b527374cf This course will take place in Basel with rules complying to COVID situation (distances and hygiene). 2021-02-17 09:00:00 UTC 2021-02-18 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • First Steps with Python in Life Sciences

    22 - 24 March 2021

    Basel, Switzerland

    Elixir node event
    First Steps with Python in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-python-in-life-sciences-440ebe81-e125-459a-8249-c99636c80aeb This course will take place in Basel with rules complying to COVID situation (distances and hygiene), but in the event of new restrictions, the participants will be informed that it will not be cancelled, but streamed. 2021-03-22 09:00:00 UTC 2021-03-24 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Long Reads Workshop 2021

    8 - 16 June 2021

    Norwich, United Kingdom

    Long Reads Workshop 2021 https://tess.elixir-europe.org/events/long-reads-workshop-2021 **This event has been postponed from 2020 due to the COVID-19 (coronavirus) pandemic. The speakers were confirmed for our 2020 event, and we are hopeful they will be able to attend in 2021.** This two-day workshop will provide a combination of presentation of use cases of long read RNAseq, technology developments from the Chief Scientific Officers of leading long read technology companies, sample processing hints and tips from the experts in sequencing facilities at Earlham Institute and Uppsala’s SciLifeLab. In addition we will provide some hands on examples of quantification, differential expression and resistance gene enrichment sequencing (e.g. RenSeq). Please email training@earlham.ac.uk if you would like to be notified as soon as registrations and abstract submissions open. Who is this event for? Research staff and students who are current users of long read technology for the production of transcriptomic data and those analysing long read RNAseq data to produce genome annotations, differential expression analyses and those using RenSeq. We particularly encourage early career researchers and PhD students to submit abstracts for selection for oral presentation. This training forms part of our BBSRC National Capability in Advanced Training 2021-06-08 10:00:00 UTC 2021-06-16 17:00:00 UTC Earlham Institute Earlham Institute, Norwich, United Kingdom Earlham Institute Norwich United Kingdom NR4 7UZ Earlham Institute training@earlham.ac.uk [] [] workshops_and_courses [] []

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