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3 events found

Event types: Workshops and courses 

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Organizer: de.NBI 

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City: Fribourg  or Basel  or Amsterdam UMC (location AMC)  or Norwich  or Utrecht  or Lund  or Magdeburg 

  • Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2020

    27 - 29 April 2020

    Magdeburg, Germany

    Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2020 https://tess.elixir-europe.org/events/tools-for-systems-biology-modeling-and-data-exchange-copasi-cellnetanalyzer-sabio-rk-fairdomhub-seek-2020 Educators: Axel von Kamp, Steffen Klamt, Sven Thiele (MPI Magdeburg), Frank T. Bergmann, Ursula Kummer (University of Heidelberg), Wolfgang Müller, Maja Rey, Andreas Weidemann, Ulrike Wittig (HITS) (de.NBI-SysBio) Date: 27. - 29 April 2020 Location: MPI Magdeburg Sandtorstrasse 1 39106 Magdeburg Contents: Key concepts of stoichiometric and kinetic modeling of biochemical networks: - stoichiometric matrix and stoichiometric networks - steady state flux distributions - principles of constraint-based modeling - metabolic flux analysis and flux optimization (flux balance analysis) - metabolic pathway analysis with elementary flux modes - metabolic network design via minimal cut sets - simulation of dynamic (kinetic) models - sensitivity analysis - carrying out parameter estimation tasks - model exchange using SBML Data and model management: - manual/programmatic access to reaction kinetics data from SABIO-RK - storage and exchange of data and models using FAIRDOMHub/SEEK - modeling specific functionalities in FAIRDOMHub/SEEK Learning goals: During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces kinetic modeling techniques which will be illustrated and exercised with COPASI. The second day continues with principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOMHub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists. The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks. Prerequisites: Some knowledge of mathematical modeling will be advantageous. The participants should bring their own laptop with MATLAB installed (if you do not have MATLAB please let us know during registration). Download and preinstallation of COPASI and CellNetAnalyzer is recommended but not mandatory. Keywords: CellNetAnalyzer (CNA), COPASI, SBML, FAIR, modeling, kinetic data access, database, data and model management Tools: CellNetAnalyzer, COPASI, Matlab, SABIO-RK, FAIRDOMHub/SEEK 2020-04-27 09:00:00 UTC 2020-04-29 17:00:00 UTC de.NBI Magdeburg, Magdeburg, Germany Magdeburg Magdeburg Germany [] [] [] workshops_and_courses [] []
  • 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 [] []
  • Applied Metaproteomics Workshop Magdeburg 2021

    22 - 26 November 2021

    Magdeburg, Germany

    Applied Metaproteomics Workshop Magdeburg 2021 https://tess.elixir-europe.org/events/applied-metaproteomics-workshop-magdeburg-2021 Educators: Dirk Benndorf, Stephan Fuchs, Robert Heyer, Kay Schallert (BiGi/MetaProtServ) Date: 22.11.2021 – 26.11.2021 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: 70 € -> The so-called “3G rule” (the course is only open to those that are vaccinated, recovered, or tested - geimpft, genesen, getestet) will be applied! Keywords: Microbiome, MPA, Metaproteomics, MetaProteomeAnalyzer, Tools: MetaproteomeAnalyzer 2021-11-22 09:00:00 UTC 2021-11-26 17:00:00 UTC de.NBI Magdeburg, Magdeburg, Germany Magdeburg Magdeburg Sachsen-Anhalt Germany [] [] [] workshops_and_courses [] []

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