3rd Tool-Training for Proteomics
28 October 2019
Bochum, Germany3rd Tool-Training for Proteomics https://www.denbi.de/training/553-3rd-tool-training-for-proteomics https://tess.elixir-europe.org/events/3rd-tool-training-for-proteomics Educators: Michael Kohl, Treesa Sunny, Michael Turewicz and Julian Uszkoreit (BioInfra.Prot) Date: Monday, 2019-10-28 Location: Ruhr University Bochum, 44801 Bochum Contents: In this one day course we will show some of BioInfra.Prot's tools provided by de.NBI, namely “PIA - Protein Inference Algorithms”, “BIONDA – A Free Biomarker Database” and “CalibraCurve”. Besides the tool based sessions we offer a "Proteomics in the Cloud" session where we show advantages of cloud based bioinformatics and give a tutorial how to access the de.NBI cloud. PIA allows to inspect and combine the results of proteomics search engines. The main focus lays on the integrated inference algorithms for identification and quantification purposes. BIONDA is a free, up-to-date and user-friendly biomarker and biomarker candidate database that facilitates any kind of research on protein biomarkers and the corresponding diseases. CalibraCurve is a tool intended for the generation of calibration curves in the context of MRM (targeted proteomics) experiments. Such calibration curves are necessary for the selection of suitable transitions. Learning goals: Attendees of the course will learn how to use the tools PIA, BIONDA and CalibraCurve effectively for their daily proteomics tasks. Additionally they will learn how to use the de.NBI cloud. Prerequisites: This course is for all researches in the field of proteomics. The attendees should have basic knowledge of LC-MS proteomics, but no prior bioinformatics skills are required. Basic knowledge of how to analyse LC-MS data are sufficient. Attendees are required to bring their own laptops. If this is not possible or laptops have very low computing capacities, please contact the organizers. Keywords: Proteomics; Data Analysis; Biomarkers; de.NBI Cloud Tools: PIA; BIONDA; CalibraCurve 2019-10-28 09:00:00 UTC 2019-10-28 17:00:00 UTC de.NBI Bochum, Bochum, Germany Bochum Bochum Arnsberg Germany    workshops_and_courses  
4th Differential analysis of quantitative proteomics data using R
18 November 2019
Bochum, Germany4th Differential analysis of quantitative proteomics data using R https://www.denbi.de/training/554-4th-differential-analysis-of-quantitative-proteomics-data-using-r https://tess.elixir-europe.org/events/4th-differential-analysis-of-quantitative-proteomics-data-using-r Educators: Michael Turewicz (bioinformatician) and Karin Schork (biostatistician) (BioInfra.Prot) Date: Monday, 18th Nov 2019 Location: Ruhr University Bochum, 44801 Bochum Contents: This course will impart knowledge about how to conduct a differential analysis of high-throughput quantitative proteomics data using R. As we start with a basic introduction to the popular statistical programming language, no prior knowledge on R is required. The statistical background on utilized methods is explained in order to enable the participants to assess their own as well as published workflows critically. In this regard the course will touch upon • statistical inference: hypotheses, type I and II error • location tests (t-test and ANOVA) • multiple testing Learning goals: • Independent usage of basic R functions including • data import and export • basic plots • statistical tests • Deeper understanding of statistical methods applied in differential analyses Prerequisites: • Basic understanding of high-dimensional data sets from quantitative proteomics or other life sciences; • No prior knowledge on R required • Please bring your own laptop for the hands-on exercises! Keywords: R; high-throughput data; omics; proteomics; differential analysis 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 2019-11-18 09:00:00 UTC 2019-11-18 17:00:00 UTC de.NBI Bochum, Bochum, Germany Bochum Bochum Arnsberg Germany      
Advanced analysis of quantitative proteomics data using R
19 November 2019
Bochum, GermanyAdvanced analysis of quantitative proteomics data using R https://www.denbi.de/training/556-advanced-r-course https://tess.elixir-europe.org/events/advanced-analysis-of-quantitative-proteomics-data-using-r Educators: Michael Turewicz (bioinformatician) and Karin Schork (biostatistician) (BioInfra.Prot) Date: Tuesday, 19th Nov 2019 Location: Ruhr University Bochum, 44801 Bochum Contents: In this course you will learn about using R for the analysis of proteomics data. We will focus on data preprocessing methods and advanced methods for data analysis. In this regard the cpurse will touch upon: • data normalization • quality control, handling of missing values • clustering, heatmaps • ROC-curves Please be aware that basic knowledge of R and methods for differential analysis of proteomics data are taught in our course “Differential analysis of quantitative proteomics data” the previous day (Monday, 18th Nov 2019, http://goo.gl/forms/mpKHnbT1Um) Learning goals: • Independent usage of R functions for • Data preprocessing • Plots and graphs • Statistical methods for data analysis • Use of additional R packages • Deeper understanding of statistical methods applied in differential analyses 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, t-test, for loop) and basic knowledge of differential analysis of proteomics data. Both can for example be gained from our course “Differential analysis of quantitative proteomics data” the previous day (Monday, 18th Nov 2019, http://goo.gl/forms/mpKHnbT1Um). • Please bring your own laptop for the hands-on exercises! Keywords: R; 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 2019-11-19 09:00:00 UTC 2019-11-19 17:00:00 UTC de.NBI Bochum, Bochum, Germany Bochum Bochum Arnsberg Germany    workshops_and_courses  
LIFS Course - ILS 2021 & LipidomicsForum 2021
5 October 2021
Regensburg, GermanyLIFS Course - ILS 2021 & LipidomicsForum 2021 https://www.denbi.de/training/1151-lifs-course-ils-2021-lipidomicsforum-2021 https://tess.elixir-europe.org/events/lifs-course-ils-2021-lipidomicsforum-2021 Educators: Jacobo Miranda Ackerman, Daniel Krause, Nils Hoffmann (de.NBI, BioInfra.Prot / LIFS) Date: October 5th, 2021, 9:00 – 12:00 (CEST) & 13:00 – 17:00 (CEST) Deadline for Workshop Registration: Until capacity is reached. Location: On-Site, Regensburg (if local COVID-19 rules allow, on-line otherwise) Contents: In the first part of the course, we will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. In the second part of the course, we will apply PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets. The third part of this course will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will inspect, check and normalize the data as well as calculate absolute quantities using internal class-specific standards with lxPostman. In part four, we will then perform a qualitative comparison of the lipidomes using the LUX Score lipidome homology. Morning 09:00 – 09:45 Welcome and Introduction 10:00 – 10:30 Targeted Lipidomics with LipidCreator and Skyline 10:30 – 12:00 LipidCreator and Skyline Exercises Afternoon 13:00 – 14:30 Shotgun Lipidomics with LipidXplorer 14:30 – 15:30 Quantification of Shotgun Lipidomics data with lxPostman 15:30 – 17:00 Lipidome comparison with LUX Score Learning goals: Participants will be able to understand and explain the shotgun MS and targeted LC-MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline. Prerequisites: Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based and desktop applications. Please note that you may need to install software on your computer to fully participate in all exercises which may require the proper rights. The workshop will be a mix of small lecture segments and hands-on exercises. The trainers will be available for questions and assistance during the workshop. Keywords: Lipidomics, Shotgun, Targeted, LC-MS Tools: PeakStrainer and LipidXplorer, LipidCreator, Skyline, lxPostman, LUX Score Registration: Please select the “LIFS Training session I & II” in the Workshops section of the conference registration. Capacity is limited to 30 participants. 2G (vaccinated or fully recovered) - with either certificate of full vaccination or certificate of recovery / positive PCR test not older than six months. Nose+mouth protection - FFP2 mask or medical mouth nose protection have to be worn inside of buildings. 2021-10-05 09:00:00 UTC 2021-10-05 17:00:00 UTC de.NBI Regensburg, Regensburg, Germany Regensburg Regensburg Oberpfalz Germany      
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