Protein Structure Fundamentals: Searching – Analyzing – Modeling
23 - 24 September 2019
Hamburg, GermanyProtein Structure Fundamentals: Searching – Analyzing – Modeling https://www.denbi.de/training/606-protein-structure-fundamentals-searching-analyzing-modeling https://tess.elixir-europe.org/events/protein-structure-fundamentals-searching-analyzing-modeling Educators: Eva Nittinger (BioData), Matthias Rarey (BioData), Ida Schomburg (BioData), Greg Landrum (CIBI) Date: 23./24.09.2019 Location: Universität Hamburg, ZBH – Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg Contents: In this workshop, you will get to know a combination of tools and webservices for searching and analyzing protein structure data. The focus will be on protein function and related interactions to small molecules. We will work with two web- and two software platforms: BRENDA, the database for enzyme structures will be used to gather information about enzyme structures. The ProteinsPlus web service contains a diverse range of software solution for the analysis of protein structures and its application in molecular modeling approaches. NAOMI ChemBio Suite contains desktop software for cheminformatics and advanced modeling. KNIME offers diverse options for the analysis of biological data and the generation of analytical workflows. Learning goals: This course is designed for life and computer scientists with interest in protein structures, but only very basic experience. Topics include: Finding and selecting protein structure data, evaluating the quality of experimental data, preprocessing structure data for modeling, first modeling steps like the analysis of binding site properties and conformational flexibility. Furthermore, we will introduce basic Cheminformatics tools. Usage of ProteinsPlus, BRENDA, NAOMI ChemBio Suite, and KNIME; all software introduced is available for free for academic use. Prerequisites: General knowledge of proteins and their role in life sciences Keywords: Protein structures, protein-ligand interactions, molecular modeling, structure-to-function relationships, cheminformatics, ProteinsPlus, BRENDA, EnzymeStructures, KNIME Tools: ProteinsPlus, BRENDA, NAOMI ChemBio Suite, KNIME 2019-09-23 09:00:00 UTC 2019-09-24 17:00:00 UTC de.NBI Hamburg, Hamburg, Germany Hamburg Hamburg Germany    workshops_and_courses  
Software Carpentry Workshop
16 - 18 October 2019
Heidelberg, GermanySoftware Carpentry Workshop https://www.denbi.de/training/486-software-carpentry-workshop https://tess.elixir-europe.org/events/software-carpentry-workshop-ab3af408-aa91-49ed-bab2-5db1f2e6d15d Educators: Malvika Sharan, Georg Zeller, Mike Smith, Thomas Schwarzl, Frank Thommen (HD-HuB), Holger Dinkel Date: 16-10-2019 - 18-10-2019 09:00-18:00 Location: ATC Computer Training Lab, EMBL Heidelberg Contents: Computation is an integral part of today's research as data has grown too large or too complex to be analysed by hand. An ever-growing fraction of science is performed computationally and many wet-lab biologists spend part of their time on the computer. Many scientists struggle with this aspect of research as they have not been properly trained in the necessary set of skills. The result is that too much time is spent using inefficient tools when progress could be faster. This course provides training in several key tools, with a focus on good development practices that encourage efficient and reproducible research computing. Topics covered include: Introduction to Python scripting Introduction to the Unix shell and usage of cluster resources Version control with Git and Github Analysis pipeline management Scientific Python & working with biological data Literate programming with Jupyter notebooks Learning goals: This course aims to teach software writing skills and best practices to researchers in biology who wish to analyse data, and to introduce a toolset that can help them in their work. The goal is to enable them to be more productive and to make their science better and more reproducible. Prerequisites: This is a course for researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will be familiar with some command line/programmatic computer usage, will want to become more confident using these tools efficiently and reproducibly. A target student will have written a for loop in some language before, but will not know what git is (or at least not be very comfortable using git). Keywords: Programming; Command Line; Version Control; Bioinformatics; Data Analysis; Cluster Computing Tools: Python; Bash; Unix/Linux; Git; GitHub; SnakeMake; Biopython; Pandas; Numpy; SciPy; Matplotlib 2019-10-16 09:00:00 UTC 2019-10-18 17:00:00 UTC de.NBI / ELIXIR Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany    workshops_and_courses  
Machine Learning in R
6 - 7 November 2019
Heidelberg, GermanyMachine Learning in R https://www.denbi.de/training/675-machine-learning-in-r https://tess.elixir-europe.org/events/machine-learning-in-r Date Nov 6 - Nov 7 2019 Location EMBL Heidelberg Tutors and helpers - Dr. Malvika Sharan - Prof Bernd Bischl - Martin Binder - Giuseppe Casalicchio Affiliation: Ludwig-Maximilians-University Munich Course Information This two-day course, on the implementation of Machine Learning in R, using mlr package will be delivered as practical sessions on programming and data analysis. The main goal of mlr is to provide a unified interface for machine learning tasks as classification, regression, cluster analysis and survival analysis in R. Sessions will be driven by many practical exercises and case studies. Before this workshop, participants are expected to review the official material introducing the principle of Machine Learning (see the prerequisite). Course Content This 2-day course will cover hands-on sessions using `mlr` and other relevant packages. Daily schedule - 09:30-12:30 3h morning, 90 min Theory + 90 min Practical - 12:30-13:30 1h Lunchbreak - 13:30-16:30 3h afternoon, 90 min Theory + 90 min Practical - 16:30-17:00 Time for general questions Day 1 Introduction to the concepts and Practical with mlr - Performance Evaluation and Resampling (Metrics, CV, ROC) - Introduction to Boosting Day 2 Introduction to the concepts and Practical with mlr - Tuning and Nested Cross-Validation - Regularization and Feature Selection Prerequisite The course is aimed at advanced R programmers, preferably with some knowledge of statistics and data modeling (See prerequisite materials from Day-1, 2, & 4). In this course, our learners will learn more about machine learning and its application and implementation through the hands-on sessions and use cases. Optional: Discussion-Based Session On The Principle of Machine Learning Anna Kreshuk (EMBL Group Leader) will lead a one-day discussion-based session on 14 October 2019 to address your questions on the prerequisite materials on the principle of Machine Learning. This will also allow you to connect with other participants of this workshop informally, and discuss the materials in smaller groups. Please register for this workshop separately: https://bio-it.embl.de/events/machine-learning-discussion-workshop-2019/. Registration Please register on this page: https://bio-it.embl.de/events/machine-learning-in-r-2019/ Please note that the maximum capacity of this course is 40 participants and registration is required to secure a place. If you have any questions, please contact Malvika Sharan. In your registration, please mention your EMBL group name, or institute's name (e.g. DKFZ, Uni-HD) if you are registering as an external participant. Costs 60,00 EUR Keywords: Machine Learning, R 2019-11-06 09:00:00 UTC 2019-11-07 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany    workshops_and_courses  
NBIS/SciLifeLab course: Introduction to Bioinformatics using NGS data
25 - 30 November 2019
Lund, SwedenNBIS/SciLifeLab course: Introduction to Bioinformatics using NGS data https://www.google.com/calendar/event?eid=N3ZubGxqcmprZHU2NGFodHZnamtuZGplbWMgYmlscy5lbGl4aXJAbQ https://tess.elixir-europe.org/events/nbis-scilifelab-course-introduction-to-bioinformatics-using-ngs-data More information will follow: https://www.scilifelab.se/education/courses%26training questions? mail firstname.lastname@example.org 2019-11-25 09:00:00 UTC 2019-11-30 00:00:00 UTC Lund, Sweden Lund Sweden  email@example.com     
NBIS course: RNAseq
26 - 29 November 2019
Lund, SwedenNBIS course: RNAseq https://www.google.com/calendar/event?eid=MWFodTBmNm10dmlqM2d0cDFxZG41c2Uzb2YgYmlscy5lbGl4aXJAbQ https://tess.elixir-europe.org/events/nbis-course-rnaseq More information will follow: https://www.scilifelab.se/education/courses%26training questions? mail firstname.lastname@example.org 2019-11-26 09:00:00 UTC 2019-11-29 00:00:00 UTC Lund, Sweden Lund Sweden  email@example.com     
CABANA Workshop: Analysis of Crop Genomics Data
2 - 6 December 2019
Bogota, ColombiaCABANA Workshop: Analysis of Crop Genomics Data http://www.ebi.ac.uk/training/events/2019/cabana-workshop-analysis-crop-genomics-data https://tess.elixir-europe.org/events/cabana-workshop-analysis-of-crop-genomics-data This course will introduce crop biologists to methods and approaches for analysing crop genomics data. 2019-12-02 08:30:00 UTC 2019-12-06 12:45:00 UTC Universidad de los Andes - UniAndes, Bogota, Colombia Universidad de los Andes - UniAndes Bogota Colombia 111711  Marco Cristancho     HDRUK
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