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  • Tools for reproducible research - ISMB/ECCB 2019

    21 July 2019

    Basel, Switzerland

    Tools for reproducible research - ISMB/ECCB 2019 https://tess.elixir-europe.org/events/tools-for-reproducible-research-0ed30b48-9c67-48f5-8616-6ca21c78c509 Educators: Bjoern Grüning (RBC), Johannes Köster, Devon Ryan Date: 21.07.2019 Location: ISMB/ECCB Basel Content: The typical data analyst must simultaneously juggle multiple projects, each having its own duration and software requirements. As few analysts have any formal training on structuring or even writing the code necessary to perform an analysis, it is unsurprising that the iterative analytic process can produce a wide assortment of almost identically named files (e.g., “final_results.txt”, “final_results.version2.txt”, “final_results.really_final.txt”), all with unclear origins and produced with a hodge-podge of similarly poorly named scripts. The near impossibility of tracing a results file to the exact process that produced it creates untold difficulties both when it comes time to publish results as well as when planning subsequent experiments months or years later (afterall, which of the “final_results” files was really the “right one”?). These issues are further compounded by software paths and other similar assumptions being hard-coded into scripts, preventing easy analysis replication elsewhere. Performing analyses in a reproducible and traceable manner is clearly needed to combat such problems. Schedule Overview 2:00 - 2:10 pm Installing conda and snakeMake 2:10 - 2:30 pm Intro to conda and bioconda (slides) 2:30 - 3:30 pm Hands-on Session: creating conda envs and installing packages from bioconda repo This practical would require installing hisat, samtools and deeptools via bioconda 3:30 - 4:00 pm Hands-on Session: writing conda recipes Topics in BioVis (including examples) Visualization of sequences, macromolecules, omics data, biological networks 4:00 - 4:15 am Coffee Break 4:15 - 4:35 pm Intro to snakemake Specific tools for visualizing large-scale biological data 4:35 - 6:00 Hands On Session: Writing a snakemake workflow wrapper for mapping, indexing and creating coverage files Learning goals: In this hands-on tutorial, we demonstrate how Conda can be used to deploy specific software versions easily, reproducibly, and without administrator credentials. Moreover, we demonstrate how Conda’s ability to create isolated software environments helps to avoid side-effects between different analyses or different steps of the same analysis. Attendees will also learn how to create conda recipes themselves, so they can contribute new packages to projects such as Bioconda. We further demonstrate how Snakemake can be used in combination with Conda and Containers to create reproducible analysis workflows and execute them on any platform from workstations to clusters and the cloud. Finally, using snakePipes as an example, we demonstrate how Conda and Snakemake can be used to define reproducible and flexible workflows for complex genomics analysis. Prerequisites: - Laptops with Linux or MacOS - Pre-installed Miniconda - install via miniconda : https://conda.io/miniconda.html - Expected audience should have basic familiarity with python, git and the command line. Keywords: Conda, Bioconda, snakemake, Bioconductor, reproducible research Tools: Conda, Bioconda, snakemake, 2019-07-21 09:00:00 UTC 2019-07-21 17:00:00 UTC de.NBI Basel, Basel, Switzerland Basel Basel Basel-Stadt Switzerland [] [] [] meetings_and_conferences [] []
  • 2nd de.NBI Cloud User Meeting

    3 - 5 September 2019

    Heidelberg, Germany

    2nd de.NBI Cloud User Meeting https://tess.elixir-europe.org/events/2nd-de-nbi-cloud-user-meeting Educators: de.NBI Cloud Group Date: 03.09 to 05.09 Location: Heidelberg What is it about? The 2nd de.NBI Cloud User Meeting is an upcoming 3-day event (03.09.2018-05.09.2018) in Heidelberg for people interested in Bioinformatics, Cloud Computing or Big Data. Due to the diversity of approaches that arise in this exciting and rapidly evolving cloud computing technology niche, this meeting should help to exchange ideas and approaches in the growing de.NBI Cloud community. We aim to advantage our attendees, from beginner to expert, with comprehensive understanding of the very broad application and benefit of the de.NBI Cloud. This event is your chance of meeting users, developers and administrators using the de.NBI Cloud. We feature topics from introduction or use case talks to introduce different technologies (OpenStack, Docker, Kubernetes, Nextflow, ….) to tutorials and workshops that will help understand how to actually apply the technology in your research. Confirmed Speakers Matthias König – Humboldt-University Berlin Alan Beccati – Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy Alexander Peltzer – Quantitative Biology Center (QBIC) Johannes Werner – Leibniz-Institute for Baltic Sea Research Jens Preussner – Max Planck Institute for Heart and Lung Research Marius Dieckmann – Bioinformatics and Systems Biology, Justus University Giessen Björn Grüning – Bioinformatics Group Freiburg University Helena Rasche – Bioinformatics Group Freiburg University Jan Krüger – Computational Metagenomics, Bielefeld University Who should attend this meeting? We welcome people from all background, no matter if you are new to the de.NBI Cloud or considering to submit a project application, to learn and network in our growing community. What to bring? Laptop Preliminary Agenda: 03.09. (13:00 – 18:00): Presentation of use cases 04.09. (09:00 – 17:00): Workshop 05.09. (09:00 – 13:00): Workshop Registration Deadline 23.08.2019 Further Information and registration at https://cloud.denbi.de/2nd-de-nbi-cloud-user-meeting/ 2019-09-03 13:00:00 UTC 2019-09-05 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] meetings_and_conferences [] []
  • Combining Workflows, Tools and Data Management - GCB 2019

    16 September 2019

    Heidelberg, Germany

    Combining Workflows, Tools and Data Management - GCB 2019 https://tess.elixir-europe.org/events/combining-workflows-tools-and-data-management-gcb-2019 Educators: Björn Grüning (RBC), Wolfgang Müller (de.NBI-SysBio) Date: 16.09.2019 Location: Marsilius-Arkaden Turm West, Room K13 Im Neuenheimer Feld **6.130.3** 69120 Heidelberg Germany Contents: There is a huge call towards FAIR data. However, what is *FAIR*? Many of us know how that FAIR means Findable, Accessible, Interoperable, Reusable. However the questions "How do I achieve FAIR?" and "How FAIR is FAIR enough?" are still open to debate. A completely different discussion is: How do I approach making my data FAIR? Making data FAIR can be tedious, manual work. Within this workshop we will demonstrate another approach, i.e. using the workflow system Galaxy, as well as Jupyter Notebooks to extract, enrich, process, and finally upload data into the FAIRDOMHub. This is built around the example use case of building an age estimator for humans from RNA data. On the way, we will give reference to the software and services we provide and the type of advice that we can give. Keywords: FAIR data, Galaxy, Jupyter Notebooks, FAIRDOMHub Tools: Galaxy, Jupyter Notebooks, FAIRDOMHub Prerequisites: None 2019-09-16 09:00:00 UTC 2019-09-16 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] meetings_and_conferences [] []
  • Getting started with the de.NBI Cloud - GCB 2019

    16 September 2019

    Heidelberg, Germany

    Getting started with the de.NBI Cloud - GCB 2019 https://tess.elixir-europe.org/events/getting-started-with-the-de-nbi-cloud-gcb-2019 Educators: Alexander Sczyrba, Peter Belmann, Sebastian Jünemann, Jan Krüger, Alex Walender (BiGi) Location: Heidelberg GCB Date: 16th September Content: The need for high-throughput data analysis has grown tremendously since the introduction of next-generation sequencing (NGS) platforms. The massive amount of data produced creates a new class of resource barriers to be overcome including limited bandwidth, storage volume and compute power. Small research labs can hardly cope with the data generated. A solution to the mere resource problem are cloud computing environments as virtually unlimited and flexible resources. The de.NBI Cloud is a full academic cloud federation, providing compute and storage re-sources free of charge for academic users. It provides a powerful IT infrastructure in combination with flexible bioinformatics workflows and analysis tools to the life science community in Germany. The de.NBI Cloud offers reliable IT security concepts and user access rules to en-sure secure data access and storage. It closes the gap of missing computational resources for life science researchers in Germany. The de.NBI Cloud project started in 2016 as collaboration between the universities of Bielefeld, Freiburg, Gießen, Heidelberg and Tübingen. The close cooperation with the ELIXIR cloud ensures the connectivity and sustainability in the international context. The de.NBI Cloud operates the major service levels: • Infrastructure as a Service (IaaS) suited for experienced power users that want full control over the compute environment; plain access to virtualized infrastructure • Platform as a Service (PaaS) suited for experienced users who utilize fully configured infrastructure for the deployment of custom workflows • Software as a Service (SaaS) suited for users without cloud experience who can use virtual machines (VMs) of pre-configured, state-of-the-art analysis tools and pipelines Cloud computing requires initial efforts and skills to port existing workflows to these new mod-els. The same holds true for emerging programming models. Cloud environments can be difficult to use by scientists with little system administration and programming skills. Challenges exist in managing cloud environments as there is a lack of tools which simplify accessing and using these environments and helping bootstrap users by providing basic software stacks. Keywords: OpenStack, Cloud Computing, virtual machines (VMs) Tools: OpenStack, BiBiGrid Prerequisites: The participants should bring their own laptop computers. The goal of the tutorial is to provide a fundamental introduction to the underlying OpenStack infrastructure. Target audience are bioinformaticians or experienced computational data analysts who would like to utilize scalable and flexible cloud resources for their research. Participants will learn how to setup a cloud project and work with virtual instances, and how to efficiently utilize cloud computing resources. We will also address networking and security issues, demonstrate how to deploy bioinformatics tools in the cloud, and how to set up a customized compute cluster in a cloud environment using BiBiGrid. All topics will be covered by short talks and practical hands-on sessions. 2019-09-16 09:00:00 UTC 2019-09-16 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] meetings_and_conferences [] []
  • Proteomics and metabolomics with OpenMS and pyOpenMS - GCB2019

    16 September 2019

    Heidelberg, Germany

    Proteomics and metabolomics with OpenMS and pyOpenMS - GCB2019 https://tess.elixir-europe.org/events/proteomics-and-metabolomics-with-openms-and-pyopenms Educators: Julianus Pfeuffer, Timo Sachsenberg Date: 16.09.2019 Location: GCB 2019. Heidelberg Contents: Computational mass spectrometry provides important tools and bioinformatic solutions for the analysis of proteomics data. Different methods for label-free quantification have been developed in recent years and were successfully applied in a wide range of studies. Targeted approaches for label-free quantification, like SWATH-MS, achieve deep proteome coverage over a large number of samples while non-targeted methods have shown great potential in unbiased discovery studies. This de.NBI training event introduces key concepts of both targeted SWATH-MS and non-targeted label-free analysis using workflow-based processing of real-life datasets. We will introduce several open-source software tools for proteomics, primarily focusing on OpenMS (http://www.OpenMS.org). In a hands-on session, we will demonstrate how to combine these tools into complex data analysis workflows including visualization of the results. Participants will have the opportunity to bring their own data and design custom analysis workflows together with instructors. For participants interested in developing their own algorithms and methods within the OpenMS framework, we provide a brief introduction to pyOpenMS – the python interface to the OpenMS development library. Training material and handouts will be prepared for both users that want to design proteomic workflows, as well as training material for algorithm and tool developers. Software Requirements: The participants should bring their own laptop computers. Installer versions of required software will be made available. Keywords: LC-MS based proteomics, OpenMS, workflows, KNIME, data analysis Tools: OpenMS/pyOpenMS, KNIME 2019-09-16 09:00:00 UTC 2019-09-16 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] meetings_and_conferences [] []
  • MOFA Workshop - GCB 2019

    16 September 2019

    Heidelberg, Germany

    MOFA Workshop - GCB 2019 https://tess.elixir-europe.org/events/mofa-workshop-gcb-2019 Educators: Oliver Stegle (HD-HuB) Date: 16.09.2019 Location: Heidelberg, Germany Contents: This tutorial provides an introduction to Multi-Omics Factor Analysis (MOFA), a novel unsupervised framework for the integration of multi-omic data sets (Argelaguet et al, Molecular Systems Biology. 2018). Intuitively, MOFA can be viewed as a versatile and statistically rigorous generalization of principal component analysis to multi-omics data. Given multiple ‘omics data types on overlapping sets of samples, MOFA infers a low-dimensional data representation in terms of (hidden) factors. These learnt factors represent the driving sources of variation across data modalities, thus facilitating the identification of molecular phenotypes and disease subgroups. In the first part of the tutorial I will give a 30-minute presentation to explain the model, its applications and limitations. The second part will consist on a hands-on activity where we will use two real-case data sets to show how MOFA can be used for integrative analysis. The first data set will be a large study of blood cancer patients (Dietrich, J Clin Invest. 2018), and the second will be a single-cell multi-omics data set (Angermueller, Nature Methods. 2016). The attendants are also encouraged to bring their own multi-omics data sets. Keywords: MOFA, R, Tools: MOFA, R, Prerequisites: A working knowledge of R is expected. The tutorial requires the installation of the following software: • R>=3.4 + Rstudio • Python>=2.7 • MOFA R package (+ dependencies) • MOFAdata R package (+ dependencies) • mofapy python package (+ dependencies) 2019-09-16 09:00:00 UTC 2019-09-16 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] meetings_and_conferences [] []
  • Integrating computational meta-omics for microbiome research - GCB 2019

    16 September 2019

    Heidelberg, Germany

    Integrating computational meta-omics for microbiome research - GCB 2019 https://tess.elixir-europe.org/events/integrating-computational-meta-omics-for-microbiome-research-gcb-2019 Educators: Dirk Benndorf (BiGi / MetaProtServ), Thilo Muth Date: 16.09.2019 Location: German Cancer Research Center Im Neuenheimer Feld 280 69120 Heidelberg Germany Contents: The field of microbiome research starts to investigate microbial functions in relation to dysbiosis (i.e. the unbalanced composition of the microbiome) being associated with health disorders and disease states. While many microbiome studies mainly rely on genome-based analyses, the integration of meta-omics data at the gene, transcript, protein and metabolite level is a holistic approach that extends the capabilities of microbiome studies. However, the potential of integrative meta-omics has not been fully exploited so far. An important reason is that bioinformatics methods are developed by different research communities. This limits the exchange of ideas and transfer of methods between researchers across different omics fields. In this workshop, we want to bring together bioinformaticians and researchers working in meta-omics and microbiome-focused disciplines. The meta-omics workshop aims to: (i) provide a platform of presenting new algorithms and software tools for integrative multi-omics approaches or related single omics technology (ii) stimulate discussions on challenges and open questions (iii) help exchanging ideas on bioinformatics methods (iv) identify what is currently lacking for integrative omics in microbiome research Abstract proposals for oral presentations (15 min talk + 5 min discussion) of tools, methods or open problems can be submitted until July 31, 2019 Draft schedule: • Abstract deadline for open speaker slots: July 31, 2019 • Response to applications for speaker slots: August 20, 2019 • Each talk is limited to 15 minutes and additional 5 minutes of discussion for each talk. Coffee break of 15 minutes after the first half of the workshop. Final plenary discussion (20 minutes). • Proposed time schedule: 13.30 – 16.30 Learning goals: In this workshop, we want to bring together bioinformaticians and researchers working in meta-omics and microbiome-focused disciplines. Prerequisites: Registration on GCB 2019. Abstract proposals for oral presentations (15 min talk + 5 min discussion) of tools, methods or open problems can be submitted until July 31, 2019 Keywords: Microbiome, Metaproteomics, MetaProteomeAnalyzer, Prophane Tools: MetaProteomeAnalyzer, Prophane Contact: Dr. Thilo Muth (Bioinformatics Unit, Robert Koch Institute, Berlin; mutht@rki.de) Dr. Dirk Benndorf (Bioprocess Engineering, Otto von Guericke University, Magdeburg; benndorf@mpi-magdeburg.mpg.de) 2019-09-16 13:00:00 UTC 2019-09-16 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] meetings_and_conferences [] []
  • Microscopy Image Analysis Course

    19 - 20 September 2019

    Heidelberg, Germany

    Microscopy Image Analysis Course https://tess.elixir-europe.org/events/microscopy-image-analysis-course Educators: Karl Rohr, Thomas Wollmann, Manuel Gunkel (HD-HuB), Qi Gao, Leonid Kostrykin Date: 19.-20.9.2019 Location: Heidelberg University IPMB (Institute of Pharmacy and Molecular Biotechnology) Im Neuenheimer Feld 364 Contents: The course gives an introduction into the field of microscopy image analysis for cell biology and the use of software tools for automated processing of image data. Basic methods for computer-based analysis of microscopy images are introduced such as image preprocessing, segmentation, feature extraction, classification, colocalization, and tracking. Concepts of software platforms with focus on ImageJ and their use for analyzing cell microscopy image data are also taught. Workflow systems for automating image analysis pipelines are also considered (e.g., KNIME, Galaxy). The course consists of lectures and practical sessions. Participants should bring their laptops for the practical sessions. The target group are researchers with a background in biology or medicine that need to analyze their data and have little or no experience in automated image analysis. Learning goals: - Introduction into cell microscopy image analysis - Application of software tools for automated analysis of image data Prerequisites: Basic knowledge in using software tools for image analysis is helpful but not mandatory Keywords: Computer-based image analysis, image preprocessing, segmentation, feature extraction, classification, colocalization, tracking Tools: Image J Course fee: Participants will be charged with a course fee of 40 Euros (to cover the lunch and infrastructure related cost). The invoice details will be shared via email. Registration: Please register directly on the HD-HuB website: https://www.hd-hub.de/course-dates/3-all/47-microscopy-image-analysis-course In the "Comments" section of the registration form, please provide some information about yourself and your motivation to attend the training (e.g. Position, Field of study/Background, Topic of work, Knowledge of image analysis methods/tools). Registration closes on August 11, 2019. The capacity is limited to 20 participants and applicants will be selected after registration closed. You will be notified of the outcome by e-mail on August 23, 2019. 2019-09-19 09:00:00 UTC 2019-09-20 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] [] [] []
  • Software Carpentry Workshop

    16 - 18 October 2019

    Heidelberg, Germany

    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 [] []
  • Data Carpentry Workshop 2020

    23 October 2019

    Heidelberg, Germany

    Data Carpentry Workshop 2020 https://tess.elixir-europe.org/events/educators-toby-hodges-florian-huber-thea-van-rossum-georg-zeller-hd-hub-fotis-e-psomopoulos-date-28-01-2019-30-01-2019-location-atc-computer-training-lab-contents-the-missing-step-between-data-collection-and-research-progress-is-a-lack-of-training-for-researchers-in-crucial-skills-for-effectively-managing-and-analysing-large-amounts-of-data-this-hands-on-workshop-teaches-researchers-the-fundamental-data-skills-they-need-to-conduct-their-work-and-provides-high-quality-domain-specific-training-covering-the-full-lifecycle-of-data-driven-research-the-domain-specific-approach-allows-participants-to-tailor-the-data-content-and-tools-to-reflect-the-specific-data-and-analysis-needs-of-different-areas-data-organisation-and-cleaning-introduction-to-r-data-analysis-and-visualisation-in-r-interacting-with-databases-from-r-data-analysis-with-applications-to-genomics-learning-goals-you-will-learn-how-to-organise-data-and-some-practices-for-more-effective-data-handling-to-effectively-clean-and-format-data-and-automatically-track-any-changes-to-use-r-to-handle-filter-and-summarise-tabular-data-to-use-the-split-apply-combine-concept-for-data-analysis-to-visualise-the-results-of-these-analyses-in-r-using-the-ggplot2-library-to-apply-all-of-the-concepts-in-an-exploratory-analysis-of-a-typical-biological-dataset-prerequisities-the-course-is-aimed-at-graduate-students-and-other-researchers-in-the-life-sciences-who-would-like-to-learn-good-practices-in-data-management-and-analysis-the-course-is-ideally-suited-to-students-without-prior-experience-in-computational-research-but-some-familiarity-with-working-with-tabular-data-on-a-computer-is-welcome-keywords-data-carpentry-r-tools-r Educators: Toby Hodges, Florian Huber, Thea Van Rossum, Georg Zeller, (HD-HuB) Fotis E. Psomopoulos Date: 28/01/2019 - 30/01/2019 Location: ATC Computer Training Lab Contents: The missing step between data collection and research progress is a lack of training for researchers in crucial skills for effectively managing and analysing large amounts of data. This hands on workshop teaches researchers the fundamental data skills they need to conduct their work, and provides high-quality, domain-specific training covering the full lifecycle of data-driven research. The domain-specific approach allows participants to tailor the data, content, and tools to reflect the specific data and analysis needs of different areas: - Data organisation and cleaning - Introduction to R - Data analysis and visualisation in R - Interacting with databases from R - Data analysis with applications to genomics Learning goals: You will learn... - how to organise data and some practices for more effective data handling - to effectively clean and format data and automatically track any changes - to use R to handle, filter, and summarise tabular data - to use the split-apply-combine concept for data analysis - to visualise the results of these analyses in R using the ggplot2 library - to apply all of the concepts in an exploratory analysis of a typical biological dataset Prerequisities: The course is aimed at graduate students and other researchers in the life sciences who would like to learn good practices in data management and analysis. The course is ideally suited to students without prior experience in computational research, but some familiarity with working with tabular data on a computer is welcome. Keywords: Data Carpentry, R Tools: R 2019-10-23 09:00:00 UTC 2019-10-23 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • Machine Learning in R

    6 - 7 November 2019

    Heidelberg, Germany

    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 [] []
  • de.NBI & ELIXIR - Train the Trainer Workshop to Learn Teaching Techniques

    11 - 12 November 2019

    Heidelberg, Germany

    de.NBI & ELIXIR - Train the Trainer Workshop to Learn Teaching Techniques https://tess.elixir-europe.org/events/de-nbi-elixir-train-the-trainer-workshop-to-learn-teaching-techniques de.NBI & ELIXIR - Train the Trainer Workshop to Learn Teaching Techniques Heidelberg Educators: Malvika Sharan, Toby Hodges (HD-HuB), Elisabeth Zielonka Date: 11-11-2019 - 12-11-2019 09:30-17:00 Location: EMBL Heidelberg Room 202 Contents: The course is aimed at everyone who is interested in becoming a better teacher. The workshop is a mix of lectures and hands-on lessons where you practise giving a short lesson using approaches learned and implement some of the teaching techniques which we will discuss. This is training for teaching, not technical training; you do not need any particular technical background, and we will not be teaching that. This workshop is based on the constantly revised and updated curriculum. We will offer two parallel tracks (The Carpentries Track and ELIXIR Track), and you will be asked to choose one track that you would like to attend during this event. The Carpentries Track to become Software Carpentry, Data Carpentry and Library Carpentry instructors, run workshops and contribute to the Carpentry training materials. ELIXIR Track is a non-programming module which will prepare you to organise or teach at the bioinformatics or wet-biology workshops. The Carpentries Track This module is aimed at those who want to become Software Carpentry and Data Carpentry instructors, run workshops and contribute to the Carpentry training materials. You don't currently have to be an instructor or a teacher to attend this workshop, but you do need to be willing and committed to becoming one and to improving your teaching techniques. Software Carpentry and Data Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on two-day workshop covers the basics of educational psychology and instructional design and looks at how to use these ideas in both intensive workshops and regular classes. Please note that after this course is over, you will be asked to do three short follow-up exercises online in order to finish qualifying as an instructor: the details are available athttps://carpentries.github.io/instructor-training/checkout/. If you have any questions about the workshop, the reading material, or anything else, please get in touch. ELIXIR (non-programming) Track ELIXIR unites Europe’s leading life science organisations in managing and safeguarding the increasing volume of data being generated by publicly funded research. It coordinates, integrates and sustains bioinformatics resources across its member states and enables users in academia and industry to access services that are vital for their research. In this module the trainer will deliver the ELIXIR curriculum aimed at the instructors interested in teaching workshops on the topics related to bioinformatics or wet-biology. 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: When possible, participants should bring a laptop that can be connected to the Internet to follow teaching materials and developing a shared note. A device for recording audio and video (mobile phones and laptops are OK) will also be useful as throughout the two days, we are going to record one another teaching in pairs or threes. It does not have to be high-quality, but it should be good enough that you can understand what someone is saying. All participants are required to abide by The Carpentries' Code of Conduct. Keywords: Train the Trainer, 2019-11-11 09:00:00 UTC 2019-11-12 17:00:00 UTC de.NBI / ELIXIR Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
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