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  • Bulk RNASeq analysis for differential expression

    9 - 20 September 2019

    Leuven, Belgium

    Elixir node event
    Bulk RNASeq analysis for differential expression https://tess.elixir-europe.org/events/bulk-rnaseq-analysis-for-differential-expression During this training you will: execute a complete workflow at command line or in GenePattern to go from raw fastq files to count files execute a complete workflow in R to detect differential expression between two conditions initiate functional annotation and interpretation of the list of differentially expressed genes   2019-09-09 09:00:00 UTC 2019-09-20 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • 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 [] []
  • Introduction to genome-wide association studies (GWAS) 2019

    18 September 2019

    Kiel, Germany

    Introduction to genome-wide association studies (GWAS) 2019 https://tess.elixir-europe.org/events/introduction-to-genome-wide-association-studies-gwas-2019 Educators: David Ellinghaus (Associated partner - CAU) Date: September 18, 2019 Time: 08:30 - 16:30 Location: Kiel, Am Botanischen Garten 1-9, Room E49 This course is designed for 15 participants. If we receive (a lot) more applications, we will choose participants based on the relevance of their application and/or a first-come-first-serve basis. Contents: Over the past decade, genetic epidemiology studies have progressed from studying single genetic variants in candidate genes to investigating millions of common genetic variants in genome-wide association studies (GWAS). Nowadays GWAS studies are moving forward to genome-wide rare variant association studies, gene-gene (GxG) and gene-environment (GxE) interaction studies as well as cross-phenotype studies including several 10k and sometimes even >100k genetic samples. Learning goals: In this one day course we will give guidance for planning of SNP array genotyping and will provide best-practices for large-scale quality control, variant annotation and association analysis of GWAS data. In the practical part of the course will work on real-world data sets and show how to automatically and manually analyze large case-control sample sets and how to annotate phenotype-associated genomic regions. Prerequisites: None Keywords: genome-wide association studies (GWAS); SNP genotype quality control; association testing 2019-09-18 08:00:00 UTC 2019-09-18 17:00:00 UTC de.NBI Kiel, Kiel, Germany Kiel Kiel Germany [] [] [] workshops_and_courses [] []
  • Eukaryote genome annotation workshop 2019

    19 September 2019

    Kiel, Germany

    Eukaryote genome annotation workshop 2019 https://tess.elixir-europe.org/events/eukaryote-genome-annotation-workshop-2019 Educators: Marc Höppner (Associated partner - CAU) Date: September 19, 2019 - 08:30 - 16:30 Location: Kiel, Am Botanischen Garten 1-9, Room E49 Contents: The constant drop in sequencing prices and the development of easy-to-use assembly programs makes it possible, even for small groups, to embark on a de novo genome project to obtain the full sequence of their species of interest. However, automatically annotating all genetic features in a eukaryotic genome, especially in non-model species with few or no sequenced closely related species, remains a challenge and standard pipelines still do not exist. Learning goals: In this one day course participants will learn about these challenges and the current strategies that can be used to try to obtain the most complete set of genes from a de novo assembled eukaryotic genome. We will also discuss how additional data, such as RNA-seq, assembled transcriptomes or proteomic data, can be used to improve the annotation, which can inform decisions on how best to spend the budget during a genome project. The practical part of the course will explain how to automatically and manually annotate a genomic region and how that information can be immediately translated into biologically relevant data for the species of interest. Prerequisites: None Keywords: eukaryotic genome, annotation, RNAseq proteomic data, assembly Contact: Marc Höppner, m.hoeppner@ikmb.uni-kiel.de This course is designed for 15 participants. If we receive (a lot) more applications, we will choose participants based on the relevance of their application and/or a first-come-first-serve basis. 2019-09-19 09:00:00 UTC 2019-09-19 17:00:00 UTC de.NBI Kiel, Kiel, Germany Kiel Kiel Germany [] [] [] workshops_and_courses [] []
  • 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 [] [] [] [] [] []
  • Metabolomics: Understanding Metabolism in the 21st Century

    23 September - 18 October 2019

    Edgbaston, United Kingdom

    Elixir node event
    Metabolomics: Understanding Metabolism in the 21st Century https://tess.elixir-europe.org/events/metabolomics-understanding-metabolism-in-the-21st-century-8c9cebe4-268d-4e19-9073-3a9d99e51df5 This online course explores metabolomics, an emerging field that aims to measure the complement of metabolites (the metabolome) in living organisms. The metabolome represents the downstream effect of an organism's... 2019-09-23 09:00:00 UTC 2019-10-18 23:59:00 UTC Online, Edgbaston, United Kingdom Online Edgbaston United Kingdom B15 2TT [] [] [] [] [] []
  • Good practice in high-throughput experiments

    30 September - 1 October 2019

    Zurich, Switzerland

    Elixir node event
    Good practice in high-throughput experiments https://tess.elixir-europe.org/events/good-practice-in-high-throughput-experiments Overview This course offers an overview of good practice in high-throughput experiments (e.g. next-generation sequencing or compound screening). Particularly we focus on pitfalls in the design of projects (e.g. 2019-09-30 09:00:00 UTC 2019-10-01 00:00:00 UTC SIB, Zurich, Switzerland SIB Zurich Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Linux Introduction

    3 October 2019

    Leuven, Belgium

    Elixir node event
    Linux Introduction https://tess.elixir-europe.org/events/linux-introduction-88e35601-7e20-4a65-8451-ad4baff0ed63 This course will give a short practical summary of the basic things one needs when using mainly the command line in Linux: Overview and distributions How to start working with Linux Short introduction to Graphical User Interface Command line basics: getting help, useful commands Linux File System: navigating, file paths, file manipulation, disk space, archiving Text editing Groups, users, security: access rights Process control This course provides several hands-on sessions 2019-10-03 09:00:00 UTC 2019-10-03 13:00:00 UTC Vlaams Supercomputer Centrum Willem de Croylaan 52, 52, Willem de Croylaan, Leuven, Belgium Willem de Croylaan 52, 52, Willem de Croylaan Leuven Vlaams-Brabant Belgium 3001 [] [] [] workshops_and_courses first_come_first_served Linux basics
  • The Brain Mosaic: Cellular heterogeneity in the CNS (2nd edition)

    10 - 11 October 2019

    Leuven, Belgium

    The Brain Mosaic: Cellular heterogeneity in the CNS (2nd edition) https://tess.elixir-europe.org/events/the-brain-mosaic-cellular-heterogeneity-in-the-cns-2nd-edition Recent advances in technology now allow us to explore multiple aspects of heterogeneity at the single cell level. Nowhere is this more important than in the Central Nervous System (CNS), where cellular heterogeneity has profound effects on all aspects of normal brain function and behavior and explains important aspects of disease pathology. With the second edition of the Brain Mosaic conference we aim to bring together leaders in this emerging discipline to discuss how it is advancing our knowledge of CNS function and disease. Speakers at this neuroscience meeting on ‘single cell’ will emphasize the multi-disciplinary nature of the field in several sessions: • Single cell sequencing and cell diversity • Spatial transcriptomics • New developments in technology and bioinformatics • CNS sequencing and relevance to disease research • Connections an activity Poster information: Format: A0 (841 x 1189 mm / 33.1 x 46.8 in), portrait orientation Deadlines: • Early Bird: 8 September 2019 • Late Registration: 26 September 2019 • Abstract deadline: 29 August 2019 2019-10-10 08:00:00 UTC 2019-10-11 18:00:00 UTC VIB Conferences KU Leuven - Promotion & Jubileumzaal, Naamsestraat 22, 22, Naamsestraat, Leuven, Belgium KU Leuven - Promotion & Jubileumzaal, Naamsestraat 22, 22, Naamsestraat Leuven Vlaams-Brabant Belgium 3000 Bioinformatics Transcriptomics Sequencing [] Evy Vierstraete +32 9 244 66 11 conferences@vib.be [] [] meetings_and_conferences [] Single cell sequencing Sequencingcell diversitySpatial transcriptomicsTranscriptomicstranscriptomicsAlzheimers Clinical Trials And StudiesAlzheimers DiseaseAmnesiaAnimal Models In DementiaAnxiety Autoimmune Disorders & Multiple SclerosisBehavioral IssuesBiopsychiatry Blood-Brain BarrierBrain DiagnosisBrain Disease & FailureBrain InjuryBrain TumourCentral Nervous SystemCerebrovascular DiseaseChild NeurologyClinical NeurophysiologyCNS TumorsCognitive DisordersDementiaDementia CareDemyelinationDiagnosis And TherapyEpilepsyGenetics Genetics And Epigenetics Geriatric NeurologyGut- Brain AxisHeadacheIntervention NeuroradiologyMeningitisMental HealthMental Health NursingMetastatisMovement DisordersMultiple SclerosisMultiple Sclerosis DiagnosisNervous SystemNeural EngineeringNeural EnhancementNeuro-Oncology NeuroanaatomyNeuroanatomyNeurocritical CareNeurodegenerationNeurodegenerative DisorderNeurodegenerative DisordersNeurogeneticsNeuroimagingNeuroimmunologyNeurological DisordersNeurological Disorders And StrokeNeurological InfectionsNeurological SurgeryNeurologistNeurologyNeuromedicinesNeuromuscular MedicineNeuronal AutoantibodiesNeuropathyNeuropeptidesNeuropharmacologyNeuroscienceNeurosurgeryNeurotoxicologyNeurotoxinsNeurotransmissionNeurotransmittersParkinsonParkinsons DiseasePediatric NeurologyPharmacology Psychiatry Psychology PsychoneuroimmunologyRecent Research And Case StudiesRehabilitation TherapyStem Cell Treatment For Neurological DisordersStrokesTraumatic Brain InjuryCNS sequencing disease researchbioinformatics• New developments in technology
  • 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 [] []
  • 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 [] []
  • Genome Engineering

    19 November 2019

    Leuven, Belgium

    Elixir node event
    Genome Engineering https://tess.elixir-europe.org/events/genome-engineering 2019-11-19 09:00:00 UTC 2019-11-19 00:00:00 UTC VIB Bioinformatics Core Provinciehuis Vlaams-Brabant, Leuven, Belgium Provinciehuis Vlaams-Brabant Leuven Belgium 3010 [] [] [] [] [] []
  • Analysis of 16S rRNA metagenomic experiments

    25 November 2019

    Leuven, Belgium

    Elixir node event
    Analysis of 16S rRNA metagenomic experiments https://tess.elixir-europe.org/events/analysis-of-16s-rrna-metagenomic-experiments Processing and statistical analysis of 16S rRNA metagenomic experiments using R & Lotus pipeline. The following analytical steps from raw data to communicable results will be on the programme: - Preparation of sequencing data, read filtering, data cleaning - Data normalization - Numerical ecology: Clustering, Ordination, Diversity, Modelling - Univariate & Multivariate Statistics - Biological interpretation 2019-11-25 09:00:00 UTC 2019-11-25 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • CABANA Workshop: Analysis of Crop Genomics Data

    2 - 6 December 2019

    Bogota, Colombia

    Elixir node event
    CABANA Workshop: Analysis of 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
  • Advanced R Shiny

    5 December 2019

    Zurich, Switzerland

    Elixir node event
    Advanced R Shiny https://tess.elixir-europe.org/events/advanced-r-shiny More information coming up 2019-12-05 09:00:00 UTC 2019-12-05 00:00:00 UTC SIB, Zurich, Switzerland SIB Zurich Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Hands on introduction to ChIP-seq and ATAC-seq analysis

    17 February 2020

    Leuven, Belgium

    Elixir node event
    Hands on introduction to ChIP-seq and ATAC-seq analysis https://tess.elixir-europe.org/events/hands-on-introduction-to-chip-seq-and-atac-seq-analysis The aim is to: have an understanding of the nature of ChIP-seq and ATAC-seq data perform a complete analysis workflow including QC, read mapping, visualization in a genome browser and peak-calling using command line and open source software for each each step  have an overview of possible downstream analyses perform a motif analysis with online web programs This training does not cover all methods available today. It does not aim at bringing users to a professional NGS analyst level but provides enough information to allow biologists understand what DNA sequencing practically is and to communicate with NGS experts for more in-depth needs. 2020-02-17 09:00:00 UTC 2020-02-17 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
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