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  • FLAMES Summer School

    9 - 20 September 2019

    Gent, Belgium

    FLAMES Summer School https://tess.elixir-europe.org/events/flames-summer-school FLAMES (Flanders Training Network for Methodology and Statistics) organizes a two-week Summer School aiming at providing practical methodological and statistical training to young researchers (particularly PhD students) from all disciplines. After the success of the FLAMES Summer School in 2013 (at KULeuven), 2014 (at UGent), 2015 (at VUB), 2016 (at UHasselt) , 2017 (at UAntwerp) and 2018 (at KULeuven) we are going to offer and even broader variety of courses from top lecturers around the world. Whether you are a complete dummy, a starter with a limited knowledge, or a more experienced researcher with a broad basic knowledge in the world of methodology and statistics, the FLAMES summer school offers courses at your level, which emphasizes everyday research practice. The program consists of 23 courses (called modules) from which participants can choose. Each module seamlessly connects theory with hands-on exercises or lab sessions, focusing on various disciplines and software packages whenever possible. The basic courses are combined in 2 recommended tracks, that directly connect to the prior knowledge of the participant. This year the FLAMES Summer School will take place at Gent University, De Sterre. 2019-09-09 09:00:00 UTC 2019-09-20 17:00:00 UTC Krijgslaan 281, Gent, Belgium Krijgslaan 281 Gent Oost-Vlaanderen Belgium Ghent University summerschool@flames-statistics.com [] [] workshops_and_courses registration_of_interest []
  • 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 [] []
  • Melbourne R package development workshop

    16 September 2019

    Melbourne, Australia

    Melbourne R package development workshop https://tess.elixir-europe.org/events/melbourne-r-package-development-workshop 2019-09-16 09:00:00 UTC 2019-09-16 17:00:00 UTC COMBINE Walter and Eliza Hall Institute, Melbourne, Australia Walter and Eliza Hall Institute Melbourne Australia Bioinformatics [] [] [] [] [] bioinformatics
  • 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 [] [] [] [] [] []
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Monash University)

    25 - 26 September 2019

    Melbourne, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Monash University) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-monash-university 2019-09-25 12:00:00 UTC 2019-09-26 16:00:00 UTC EMBL-ABR L1.02, 44 Exhibition Walk Matheson Library Monash University Clayton, VIC, Melbourne, Australia L1.02, 44 Exhibition Walk Matheson Library Monash University Clayton, VIC Melbourne Australia Bioinformatics Monash University [] [] [] [] SnakemakeNextflowbioinformatics
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Hudson Institute)

    25 - 26 September 2019

    Melbourne, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Hudson Institute) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-c253f254-38a1-4de9-b3cf-8abf216453db 2019-09-25 12:00:00 UTC 2019-09-26 16:00:00 UTC EMBL-ABR Boardroom 1, Level 3 Hudson Institute of Medical Research 27-31 Wright Street Clayton, VIC 3168, Melbourne, Australia Boardroom 1, Level 3 Hudson Institute of Medical Research 27-31 Wright Street Clayton, VIC 3168 Melbourne Australia Bioinformatics [] [] [] [] [] bioinformaticsNextflowSnakemake
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (University of Melbourne)

    25 - 26 September 2019

    Melbourne, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (University of Melbourne) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-23941db7-c610-4aaf-8789-f55c938edb0d 2019-09-25 12:00:00 UTC 2019-09-26 16:00:00 UTC EMBL-ABR Melbourne Bioinformatics 187 Grattan St University of Melbourne CARLTON, VIC 3053, Melbourne, Australia Melbourne Bioinformatics 187 Grattan St University of Melbourne CARLTON, VIC 3053 Melbourne Australia Bioinformatics University of Melbourne [] [] [] [] bioinformaticsSnakemakeNextflow
  • 4th Disease Maps Community Meeting - DMCM2019

    2 - 4 October 2019

    Sevilla, Spain

    Elixir node event
    4th Disease Maps Community Meeting - DMCM2019 https://tess.elixir-europe.org/events/4th-disease-maps-community-meeting-dmcm2019 The [4th Disease Maps Community Meeting] (http://disease-maps.org/DMCM2019) is hosted by the [Clinical Bioinformatics Area] (http://www.clinbioinfosspa.es/), FPS, Hospital Virgen del Rocio. **Invited Talks** * _Schizophrenia Map: Data to knowledge to data_ **Jessica Dale Tenenbaum**, Duke University at Durham, North Carolina, USA * _Logic modeling to integrate disease maps and various omics data_ **Julio Saez-Rodriguez**, RWTH-Aachen University Hospital, Aachen, Germany * _Toward whole-cell computational models for precision medicine_ **Jonathan Karr**, Icahn School of Medicine at Mount Sinai, New York, USA * _Computational approaches to tackle chemoresistance in high-grade serous ovarian cancer_ **Sampsa Hautaniemi**, Faculty of Medicine, University of Helsinki, Finland **Afternoon discussion sessions** Afternoon breakout discussion sessions are planned following the example of the 2nd Disease Maps Community Meeting in Luxembourg. We invite proposals: a title and a brief description of the topic (1 page maximum). 4-6 topics will be selected, introduced 2nd October and discussed 3rd and 4th October with summaries presented at the end to all the participants. **Abstract subimission and registration** http://disease-maps.org/DMCM2019 2019-10-02 09:30:00 UTC 2019-10-04 13:30:00 UTC Disease Maps Project Centro de Documentación Clínica Avanzada, s/n, Avda de Manuel Siurot, Sevilla, Spain Centro de Documentación Clínica Avanzada, s/n, Avda de Manuel Siurot Sevilla Spain 41013 Systems medicine Translational medicine Bioinformatics Fundación Progreso y Salud (FPS)Hospital Virgen del Rocio disease-maps-coord@googlegroups.com [] [] meetings_and_conferences [] BioinformaticsClinical BioinformaticsDiseasesDisease mapsTranslational Bioinformaticssystems medicine
  • Joint SIB / NBIS Autumn School Single Cell Analysis

    13 - 19 October 2019

    Leysin

    Elixir node event
    Joint SIB / NBIS Autumn School Single Cell Analysis https://tess.elixir-europe.org/events/nbis-sib-collaborative-course-single-cell-transcriptomics #training #url: https://www.sib.swiss/training/course/2019-10_single-cell contact: education@nbis.se This course is organised by NBIS/SciLifeLab and the SIB PhD Training Network. Priority is given to their members, but is open to everyone. Overview Single-cell analysis of the various -omics makes possible to discover mechanisms, strains, expressions that would not be noticed when studying bulk cell populations. New developments lead more and more research groups to use this technology and this Autumn School will provide an overview of the various methods and fields of application through lectures and hands-on exercises. Generally, the afternoons will be dedicated to practical exercises where you will be able to apply the theoretical concepts learned during the morning session. Sometimes there will be a mix of both. One afternoon will be devoted to a social activity. See the preliminary program below for more details... Audience This course is addressed to PhD students, postdocs and scientists starting to work with single cell technologies and analysis. Learning objectives The first objective of this school is to provide participants with a broad knowledge of single cell analysis that would enable them to understand its application in general. This would be achieved via the multiple lectures provided by our lecturers throughout the week. The second objective is to enable participants to apply single cell analysis in their own research. This would be achieved by all the exercises that would follow the theoretical lectures. The third objective is networking with the lecturers and also the other participants that will most likely share similar interests. Prerequisites Knowledge / competencies Students should have intermediate to advanced R skills (able to read, understand and write R scripts), know how to use common R/Bioconductor packages, be familiar with the typical steps involved in a bulk RNA-seq (both experimental and data analysis parts). Technical Students should be able to bring their own laptop with R and RStudio installed. A list of required R-packages will be sent before the course and these should be installed prior to the course start. Program Sunday ≈17-18h: arrival of the participants, check-in Welcome and dinner Monday: Transcriptomics Introductory lecture: Vincent Gardeux, Laboratory of Systems and Genetics, EPFL / SIB, Lausanne, Switzerland. Quantification, QC & Normalization: Davide Risso, Department of Statistical Sciences, University of Padova, Italy. Dimensionality reduction: Paulo Czarnewski, NBIS, Uppsala University, SciLifeLab, Uppsala, Sweden. Tuesday: Transcriptomics Batch correction: Panagiotis Papasaikas, Computational Biology Group, Friedrich Miescher Institute for Biomedical Research / SIB, Basel. Switzerland. Clustering - methods overview: Charlotte Soneson, Computational Biology Group, Friedrich Miescher Institute for Biomedical Research / SIB, Basel, Switzerland. Cell fate mapping and trajectories: Robrecht Cannoodt, VIB-UGent Center for Inflammation Research, Gent, Belgium. Wednesday: Transcriptomics Differential expression: Charlotte Soneson, Computational Biology, Friedrich Miescher Institute for Biomedical Research / SIB, Basel, Switzerland. Afternoon: Team activity Evening: Keynote lecture: Alejandro Sifrim, Laboratory of Reproductive Genomics, KU Leuwen, Belgium. Thursday: Proteomics Transcriptome + proteome: Johan Reimegård, Uppsala University, SciLifeLab, Uppsala, Sweden. Differential abundance and differential state analysis of single cell cytometry data: Mark Robinson & Helena Crowell, Statistical Genomics, University of Zurich / SIB, Zurich, Switzerland. Friday: Other omics and integration Spatial mapping of scRNAseq: Lars Borm, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. Lineage tracing and scRNA: Maria Florescu, Hubrecht Institute, Developmental Biology and Stem Cell Research, Utrecht, Netherlands. Data integration methods: Sebastien Smallwood, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. End of the event around 14h30. Application Before applying, be sure your profile matches the prerequisites and do not forget to take this survey. If you do not take the survey, your application will not be taken into consideration. Please use the same email address for the application and the survey. Registration fees are the following: 250 Swiss Francs for members of the SIB PhD Training Network and for PhD students enrolled at a Swedish University, 600 Swiss Francs for other academics, 1200 Swiss Francs for for-profit institutions. This includes full course fees, full board accommodation at the hotel and coffee breaks. Deadline for application and free-of-charge cancellation is set is set to 16 September 2019. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions. You will be informed by email of your registration confirmation. Click to apply Venue and Time Location: Hotel Central Residence & Spa, Leysin, Switzerland. Arrival: Sunday before 18h Departure: Friday around 14h30 Additional information Coordination: Björn Nystedt (NBIS/SciLifeLab), Grégoire Rossier (SIB). Scientific Committe: Åsa Björklund (NBIS/SciLifeLab), Michael Stadler & Charlotte Soneson (SIB and FMI Basel), Vincent Gardeux (EPFL). For more information, please contact Grégoire Rossier. 2019-10-13 09:00:00 UTC 2019-10-19 00:00:00 UTC Leysin Leysin [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Joint SIB / SciLifeLab Autumn School Single Cell Analysis

    13 - 18 October 2019

    Leysin, Switzerland, Switzerland

    Elixir node event
    Joint SIB / SciLifeLab Autumn School Single Cell Analysis https://tess.elixir-europe.org/events/joint-sib-scilifelab-autumn-school-single-cell Application is now closed. This course is organised by NBIS/SciLifeLab and the SIB PhD Training Network. Priority is given to their members, but is open to everyone. 2019-10-13 09:00:00 UTC 2019-10-18 00:00:00 UTC SIB, Leysin, Switzerland, Switzerland SIB Leysin, Switzerland Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] #trainingtraining
  • 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 [] []
  • 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
  • A tour of machine learning: classification

    13 - 14 January 2020

    Gent, Belgium

    Elixir node event
    A tour of machine learning: classification https://tess.elixir-europe.org/events/a-tour-of-machine-learning-classification-b217275f-0a31-4994-b5c6-be3d999cc9f7 Machine learning has become ubiquitous in biotechnology (as in many other fields), fueled largely by the increasing availability and amount of data. Learning algorithms can figure out how to perform important tasks by generalizing examples. Typical applications are diagnoses/prognoses, gene/protein annotation, drug design, image recognition, text mining and many others. However, building successful machine learning models requires a substantial amount of “black art” that is hard to find in textbooks. This course is an interactive Jupyter Notebook (Python) that will teach you how to build successful machine learning models. No background in machine learning is assumed, just a keen interest. 2020-01-13 09:00:00 UTC 2020-01-14 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []
  • FAIRplus Innovation and SME Forum: Implementing FAIR data principles in industrial life science research

    29 January 2020

    Hinxton, United Kingdom

    FAIRplus Innovation and SME Forum: Implementing FAIR data principles in industrial life science research https://tess.elixir-europe.org/events/fairplus-innovation-and-sme-forum The agenda includes: Introduction to FAIRplus Guidelines for making data FAIR Flastalks from SMEs Hands-on session on FAIRification   Who should attend: Biotech companies owning data potentially in need of FAIRification  Technology companies who are planning to provide FAIRification services  Academic groups interested in FAIRification for their data collections       2020-01-29 09:00:00 UTC 2020-01-29 00:00:00 UTC Wellcome Genome Campus, Hinxton, United Kingdom Wellcome Genome Campus Hinxton United Kingdom [] [] [] [] [] []
  • ELIXIR Scientific Advisory Board meeting 2020

    11 - 12 February 2020

    Hinxton, United Kingdom

    ELIXIR Scientific Advisory Board meeting 2020 https://tess.elixir-europe.org/events/elixir-scientific-advisory-board-meeting-2020 The ELIXIR Scientific Advisory Board will hold their annual meeting from 11-12 February 2020 at the Wellcome Genome Campus in Hinxton, UK. Details of agenda and registration will be made available to participants. Contacts For all logistical inquiries, please contact: Melissa Balzano (melissa.balzano@elixir-europe.org)  Tel: +44 (0)1223 494305 For all documentation inquiries, please contact: Joana Wingender (joana.wingender@elixir-europe.org)  Tel: +44 (0)1223 492670 2020-02-11 09:00:00 UTC 2020-02-12 17:00:00 UTC Wellcome Genome Campus, Hinxton, United Kingdom Wellcome Genome Campus Hinxton United Kingdom [] [] [] meetings_and_conferences [] []
  • 13th ELIXIR Board meeting (Hinxton)

    22 - 23 April 2020

    Hinxton, United Kingdom

    13th ELIXIR Board meeting (Hinxton) https://tess.elixir-europe.org/events/thirteenth-elixir-board-meeting-hinxton The thirteenth ELIXIR Board will take place at the Wellcome Genome Campus in Hinxton, UK From 29 - 30 April 2020. This meeting is only open to the ELIXIR Board and Observers. Agenda items and meeting documentation will be made available to Board members in due time.  Any inquiries regarding ELIXIR Board meetings should be sent to info@elixir-europe.org. 2020-04-22 09:00:00 UTC 2020-04-23 00:00:00 UTC Wellcome Genome Campus, Hinxton, United Kingdom Wellcome Genome Campus Hinxton United Kingdom CB10 1SD [] [] [] meetings_and_conferences [] []
  • Mass spectrometry data processing

    2 - 3 June 2020

    Gent, Belgium

    Elixir node event
    Mass spectrometry data processing https://tess.elixir-europe.org/events/mass-spectrometry-data-processing-f80a1c34-fcd4-40bf-83df-1ba4b05dd38e Obtain a good understanding of the origins and properties of mass spec data Obtain an understanding of the processing of mass spec data, aimed at identifying and quantifying peptides and proteins Gain sufficient understanding of the software tools and database used, and of the issues and caveats involved, to critically analyse and assess results from mass spectrometry based proteomics experiments 2020-06-02 09:00:00 UTC 2020-06-03 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []
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