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  • NGS Platforms: how data generation impacts bioinformatics analysis? - Quality Control (1 day)

    23 September 2019

    Brisbane, Australia

    NGS Platforms: how data generation impacts bioinformatics analysis? - Quality Control (1 day) https://tess.elixir-europe.org/events/analysis-of-ngs-data-workshops-with-galaxy-fe6e1892-806d-4078-979a-71e5b2ae842a 2019-09-23 09:00:00 UTC 2019-09-23 17:00:00 UTC QFAB Translational Research Institute, 37, Kent Street, Brisbane, Australia Translational Research Institute, 37, Kent Street Brisbane Brisbane City Australia Bioinformatics [] [] [] [] [] bioinformaticsGalaxy
  • Genome assembly using Galaxy (1 day)

    24 September 2019

    Brisbane, Australia

    Genome assembly using Galaxy (1 day) https://tess.elixir-europe.org/events/analysis-of-ngs-data-workshops-with-galaxy-5e8d0966-8ee8-4d64-8663-c49d25525a60 2019-09-24 09:00:00 UTC 2019-09-24 17:00:00 UTC QFAB Translational Research Institute, 37, Kent Street, Brisbane, Australia Translational Research Institute, 37, Kent Street Brisbane Brisbane City Australia Bioinformatics [] [] [] [] [] bioinformaticsGalaxy RNA-Seq
  • RNA Seq analysis using Galaxy (1 day)

    25 September 2019

    Brisbane, Australia

    RNA Seq analysis using Galaxy (1 day) https://tess.elixir-europe.org/events/analysis-of-ngs-data-workshops-with-galaxy-ad768f51-e8ab-4c04-83a3-388fec5ae25b 2019-09-25 09:00:00 UTC 2019-09-25 17:00:00 UTC QFAB Translational Research Institute, 37, Kent Street, Brisbane, Australia Translational Research Institute, 37, Kent Street Brisbane Brisbane City Australia Bioinformatics [] [] [] [] [] bioinformaticsGalaxy RNA-Seq
  • Variant detection using Galaxy (1 day)

    26 September 2019

    Brisbane, Australia

    Variant detection using Galaxy (1 day) https://tess.elixir-europe.org/events/analysis-of-ngs-data-workshops-with-galaxy-377372e4-b0dd-425d-8ae7-1ef5d902d26b 2019-09-26 09:00:00 UTC 2019-09-26 17:00:00 UTC QFAB Translational Research Institute, 37, Kent Street, Brisbane, Australia Translational Research Institute, 37, Kent Street Brisbane Brisbane City Australia Bioinformatics [] [] [] [] [] bioinformaticsGalaxy RNA-Seq
  • Metagenomics analysis using Galaxy (1 day)

    27 September 2019

    Brisbane, Australia

    Metagenomics analysis using Galaxy (1 day) https://tess.elixir-europe.org/events/analysis-of-ngs-data-workshops-with-galaxy-aa7d8414-431f-4b57-8416-bb05ac1389da 2019-09-27 09:00:00 UTC 2019-09-27 17:00:00 UTC QFAB Translational Research Institute, 37, Kent Street, Brisbane, Australia Translational Research Institute, 37, Kent Street Brisbane Brisbane City Australia Bioinformatics [] [] [] [] [] bioinformaticsGalaxy RNA-Seq
  • 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 [] [] [] [] []
  • 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 [] []
  • ELIXIR Norway All Hands Meeting

    22 - 24 October 2019

    Oslo, Norway

    Elixir node event
    ELIXIR Norway All Hands Meeting https://tess.elixir-europe.org/events/elixir-norway-all-hands-meeting-2019 Yearly gathering of all hands involved in ELIXIR Norway, including our SAC and stakeholder panel. Registration here by 22 September: https://forms.gle/hprhrTnthstT46E37 Schedule: 22 October 0900 - 23 October 1200: Pre-meeting on workflows and data management (WP4) 23 October 1200 - 24 October 1300: ELIXIR Norway all hands meeting (All) 24 October 1300 - 25 October 1300: Meeting with SAC and stakeholders (node leaders, WP leaders, coordinators 25 October 1300 - 25 October 1600: Board meeting (Head of Node, Node coordinator) 2019-10-22 09:00:00 UTC 2019-10-24 13:00:00 UTC ELIXIR Norway Thon Hotel Opera, 4, Dronning Eufemias gate, Oslo, Norway Thon Hotel Opera, 4, Dronning Eufemias gate Oslo Norway [] christine.stansberg@uib.no [] ELIXIR Norway staffELIXIR Norway SACELIXIR Norway stakeholder panel meetings_and_conferences [] []
  • 3rd Tool-Training for Proteomics

    28 October 2019

    Bochum, Germany

    3rd Tool-Training for Proteomics https://tess.elixir-europe.org/events/3rd-tool-training-for-proteomics Educators: Michael Kohl, Treesa Sunny, Michael Turewicz and Julian Uszkoreit (BioInfra.Prot) Date: Monday, 2019-10-28 Location: Ruhr University Bochum, 44801 Bochum Contents: In this one day course we will show some of BioInfra.Prot's tools provided by de.NBI, namely “PIA - Protein Inference Algorithms”, “BIONDA – A Free Biomarker Database” and “CalibraCurve”. Besides the tool based sessions we offer a "Proteomics in the Cloud" session where we show advantages of cloud based bioinformatics and give a tutorial how to access the de.NBI cloud. PIA allows to inspect and combine the results of proteomics search engines. The main focus lays on the integrated inference algorithms for identification and quantification purposes. BIONDA is a free, up-to-date and user-friendly biomarker and biomarker candidate database that facilitates any kind of research on protein biomarkers and the corresponding diseases. CalibraCurve is a tool intended for the generation of calibration curves in the context of MRM (targeted proteomics) experiments. Such calibration curves are necessary for the selection of suitable transitions. Learning goals: Attendees of the course will learn how to use the tools PIA, BIONDA and CalibraCurve effectively for their daily proteomics tasks. Additionally they will learn how to use the de.NBI cloud. Prerequisites: This course is for all researches in the field of proteomics. The attendees should have basic knowledge of LC-MS proteomics, but no prior bioinformatics skills are required. Basic knowledge of how to analyse LC-MS data are sufficient. Attendees are required to bring their own laptops. If this is not possible or laptops have very low computing capacities, please contact the organizers. Keywords: Proteomics; Data Analysis; Biomarkers; de.NBI Cloud Tools: PIA; BIONDA; CalibraCurve 2019-10-28 09:00:00 UTC 2019-10-28 17:00:00 UTC de.NBI Bochum, Bochum, Germany Bochum Bochum Arnsberg Germany [] [] [] workshops_and_courses [] []
  • 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 [] []
  • Assembly of long-read sequencing (2 days)

    12 - 13 November 2019

    Brisbane, Australia

    Assembly of long-read sequencing (2 days) https://tess.elixir-europe.org/events/assembly-of-long-read-sequencing-2-days-a1383ac8-7ceb-429e-9360-61be939cbcdb 2019-11-12 09:00:00 UTC 2019-11-13 17:00:00 UTC QFAB Brisbane, Australia Brisbane Australia Bioinformatics [] [] [] [] [] bioinformatics RNA-SeqGalaxy
  • 4th Differential analysis of quantitative proteomics data using R

    18 November 2019

    Bochum, Germany

    4th Differential analysis of quantitative proteomics data using R https://tess.elixir-europe.org/events/4th-differential-analysis-of-quantitative-proteomics-data-using-r Educators: Michael Turewicz (bioinformatician) and Karin Schork (biostatistician) (BioInfra.Prot) Date: Monday, 18th Nov 2019 Location: Ruhr University Bochum, 44801 Bochum Contents: This course will impart knowledge about how to conduct a differential analysis of high-throughput quantitative proteomics data using R. As we start with a basic introduction to the popular statistical programming language, no prior knowledge on R is required. The statistical background on utilized methods is explained in order to enable the participants to assess their own as well as published workflows critically. In this regard the course will touch upon • statistical inference: hypotheses, type I and II error • location tests (t-test and ANOVA) • multiple testing Learning goals: • Independent usage of basic R functions including • data import and export • basic plots • statistical tests • Deeper understanding of statistical methods applied in differential analyses Prerequisites: • Basic understanding of high-dimensional data sets from quantitative proteomics or other life sciences; • No prior knowledge on R required • Please bring your own laptop for the hands-on exercises! Keywords: R; high-throughput data; omics; proteomics; differential analysis Tools: download and more information on R here: https://cran.r-project.org/ We recommend using an editor such as RStudio, see www.rstudio.com 2019-11-18 09:00:00 UTC 2019-11-18 17:00:00 UTC de.NBI Bochum, Bochum, Germany Bochum Bochum Arnsberg Germany [] [] [] [] [] []
  • Advanced analysis of quantitative proteomics data using R

    19 November 2019

    Bochum, Germany

    Advanced analysis of quantitative proteomics data using R https://tess.elixir-europe.org/events/advanced-analysis-of-quantitative-proteomics-data-using-r Educators: Michael Turewicz (bioinformatician) and Karin Schork (biostatistician) (BioInfra.Prot) Date: Tuesday, 19th Nov 2019 Location: Ruhr University Bochum, 44801 Bochum Contents: In this course you will learn about using R for the analysis of proteomics data. We will focus on data preprocessing methods and advanced methods for data analysis. In this regard the cpurse will touch upon: • data normalization • quality control, handling of missing values • clustering, heatmaps • ROC-curves Please be aware that basic knowledge of R and methods for differential analysis of proteomics data are taught in our course “Differential analysis of quantitative proteomics data” the previous day (Monday, 18th Nov 2019, http://goo.gl/forms/mpKHnbT1Um) Learning goals: • Independent usage of R functions for • Data preprocessing • Plots and graphs • Statistical methods for data analysis • Use of additional R packages • Deeper understanding of statistical methods applied in differential analyses Prerequisites: • Basic understanding of high-dimensional data sets from quantitative proteomics or other life sciences; • Basic knowledge of R (e.g. data import, basic plots, t-test, for loop) and basic knowledge of differential analysis of proteomics data. Both can for example be gained from our course “Differential analysis of quantitative proteomics data” the previous day (Monday, 18th Nov 2019, http://goo.gl/forms/mpKHnbT1Um). • Please bring your own laptop for the hands-on exercises! Keywords: R; high-throughput data; omics; proteomics; data analysis, graphics, data preprocessing Tools: download and more information on R here: https://cran.r-project.org/ We recommend using an editor such as RStudio, see www.rstudio.com 2019-11-19 09:00:00 UTC 2019-11-19 17:00:00 UTC de.NBI Bochum, Bochum, Germany Bochum Bochum Arnsberg Germany [] [] [] workshops_and_courses [] []
  • 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
  • RNA-Seq using R (2 days - Knowledge of R required)

    3 - 4 December 2019

    Brisbane, Australia

    RNA-Seq using R (2 days - Knowledge of R required) https://tess.elixir-europe.org/events/analysis-of-ngs-data-workshops-advanced-393853d7-8b13-4f51-b774-afb159f5d818 2019-12-03 09:00:00 UTC 2019-12-04 17:00:00 UTC QFAB Translational Research Institute, 37, Kent Street, Brisbane, Australia Translational Research Institute, 37, Kent Street Brisbane Brisbane City Australia Bioinformatics [] [] [] [] [] bioinformaticsGalaxy RNA-Seq
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