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  • Data Interpretation and Reporting with R

    11 May 2016

    Brisbane, Australia

    Data Interpretation and Reporting with R https://tess.elixir-europe.org/events/data-interpretation-and-reporting-with-r This hands-on workshop will introduce users of the R software environment to the techniques involved in generating reproducible, dynamic data analyses and reports. Using literate programming approaches, participants will learn to build automated reusable reports in R. Practical exercises will include integration and manipulation of datasets, generation of summary statistics about a dataset, and how to produce high-quality tables and charts. Recommended participants Biologists and bioinformaticians wishing to structure and interpret data and generate dynamic reports using R. Prior expertise with R and the command line interface is required, to a level equivalent of that provided by the QFAB workshop “Introduction to R”. What will I learn? During this course you will learn about: Building dynamic reports for reproducible research with literate programming techniques Reformatting data and summarising and integrating datasets Generating high-quality graphic presentations of data Producing reusable scripts in R After this course you should be able to: Import tabular data files into R Use R to merge data from two or more files based on common fields Extract data from a table and summarise it in both text and graphical formats Create a knitR template that combines automated data analysis with free-form text interpretation 2016-05-11 09:00:00 UTC 2016-05-11 00:00:00 UTC University of Queensland University of Queensland, Brisbane, Australia University of Queensland Brisbane Australia Data architecture, analysis and design [] [] [] workshops_and_courses [] ABRRQFAB
  • Differential Gene Expression Analysis with R (microarray and NGS)

    25 May 2016

    Brisbane, Australia

    Differential Gene Expression Analysis with R (microarray and NGS) https://tess.elixir-europe.org/events/differential-gene-expression-analysis-with-r-microarray-and-ngs This hands-on workshop will introduce users of the R software environment to the specific skills and applications used in the analysis of microarray and next-generation sequencing (NGS) data. Practical exercises will include quality control and normalisation of data for differential gene expression, and linking genomic information to external public datasets. Recommended participants Biologists and bioinformaticians wishing to use R for RNA expression analysis. Prior expertise with R and the command line interface is required, to a level equivalent of that provided by the QFAB workshop “Introduction to R”. What will I learn? During this course you will learn about: Pre-processing and quality control of microarray and RNA-Seq data The use of R packages for the identification of differentially-expressed genes from expression data Systems biology interpretation of gene lists using pathway analysis Integration of expression and genome data with Ensembl databases After this course you should be able to: Import Affymetrix CEL files to R as data objects Carry out standard QC tests on microarray and RNA-Seq datasets Use the limma-voom R package to produce lists of differentially expressed genes between pairs of samples Identify over-represented gene ontology categories in gene lists using the GOStats package 2016-05-25 09:00:00 UTC 2016-05-25 00:00:00 UTC University of Queensland, Brisbane, Australia University of Queensland Brisbane Australia Sequencing Gene expression Data architecture, analysis and design [] [] [] workshops_and_courses [] ABRQFABR
  • Introduction to Molecular Modelling & Visualisation for Life Sciences

    4 July 2016

    University of Melbourne, Australia

    Introduction to Molecular Modelling & Visualisation for Life Sciences https://tess.elixir-europe.org/events/introduction-to-molecular-modelling-visualisation-for-life-sciences This VLSCI workshop introduces beginners to molecular modelling and visualisation techniques using packages such as VMD and NAMD. After introductory talks, participants will be given practical exercises to visualise molecules as well as learn how to submit jobs to the VLSCI clusters. 2016-07-04 09:00:00 UTC 2016-07-04 00:00:00 UTC VLSCI - University of Melbourne Lab-14, VLSCI, University of Melbourne, Australia Lab-14, VLSCI University of Melbourne Australia Computational chemistry Computational biology Molecular modelling Molecular dynamics Data architecture, analysis and design [] [] [] workshops_and_courses [] ABRVLSCIComputationalBiologyMolecularInteractions
  • Cleaning & Exploring your data with Open Refine at USYD Camperdown

    27 September 2016

    Sydney, Australia

    Cleaning & Exploring your data with Open Refine at USYD Camperdown https://tess.elixir-europe.org/events/cleaning-exploring-your-data-with-open-refine-at-usyd-camperdown This three hour workshop presented by Intersect Australia introduces Open Refine which is a powerful tool for cleaning, normalisation and exploration of datasets. In this tutorial attendees will work through the various features of Refine, including importing data, faceting, clustering, and calling into remote APIs, by working on a fictional but plausible humanities research project. Who can access Intersect training services? * Researchers, research groups, and Higher-Degree Research students from any Intersect member organisation. * For people and organisations outside the Intersect membership, training can be provided on a fee-for-service basis. Please email: training@intersect.org.au 2016-09-27 09:00:00 UTC 2016-09-27 00:00:00 UTC University of Sydney Camperdown, Sydney, Australia Camperdown Sydney Australia Data architecture, analysis and design Data management [] [] [] workshops_and_courses [] ABRDatamanipulation
  • Workshop on Research Objects (RO2018)

    29 October 2018

    Amsterdam, Netherlands

    Workshop on Research Objects (RO2018) https://tess.elixir-europe.org/events/workshop-on-research-objects-ro2018 In this workshop we will explore recent advancements in Research Objects and publishing of research data. **Deadlines**: * 2018-07-01 Abstracts due * 2018-07-15 Research articles and software/data articles due A travel bursary is available for accepted speakers, sponsored by [BioExcel](http://bioexcel.eu) (H2020-675728) ## Research Objects Scholarly Communication has evolved significantly in recent years, with an increasing focus on **Open Research**, [FAIR](https://doi.org/10.1038/sdata.2016.18)data sharing and community-developed open source methods. A question remains on how to publish, archive and explore digital research outputs. A number of initiatives have begun to explore how to package and describe research outputs, data, methods, workflows, provenance and structured metadata, reusing existing Web standards and formats. Such efforts aim to address the challenges of structuring multi-part research outcomes with their context, handling distributed and living content and porting and safely exchange what we collectively can call **Research Objects** between platforms and between researchers. In the workshop **RO2018**, part of [IEEE eScience 2018](https://www.escience2018.com) in Amsterdam, we will explore recent advancements in Research Objects and publishing of research data with peer-reviewed presentations, invited talks, short demos, lightning talks and break-out sessions to further build relationships across scientific domains and RO practitioners. ## Call for Papers RO2018 welcomes submissions of academic abstracts (1-2 pages), data/software articles (3-6 pages) and short research articles (4-8 pages) on cross-cutting case studies or specific research on topics including, but not limited to: FAIR metrics; platforms, infrastructure and tools; lifecycles; access control and secure exchange; examples of exploitation and application; executable containers; metadata, packaging and formats; credit, attribution and peer review; dealing with scale and distribution; driving adoption within current scholarly communications and alignments with community efforts; and domain-specific and cross-domain Research Objects. Further details on submitting: [http://www.researchobject.org/ro2018/submitting-to-ro2018/](http://www.researchobject.org/ro2018/submitting-to-ro2018/) ## Timeline 2018-07-01 Abstracts due 2018-07-15 Research articles and software/data articles due 2018-08-31 Notification of acceptance 2018-08-31 IEEE eScience 2018 early-bird registration deadline 2018-10-29 RO2018 workshop at IEEE eScience 2018 2018-10-29 09:00:00 UTC 2018-10-29 17:00:00 UTC The University of Manchester, researchobject.org, IEEE Mövenpick Hotel Amsterdam City Centre, 11, Piet Heinkade, Amsterdam, Netherlands Mövenpick Hotel Amsterdam City Centre, 11, Piet Heinkade Amsterdam Amsterdam Netherlands Workflows Software engineering Ontology and terminology Informatics Data submission, annotation and curation Data identity and mapping Data integration and warehousing Data architecture, analysis and design Data management Computer science [] For any questions, email the Workshop Organizers at ro2018@easychair.org BioExcel [] workshops_and_courses [] digital archivesdata repositorylinked dataWorkflows
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