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307 events found

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  • Machine Learning for Image Analysis

    29 - 31 October 2018

    Heidelberg, Germany

    Elixir node event
    Machine Learning for Image Analysis https://tess.elixir-europe.org/events/machine-learning-for-image-analysis This is a blended learning course on Machine Learning for Image Analysis, consisting of three online sessions with associated hands-on exercises prior to the workshop, a three day face-to-face workshop at EMBL Heidelberg and two optional online sessions with associated hands-on exercises after the workshop. The course is organised jointly by CORBEL, EMBL, German BioImaging and NEUBIAS. 2018-10-29 09:00:00 UTC 2018-10-31 16:15:00 UTC EMBL, Heidelberg, Germany EMBL Heidelberg Germany 69117 [] Charlotte Pearton [] [] [] [] HDRUK
  • Introduction to Genomic Variant Interpretation

    6 - 7 November 2018

    Sheffield, United Kingdom

    Introduction to Genomic Variant Interpretation https://tess.elixir-europe.org/events/introduction-to-identifying-and-characterising-variants-from-ngs-data-d9eff52c-bd15-4e71-a1b8-a008ca616d24 This course covers state-of-the-art and best-practice tools for the analysis of genomes. We describe, and give hands-on experience of, the entire analysis workflow from raw data generated by a sequencing machine to deriving variant calls (e.g. Single Nucleotide Variants) that are ready for downstream analysis, interpretation and prioritisation. We will describe the steps involved to go from sequencing library to a prioritised, clinically-relevant list of DNA variants. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control, variant-calling and annotation. 2018-11-06 09:30:00 UTC 2018-11-07 17:00:00 UTC Bartolome House, Computer Room ALG04, Sheffield, United Kingdom Bartolome House, Computer Room ALG04 Sheffield United Kingdom S3 7ND [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • CABANA Train the Trainer Workshop

    15 - 16 November 2018

    Bogota, Colombia

    Elixir node event
    CABANA Train the Trainer Workshop https://tess.elixir-europe.org/events/cabana-train-the-trainer-workshop This course will provide new trainers with knowledge, skills, guidance and tips for developing and delivering training. 2018-11-15 09:30:00 UTC 2018-11-16 17:00:00 UTC Universidad de los Andes - UniAndes, Bogota, Colombia Universidad de los Andes - UniAndes Bogota Colombia 111711 [] Alejandro Reyes [] [] [] [] HDRUK
  • Nucleic acids model building workshop

    16 November 2018

    Prague, Czechia

    Elixir node event
    Nucleic acids model building workshop https://tess.elixir-europe.org/events/nucleic-acids-model-building-workshop Workshop will concentrate on using the dinucleotide conformers (NtC) as a tool enabling more reliable solution of crystal and cryo-EM structures of nucleic acids. The current version of the dnatco.org web server as well as the development version introducing a universal (for both DNA and RNA) set of NtC classes will be demonstrated. We will show prototype of the procedure(s) to fit our library of the dinucleotide conformers to electron density, as well as method of building NA models with the user specified NtC sequence, and morphing between two NA structures. All that by using MacroMoleculeBuilder (MMB) by Samuel Flores. Sam will be present to show these new functions. Importantly, we also work with Paul Emsley on new Coot features. We currently concentrate on initial model building by fitting into experimental electron density and validation using the NtC. Paul is unavailable for the meeting but we shall be able to present and discuss all new and planned Coot features concentrating on the synergy between different tools. Your presence would be extremely important to be able to look at the initial model building and validation from user's perspective and suggest improvements of an early phase of building a truly useful tool. It will be great if you bring your own problem to test the emerging system. We will try to cover two nights (Nov 15-16 and 16-17) in a hotel including breakfast ( www.hotel-ilf.cz ). There is also no registration fee for the workshop thanks to the support provided by the ELIXIR-CZ. For more details contact Jiří Černý ( jiri.cerny@ibt.cas.cz ), ideally till November 7. 2018-11-16 10:00:00 UTC 2018-11-16 22:00:00 UTC Biocev V Sadech 1/1, 1, V Sadech, Prague, Czechia V Sadech 1/1, 1, V Sadech Prague Hlavní město Praha Czechia 16000 Nucleic acid structure analysis Nucleic acids Structural biology [] [] [] meetings_and_conferencesworkshops_and_courses registration_of_interest []
  • Untapping diversity through Metagenomics: An Introductory Workshop

    3 - 6 December 2018

    Bogota, Colombia

    Elixir node event
    Untapping diversity through Metagenomics: An Introductory Workshop https://tess.elixir-europe.org/events/untapping-diversity-through-metagenomics-an-introductory-workshop In this course participants will learn the basics of metagenomics, covering experimental design and workflows, moving through to microbiome analysis via amplicon sequencing and shotgun metagenomics. 2018-12-03 08:30:00 UTC 2018-12-06 17:30:00 UTC Universidad de los Andes - UniAndes, Bogota, Colombia Universidad de los Andes - UniAndes Bogota Colombia 111711 [] Alejandro Reyes [] [] [] [] []
  • CABANA Workshop: Untapping diversity through Metagenomics: An Introductory Workshop

    3 - 6 December 2018

    Bogota, Colombia

    Elixir node event
    CABANA Workshop: Untapping diversity through Metagenomics: An Introductory Workshop https://tess.elixir-europe.org/events/cabana-workshop-untapping-diversity-through-metagenomics-an-introductory-workshop In this course participants will learn the basics of metagenomics, covering experimental design and workflows, moving through to microbiome analysis via amplicon sequencing and shotgun metagenomics. 2018-12-03 08:30:00 UTC 2018-12-06 17:30:00 UTC Universidad de los Andes - UniAndes, Bogota, Colombia Universidad de los Andes - UniAndes Bogota Colombia 111711 [] Alejandro Reyes [] [] [] [] HDRUK
  • Introduction to R

    10 December 2018

    Sheffield, United Kingdom

    Introduction to R https://tess.elixir-europe.org/events/introduction-to-r-547c0a39-1293-4c80-a1f4-aee7d7ea3206 R is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research. In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided. 2018-12-10 09:30:00 UTC 2018-12-10 17:00:00 UTC Pam Liversidge Design Studio 1 - D06, Sheffield, United Kingdom Pam Liversidge Design Studio 1 - D06 Sheffield United Kingdom S1 3JD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Introduction to RNA-seq

    17 December 2018

    Sheffield, United Kingdom

    Introduction to RNA-seq https://tess.elixir-europe.org/events/introduction-to-rna-seq-dc2e12e3-0a12-4693-8997-63651830ecf9 High-throughput RNA-sequencing is now the standard technique for quantifying transcript abundance in a biological sample of interest. In this course we will describe the processes that take place once you submit a library for RNA sequencing, and what data you should expect to receive from the Bioinformatics Core. We will describe the steps involved to go from sequencing library to a list of genes that show statistically significant differences between your biological conditions of interest. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control and assessing differential expression. We will also showcase some web sites you can use for enrichment and pathways analysis. 2018-12-17 09:30:00 UTC 2018-12-17 17:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Introduction to RNA-seq analysis in R

    14 January 2019

    Sheffield, United Kingdom

    Introduction to RNA-seq analysis in R https://tess.elixir-europe.org/events/introduction-to-rna-seq-analysis-in-r-59e3e3ee-b3da-4704-af24-63173b7bafde In this workshop, you will be learning how to analyse RNA-seq count data, using R. This will include reading the data into R, quality control and performing differential expression analysis and gene set testing, with a focus on the edgeR analysis workflow. You will learn how to generate common plots for analysis and visualisation of gene expression data, such as boxplots and heatmaps. You will also be learning how alignment and counting of raw RNA-seq data can be performed in R. This workshop is aimed at biologists interested in learning how to perform differential expression analysis of RNA-seq data when reference genomes are available.. 2019-01-14 09:30:00 UTC 2019-01-14 17:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Ensembl Browser Workshop, DKFZ Heidelberg, 29 January 2019

    29 January 2019

    Heidelberg, Germany

    Elixir node event
    Ensembl Browser Workshop, DKFZ Heidelberg, 29 January 2019 https://tess.elixir-europe.org/events/ensembl-browser-workshop-dkfz-heidelberg-29-january-2019 Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart. 2019-01-29 09:00:00 UTC 2019-01-29 17:00:00 UTC Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC), Heidelberg, Germany Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) Heidelberg Germany 69120 [] Astrid Gall [] [] [] [] HDRUK
  • Ensembl Browser Workshop, DKFZ Heidelberg, 30 January 2019

    30 January 2019

    Heidelberg, Germany

    Elixir node event
    Ensembl Browser Workshop, DKFZ Heidelberg, 30 January 2019 https://tess.elixir-europe.org/events/ensembl-browser-workshop-dkfz-heidelberg-30-january-2019 Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart. 2019-01-30 09:00:00 UTC 2019-01-30 17:00:00 UTC Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC), Heidelberg, Germany Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) Heidelberg Germany 69120 [] Astrid Gall [] [] [] [] HDRUK
  • Ensembl browser and REST API course, Gebze Tech University

    4 - 6 February 2019

    Gebze, Turkey

    Elixir node event
    Ensembl browser and REST API course, Gebze Tech University https://tess.elixir-europe.org/events/ensembl-browser-and-rest-api-course-gebze-tech-university Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart. Then learn to flexibly access these data using the Ensembl REST APIs in Python, Perl or R. 2019-02-04 09:00:00 UTC 2019-02-06 17:00:00 UTC Gebze Technical University, Gebze, Turkey Gebze Technical University Gebze Turkey 41400 [] Emily Perry [] [] [] [] HDRUK
  • Introduction to R

    7 February 2019

    Sheffield, United Kingdom

    Introduction to R https://tess.elixir-europe.org/events/introduction-to-r-1a71189d-660b-4509-b4b3-c3298dcefd0e R is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research. In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided. 2019-02-07 09:30:00 UTC 2019-02-07 17:00:00 UTC The Diamond - Workroom 2, Sheffield, United Kingdom The Diamond - Workroom 2 Sheffield United Kingdom S1 3JD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Ensembl Browser Workshop, Bogota, 11 February 2019

    11 February 2019

    Bogota, Colombia

    Elixir node event
    Ensembl Browser Workshop, Bogota, 11 February 2019 https://tess.elixir-europe.org/events/ensembl-browser-workshop-bogota-11-february-2019 Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart. 2019-02-11 09:00:00 UTC 2019-02-11 17:00:00 UTC Universidad de los Andes - UniAndes, Bogota, Colombia Universidad de los Andes - UniAndes Bogota Colombia 111711 [] Astrid Gall [] [] [] [] HDRUK
  • Ensembl REST API Workshop, Bogota, 12 February 2018

    12 February 2019

    Bogota, Colombia

    Elixir node event
    Ensembl REST API Workshop, Bogota, 12 February 2018 https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-bogota-12-february-2018 Work with Ensembl to master the Ensembl REST APIs and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments. 2019-02-12 09:00:00 UTC 2019-02-12 15:00:00 UTC Universidad de los Andes - UniAndes, Bogota, Colombia Universidad de los Andes - UniAndes Bogota Colombia 111711 [] Astrid Gall [] [] [] [] []
  • Ensembl REST API Workshop, Bogota, 12 February 2019

    12 February 2019

    Bogota, Colombia

    Elixir node event
    Ensembl REST API Workshop, Bogota, 12 February 2019 https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-bogota-12-february-2019 Work with Ensembl to master the Ensembl REST APIs and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments. 2019-02-12 09:00:00 UTC 2019-02-12 15:00:00 UTC Universidad de los Andes - UniAndes, Bogota, Colombia Universidad de los Andes - UniAndes Bogota Colombia 111711 [] Astrid Gall [] [] [] [] HDRUK
  • RNA-seq Analysis for Beginners

    4 March 2019

    Sheffield, United Kingdom

    RNA-seq Analysis for Beginners https://tess.elixir-europe.org/events/introduction-to-rna-seq-15076391-e5f2-4c5c-8ea3-5b925a66b8a3 High-throughput RNA-sequencing is now the standard technique for quantifying transcript abundance in a biological sample of interest. In this course we will describe the processes that take place once you submit a library for RNA sequencing, and what data you should expect to receive from the Bioinformatics Core. We will describe the steps involved to go from sequencing library to a list of genes that show statistically significant differences between your biological conditions of interest. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control and assessing differential expression. We will also showcase some web sites you can use for enrichment and pathways analysis. 2019-03-04 09:30:00 UTC 2019-03-04 17:00:00 UTC Pam Liversidge Building, Design Studio 1, D06, Sheffield, United Kingdom Pam Liversidge Building, Design Studio 1, D06 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Data Manipulation and Visualisation

    29 March 2019

    Sheffield, United Kingdom

    Data Manipulation and Visualisation https://tess.elixir-europe.org/events/data-manipulation-and-visualisation R is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research. In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided. 2019-03-29 09:30:00 UTC 2019-03-29 17:00:00 UTC Bartolome House, Computer Room ALG04, Sheffield, United Kingdom Bartolome House, Computer Room ALG04 Sheffield United Kingdom S3 7ND [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Introduction to RNA-seq

    11 April 2019

    Sheffield, United Kingdom

    Introduction to RNA-seq https://tess.elixir-europe.org/events/introduction-to-rna-seq-03705bbf-08b1-4e5d-b3ff-d48069b094b4 High-throughput RNA-sequencing is now the standard technique for quantifying transcript abundance in a biological sample of interest. In this course we will describe the processes that take place once you submit a library for RNA sequencing, and what data you should expect to receive from the Bioinformatics Core. We will describe the steps involved to go from sequencing library to a list of genes that show statistically significant differences between your biological conditions of interest. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control and assessing differential expression. We will also showcase some web sites you can use for enrichment and pathways analysis. 2019-04-11 08:30:00 UTC 2019-04-11 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Introduction to identifying and characterising somatic variants

    10 May 2019

    Sheffield, United Kingdom

    Introduction to identifying and characterising somatic variants https://tess.elixir-europe.org/events/introduction-to-identifying-and-characterising-somatic-variants This course covers state-of-the-art and best-practice tools for the analysis of genomes. We describe, and give hands-on experience of, the entire analysis workflow from raw data generated by a sequencing machine to deriving variant calls (e.g. Single Nucleotide Variants) that are ready for downstream analysis, interpretation and prioritisation. We will describe the steps involved to go from sequencing library to a prioritised, clinically-relevant list of DNA variants. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control, variant-calling and annotation. 2019-05-10 08:30:00 UTC 2019-05-10 16:00:00 UTC Pam Liversidge Design Studio 1 - D06, Sheffield, United Kingdom Pam Liversidge Design Studio 1 - D06 Sheffield United Kingdom S1 3JD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Introduction to Genomic Variant Interpretation

    30 - 31 May 2019

    Sheffield, United Kingdom

    Introduction to Genomic Variant Interpretation https://tess.elixir-europe.org/events/introduction-to-identifying-and-characterising-variants-from-ngs-data-bfeba574-0bba-47f5-9de9-fdabc6d50ce4 This course covers state-of-the-art and best-practice tools for the analysis of genomes. We describe, and give hands-on experience of, the entire analysis workflow from raw data generated by a sequencing machine to deriving variant calls (e.g. Single Nucleotide Variants) that are ready for downstream analysis, interpretation and prioritisation. We will describe the steps involved to go from sequencing library to a prioritised, clinically-relevant list of DNA variants. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control, variant-calling and annotation. 2019-05-30 08:30:00 UTC 2019-05-31 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • RNA-seq Analysis for Beginners

    10 June 2019

    Sheffield, United Kingdom

    RNA-seq Analysis for Beginners https://tess.elixir-europe.org/events/rna-seq-analysis-for-beginners High-throughput RNA-sequencing is now the standard technique for quantifying transcript abundance in a biological sample of interest. In this course we will describe the processes that take place once you submit a library for RNA sequencing, and what data you should expect to receive from the Bioinformatics Core. We will describe the steps involved to go from sequencing library to a list of genes that show statistically significant differences between your biological conditions of interest. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control and assessing differential expression. We will also showcase some web sites you can use for enrichment and pathways analysis. 2019-06-10 08:30:00 UTC 2019-06-10 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Data Manipulation and Visualisation

    21 June 2019

    Sheffield, United Kingdom

    Data Manipulation and Visualisation https://tess.elixir-europe.org/events/data-manipulation-and-visualisation-624117fd-575d-40d8-bfb0-a3ce7edbdf82 R is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research. In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided. 2019-06-21 08:30:00 UTC 2019-06-21 16:00:00 UTC Heart of the Campus, Sheffield Hallam University, Sheffield, United Kingdom Heart of the Campus, Sheffield Hallam University Sheffield United Kingdom S10 2BP [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Introduction to RNA-seq analysis in R

    24 June 2019

    Sheffield, United Kingdom

    Introduction to RNA-seq analysis in R https://tess.elixir-europe.org/events/introduction-to-rna-seq-analysis-in-r-4ff2ae93-b96a-4dc0-8f92-957042a88c1d In this workshop, you will be learning how to analyse RNA-seq count data, using R. This will include reading the data into R, quality control and performing differential expression analysis and gene set testing, with a focus on the edgeR analysis workflow. You will learn how to generate common plots for analysis and visualisation of gene expression data, such as boxplots and heatmaps. You will also be learning how alignment and counting of raw RNA-seq data can be performed in R. This workshop is aimed at biologists interested in learning how to perform differential expression analysis of RNA-seq data when reference genomes are available.. 2019-06-24 08:30:00 UTC 2019-06-24 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Best practices in Research Data Management for Biological Sciences

    2 - 2 July 2018

    Sheffield, United Kingdom

    Best practices in Research Data Management for Biological Sciences https://tess.elixir-europe.org/events/best-practices-in-research-data-management-for-biological-sciences-83cdb669-83d2-4502-90c3-8b49df4e1a22 As a researcher, you will encounter research data in many forms, ranging from measurements, numbers and images to documents and publications. Whether you create, receive or collect data, you will certainly need to organise it at some stage of your project. This workshop will provide an overview of some basic principles on how we can work with data more effectively. We will discuss the best practices for research data management and organisation so that our research is auditable and reproducible by ourselves, and others, in the future. 2019-07-02 11:30:00 UTC 2018-07-02 15:30:00 UTC Bartolome House, Seminar Room EG03, Sheffield, United Kingdom Bartolome House, Seminar Room EG03 Sheffield United Kingdom S3 7ND [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Sharing Bioinformatics Training and Building a Region-wide Programme

    9 - 10 July 2019

    Sheffield, United Kingdom

    Sharing Bioinformatics Training and Building a Region-wide Programme https://tess.elixir-europe.org/events/sharing-bioinformatics-training-and-building-a-region-wide-programme High-throughput genomic data analysis is now a defining skill in the life sciences. There is already a shortage of researchers who can bridge the gap between computational approaches to data and biological insights, and this demand is only getting stronger. Bioinformatics training is under-provisioned in the North of England, with many small Bioinformatics teams at different institutes lacking the resources to deliver a full Bioinformatics training programme. 2019-07-09 09:30:00 UTC 2019-07-10 14:30:00 UTC Sheffield, United Kingdom Sheffield United Kingdom [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • 2nd de.NBI Cloud User Meeting

    3 - 5 September 2019

    Heidelberg, Germany

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

    16 September 2019

    Heidelberg, Germany

    Combining Workflows, Tools and Data Management - GCB 2019 https://tess.elixir-europe.org/events/combining-workflows-tools-and-data-management-gcb-2019 Educators: Björn Grüning (RBC), Wolfgang Müller (de.NBI-SysBio) Date: 16.09.2019 Location: Marsilius-Arkaden Turm West, Room K13 Im Neuenheimer Feld **6.130.3** 69120 Heidelberg Germany Contents: There is a huge call towards FAIR data. However, what is *FAIR*? Many of us know how that FAIR means Findable, Accessible, Interoperable, Reusable. However the questions "How do I achieve FAIR?" and "How FAIR is FAIR enough?" are still open to debate. A completely different discussion is: How do I approach making my data FAIR? Making data FAIR can be tedious, manual work. Within this workshop we will demonstrate another approach, i.e. using the workflow system Galaxy, as well as Jupyter Notebooks to extract, enrich, process, and finally upload data into the FAIRDOMHub. This is built around the example use case of building an age estimator for humans from RNA data. On the way, we will give reference to the software and services we provide and the type of advice that we can give. Keywords: FAIR data, Galaxy, Jupyter Notebooks, FAIRDOMHub Tools: Galaxy, Jupyter Notebooks, FAIRDOMHub Prerequisites: None 2019-09-16 09:00:00 UTC 2019-09-16 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] meetings_and_conferences [] []
  • SeqAn3 – a modern C++ library for efficient sequence analysis - GCB 2019

    16 September 2019

    Heidelberg, Germany

    SeqAn3 – a modern C++ library for efficient sequence analysis - GCB 2019 https://tess.elixir-europe.org/events/seqan3-a-modern-c-library-for-efficient-sequence-analysis-gcb-2019 Educators: • René Rahn (CIBI) Date: • 16.09.2019 Location: • GCB 2019, Heidelberg Contents: Technological advances in sequencing and computer science have made it possible to generate enormous volumes of data in continuously decreasing time intervals, demanding highly efficient and fast algorithms and intelligent data structures for their analysis. However, implementation and maintenance of these is difficult, and thus can become a critical bottleneck for the time cost-effectiveness of many research projects. To counter this gap, we develop SeqAn a general purpose and generic C++ software library, whose focus lies on sequence analysis. SeqAn contains a wide range of accelerated and most competitive algorithms, data structures and file formats. Recently, we started with SeqAn3 a major redesign of the API, based on bleeding-edge features from C++ ≥ 17/20. The goal of this endeavour is to simplify the programming interface to provide an easy access to complex and system dependent algorithms and data structures. In this de.NBI/ELIXIR hands-on tutorial, we will demonstrate the supremacy to other “bio”-packages and programming languages and convince you of, both the simplicity of our new API and the gains in performance. As a showcase, we will implement a read mapper using SeqAn3 and show how application development can be simplified with our software including vectorised and paralleised algorithms. This tutorial is mostly suited for computational biologist and bioinformaticians with research focus on sequence analysis (e.g., genomics, metagenomics, assembly, read alignment, variant detection, etc.) Attendees should have an intermediate knowledge in programming. Some basic C++- knowledge is strongly recommended. Learning goals: • What SeqAn 3 is and is capable of • How to write tools with SeqAn 3 • Modern C++ features like Concepts, Ranges, and many more Prerequisites: Attendees must bring their own laptop. • MacOS (g++-7 or higher) or Linux or BSD (g++-7 or higher) • Git • Cmake-3.0 or higher • [optional] VirtualBox (We will provide a fully integrated Ubuntu VM with all necessary software pre-installed) Draft schedule: 09:00 – 09:30: [talk] introduction to SeqAn3 09:30 – 09:45: [talk] present the hands on workshop 09:45 – 10:30: [hands-on] set-up and programming 10:30 – 11:00: coffee break 11:00 – 12:30: [hands-on] programming 12:30 – 13:30: lunch 13:30 – 15:00: [hands-on] programming 15:00 – 15:30: coffee break 15:30 – 16:30: [hands-on] programming and testing the application 16:30 – 17:00: [talk] the future of SeqAn3 Keywords: • Modern C++, SeqAn3 Tools: • No special tools are required or used. Contact: • rene.rahn@fu-berlin.de 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 [] []
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