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12 events found

Country: Germany  or United Kingdom 

  • Mathematics of life (Virtual)

    27 September - 1 October 2021

    Hinxton, United Kingdom

    Elixir node event
    Mathematics of life (Virtual) https://tess.elixir-europe.org/events/mathematics-of-life-virtual This course will provide participants with an introduction to network analysis as well as modelling resources, tools and approaches used in systems biology. 2021-09-27 09:00:00 UTC 2021-10-01 17:00:00 UTC Virtual, Hinxton, United Kingdom Virtual Hinxton United Kingdom CB10 1SD [] Jane Reynolds [] [] [] [] HDRUK
  • Using the Ensembl Genome Browser (ONLINE TRAINING)

    30 September 2021

    Cambridge, United Kingdom

    Elixir node event
    Using the Ensembl Genome Browser (ONLINE TRAINING) https://tess.elixir-europe.org/events/using-the-ensembl-genome-browser-online-training-f8a26f20-facb-424d-9f7b-6fd21fdf3d5c PLEASE NOTE The Bioinformatics Team are presently teaching many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. The [Ensembl Project](http://www.ensembl.org) provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information. This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3997805&course-title=Using%20the%20Ensembl%20Genome%20Browser).'' 2021-09-30 08:30:00 UTC 2021-09-30 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Gene transcripts Gene structure Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Ensembl REST API workshop (ONLINE TRAINING)

    4 October 2021

    Cambridge, United Kingdom

    Elixir node event
    Ensembl REST API workshop (ONLINE TRAINING) https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-online-training-7f1575d1-0b50-4e85-b3ab-78e4fdd97932 PLEASE NOTE The Bioinformatics Team are presently teaching many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. The [Ensembl project](http://www.ensembl.org/) provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl [REST APIs](http://rest.ensembl.org/), including understanding the major endpoints and how to write scripts to call them. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3997816&course-title=Ensembl%20REST%20API%20Workshop).'' 2021-10-04 08:30:00 UTC 2021-10-04 15:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Bioinformaticians and wet-lab biologists who can programGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • LIFS Course - ILS 2021 & LipidomicsForum 2021

    5 October 2021

    Regensburg, Germany

    LIFS Course - ILS 2021 & LipidomicsForum 2021 https://tess.elixir-europe.org/events/lifs-course-ils-2021-lipidomicsforum-2021 Educators: Jacobo Miranda Ackerman, Daniel Krause, Nils Hoffmann (de.NBI, BioInfra.Prot / LIFS) Date: October 5th, 2021, 9:00 – 12:00 (CEST) & 13:00 – 17:00 (CEST) Deadline for Workshop Registration: Until capacity is reached. Location: On-Site, Regensburg (if local COVID-19 rules allow, on-line otherwise) Contents: In the first part of the course, we will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. In the second part of the course, we will apply PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets. The third part of this course will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will inspect, check and normalize the data as well as calculate absolute quantities using internal class-specific standards with lxPostman. In part four, we will then perform a qualitative comparison of the lipidomes using the LUX Score lipidome homology. Morning 09:00 – 09:45 Welcome and Introduction 10:00 – 10:30 Targeted Lipidomics with LipidCreator and Skyline 10:30 – 12:00 LipidCreator and Skyline Exercises Afternoon 13:00 – 14:30 Shotgun Lipidomics with LipidXplorer 14:30 – 15:30 Quantification of Shotgun Lipidomics data with lxPostman 15:30 – 17:00 Lipidome comparison with LUX Score Learning goals: Participants will be able to understand and explain the shotgun MS and targeted LC-MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline. Prerequisites: Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based and desktop applications. Please note that you may need to install software on your computer to fully participate in all exercises which may require the proper rights. The workshop will be a mix of small lecture segments and hands-on exercises. The trainers will be available for questions and assistance during the workshop. Keywords: Lipidomics, Shotgun, Targeted, LC-MS Tools: PeakStrainer and LipidXplorer, LipidCreator, Skyline, lxPostman, LUX Score Registration: Please select the “LIFS Training session I & II” in the Workshops section of the conference registration. Capacity is limited to 30 participants. 2G (vaccinated or fully recovered) - with either certificate of full vaccination or certificate of recovery / positive PCR test not older than six months. Nose+mouth protection - FFP2 mask or medical mouth nose protection have to be worn inside of buildings. 2021-10-05 09:00:00 UTC 2021-10-05 17:00:00 UTC de.NBI Regensburg, Regensburg, Germany Regensburg Regensburg Oberpfalz Germany [] [] [] [] [] []
  • Experimental Design (Online)

    20 October 2021

    Cambridge, United Kingdom

    Elixir node event
    Experimental Design (Online) https://tess.elixir-europe.org/events/experimental-design-online-9bdf4bdf-ddbe-4574-bf7c-6fa46b49475d PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. Modern technologies are able to deliver an unprecedented amount of data rapidly. However, without due care and attention early in the experimental process, such data are meaningless if they cannot adequately answer the intended research question. This course is aimed at those planning high-throughput experiments and highlights the kinds of questions they should be asking themselves. The course consists of a lecture and small-group discussions led by a member of the Genomics or Bioinformatics Cores. This event is part of a series of training courses organized in collaboration with the Bioinformatics Core Facility at [CRUK Cambridge Institute](http://www.cruk.cam.ac.uk/). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4024508&course-title=Experimental%20Design).'' 2021-10-20 08:30:00 UTC 2021-10-20 15:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Next Generation Sequencing Platforms and Bioinformatics Analysis (ONLINE LIVE TRAINING)

    26 - 27 October 2021

    Cambridge, United Kingdom

    Elixir node event
    Next Generation Sequencing Platforms and Bioinformatics Analysis (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/next-generation-sequencing-platforms-and-bioinformatics-analysis-online-live-training-e3757e4e-fa87-48a9-b5bf-256dd59b045b PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. Day 1 will introduce you to next generation sequencing technologies (NGS) and how they work, providers, common bioinformatics workflows, standardised file types, quality control. This session will include an introduction to Galaxy. [Galaxy](https://galaxyproject.org/) is an open, web-based platform for data-intensive life science research that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses. Day 2 will be hands-on practicals on using Galaxy to explore sequencing quality control, before and after removal of low quality samples. This forms the core of all NGS analyses and this day will conclude with how this data pipes into gene expression studies, variant calling and genome assemblies. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4036128&course-title=NGS%20Platforms%20and%20Bioinformatics%20Analysis).'' 2021-10-26 08:00:00 UTC 2021-10-27 11:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Biologistswet-lab scientistsbioinformatics and other life scientists planning to work with next-generation sequencing data.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Metagenomics bioinformatics

    9 - 12 November 2021

    Cambridge, United Kingdom

    Elixir node event
    Metagenomics bioinformatics https://tess.elixir-europe.org/events/metagenomics-bioinformatics-57053a63-9889-4fee-bb77-70394c57f080 EMBL-EBI plans to deliver the majority of its 2021 events face-to-face with a small number of virtual events. Please note that some events that are currently listed as ‘on-site’ might need to be delivered virtually, depending on the prevailing status of the pandemic at the time. More courses will be added to this programme as our plans develop further. 2021-11-09 09:00:00 UTC 2021-11-12 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • Metagenomics bioinformatics (Virtual)

    9 - 12 November 2021

    Cambridge, United Kingdom

    Elixir node event
    Metagenomics bioinformatics (Virtual) https://tess.elixir-europe.org/events/metagenomics-bioinformatics-virtual-24fa1698-1f9b-4529-893a-8fe88b17b165 Gain knowledge of the tools, processes and analysis approaches used in the field of metagenomics. This course will cover the metagenomics data analysis workflow from the point of newly generated sequence data. Participants will explore the use of publicly available resources and tools to manage, share, analyse and interpret metagenomics data. 2021-11-09 09:00:00 UTC 2021-11-12 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • Introduction to Statistical Analysis (Online)

    9 November 2021

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Statistical Analysis (Online) https://tess.elixir-europe.org/events/introduction-to-statistical-analysis-online-296374b8-5b8c-4190-a0dc-86057641cd04 PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. This course provides a refresher on the foundations of statistical analysis. The emphasis is on interpreting the results of a statistical test, and being able to determine the correct test to apply. Practicals are conducted using a series of online apps, and we will not teach a particular statistical analysis package, such as R. For courses that teach R, please see the links under "Related courses" . This event is part of a series of training courses organized in collaboration with the Bioinformatics Core Facility at [CRUK Cambridge Institute](http://www.cruk.cam.ac.uk/). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to Book or register Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4007755&course-title=Introduction%20to%20Statistical%20Analysis).'' 2021-11-09 09:30:00 UTC 2021-11-09 17:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • 3rd de.NBI/ELIXIR-DE metaRbolomics Hackathon

    22 - 24 November 2021

    Lutherstadt Wittenberg, Germany

    3rd de.NBI/ELIXIR-DE metaRbolomics Hackathon https://tess.elixir-europe.org/events/3rd-de-nbi-elixir-de-metarbolomics-hackathon de.NBI Organisers: Marr / Schmidt / Meier / Neumann Date: 22.11. - 24.11.2021 Location: Leucorea, Lutherstadt Wittenberg Information on travel and accommodation: https://docs.google.com/document/d/1tM9mzGmTNT11p3cYRdHjm-CT3gb-yEDbZ-xoAUKixGs Workshop goals: Aim of the workshop is to improve the interoperability of packages (e.g. using common data structures and interfaces), combine efforts (use single implementation of common functions), create and demonstrate complex workflows by integrating existing tools, identify gaps in the metaRbolomics ecosystem that need to be covered. We will also have enough discussion time to ponder challenges of the future, taking metaRbolomics into the next decade. Prerequisites: Laptop, understanding in Metabolomics, R language skills Keywords: Metabolomics, mass spectrometry, R, Bioconductor, data processing, metabolite annotation, metabolite identification 2021-11-22 09:00:00 UTC 2021-11-24 17:00:00 UTC de.NBI Lutherstadt Wittenberg, Lutherstadt Wittenberg, Germany Lutherstadt Wittenberg Lutherstadt Wittenberg Germany [] [] [] workshops_and_courses [] []
  • Applied Metaproteomics Workshop Magdeburg 2021

    22 - 26 November 2021

    Magdeburg, Germany

    Applied Metaproteomics Workshop Magdeburg 2021 https://tess.elixir-europe.org/events/applied-metaproteomics-workshop-magdeburg-2021 Educators: Dirk Benndorf, Stephan Fuchs, Robert Heyer, Kay Schallert (BiGi/MetaProtServ) Date: 22.11.2021 – 26.11.2021 Location: Magdeburg, Germany (Universitätsplatz 2, Building 28.205) Contents: Microbiome research is rapidly increasing. Meta-Omics data provide insights into microbial community influencing human health and biochemical cycle. Metaproteomics focusses on proteins representing the expressed genes and functions. In contrast to metagenomics or metatranscriptomics, the extraction and the analysis of proteins from human or environmental samples is challenging. The de.NBI course on Applied Metaproteomics trains the participants to apply a complete workflow starting from design of experiments via sample preparation to measurement and bioinformatics analysis of high-resolution MS data. Maximum 10 participants are strongly encouraged to analyze their own samples to start their own metaproteomics project. The workshop takes place at chair of bioprocess engineering at Otto-von-Guericke University Magdeburg. The team of microbial communities head by Dr. Dirk Benndorf is well experienced in metaproteomics. The samples will be measured on newly purchased timsTOF Pro MS. His group devellopes the MetaProteomAnalyzer service facilitating the analysis of of metaproteomic data. The provision of service is supported by the German Network for Bioinformatics Infrastructure - de.NBI. Monday 09:00-10:00 Arrival 10:00-11:00 Introduction to metaproteomics (lecture: Dirk Benndorf) 11:00-12:00 Design of experiments and sample preparation (lecture: Robert Heyer) 12:00-13:00 Lunch 13:00-18:00 Sample preparation I (protein extraction, protein quantification: Robert Heyer) during the afternoon short presentations of participant´s about their samples (each participant max. 10 min) Tuesday 08:00-11:00 Sample preparation II (FASP digest, SDS-PAGE: Robert Heyer) 11:00-13:00 Introduction to high resolution mass spectrometry (lecture: Dirk Benndorf) 13:00-14:00 Lunch 13:00-14:00 Sample preparation II (peptide extraction: Robert Heyer) 14:00-16:00 Introduction to the MPA 2.0 (lecture: Kay Schallert) non-stop: measurement of participant’s samples I Wednesday non-stop: measurement of participant’s samples I: Dirk Benndorf, Patrick Hellwig 09:00-11:00 MPA 2.0 exercise I (working with a small reference dataset, db searching, metaprotein concept: Kay Schallert, Robert Heyer) 11:00-13:00 MPA 2.0 exercise II (loading user db, BLAST search of unknown hits, quantitative comparison of datasets, visualization and data export: Kay Schallert, Robert Heyer) 13:00-14:00 Lunch 14:00-17:00 Prophane workflow (lecture and training: Stefan Fuchs, external speaker) Thursday 09:00-13:00 MPA 2.0 exercise III (analyzing own data: Kay Schallert, Robert Heyer) 13:00-14:00 Lunch 14:00-17:00 Training at MS (calibration, setup of LC-MS methods, solvent exchange, trouble shooting, Patrick Hellwig) Friday 08:00-10:00 MPA 2.0 exercise IV (visualization of data: Robert Heyer) 10:00-12:00 Individual discussion of results and preparation of presentations (Dirk Benndorf, Robert Heyer, Kay Schallert) 12:00-13:00 Short presentations of participant‘s results and conclusion 13:00 Lunch and departure Learning goals: To apply a complete workflow starting from design of experiments via sample preparation to measurement and bioinformatics analysis of high-resolution MS data. Prerequisites: Fee: 70 € -> The so-called “3G rule” (the course is only open to those that are vaccinated, recovered, or tested - geimpft, genesen, getestet) will be applied! Keywords: Microbiome, MPA, Metaproteomics, MetaProteomeAnalyzer, Tools: MetaproteomeAnalyzer 2021-11-22 09:00:00 UTC 2021-11-26 17:00:00 UTC de.NBI Magdeburg, Magdeburg, Germany Magdeburg Magdeburg Sachsen-Anhalt Germany [] [] [] workshops_and_courses [] []
  • Managing your Research Data (Online)

    3 December 2021

    Cambridge, United Kingdom

    Elixir node event
    Managing your Research Data (Online) https://tess.elixir-europe.org/events/managing-your-research-data-online-76810eb7-4087-4495-8dab-9322044fe215 PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors to assist you with instant and personalised feedback and to help you to run/execute the scripts which we will be using during the course. We continue to monitor advice from the UK government and the University of Cambridge on resuming in-person teaching back in the training room. How much data would you lose if your laptop was stolen? Have you ever emailed your colleague a file named 'final_final_versionEDITED'? Have you ever struggled to import your spreadsheets into R? Would you be able to write a Data Management Plan as part of a grant proposal? 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. Course materials are available [here](https://datachampcam.github.io/avoid-data-disaster/) This event is part of a series of training courses organized in collaboration with the Bioinformatics Core Facility at [CRUK Cambridge Institute](http://www.cruk.cam.ac.uk/). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=4011883&course-title=Managing%20your%20Research%20Data).'' 2021-12-03 10:00:00 UTC 2021-12-03 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK

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