Register event
  • Protein New Developments in Protein Structure Modelling for Biological and Clinical Research

    7 - 8 December 2015

    Protein New Developments in Protein Structure Modelling for Biological and Clinical Research https://tess.elixir-europe.org/events/protein-new-developments-in-protein-structure-modelling-for-biological-and-clinical-research Hand on training workshop (7 Dec 2015) & Hot Topic Meeting (8 Dec 2015) The Biochemical Society at Charles Darwin House, London Organised by Christine Orengo (UCL) and Mike Sternberg (Imperial) Protein modelling has become increasingly important with the explosion in the number of determined genomes and the challenges of interpreting clinical studies of human variation such as being obtained from the Genomics England initiative. The hot topic meeting will review the status of a wide range of modelling tools highlighting the underpinning principles, how to get the most out of the features available and the directions for development. We will describe resources for analysis of multiple sequence alignments (JALVIEW), classification and annotation of protein families (CATH, SCOP and SUPERFAMILY), protein structure prediction (FUGUE, SWISSMODEL, PHYRE2 and the PSIPRED workbench) and an integrated resource of protein annotation (GENOME3D). Additionally, several of the speakers have developed enhanced methods to predict whether a missense mutation is expected to be disease associated and these tools will be reported (FATHMM, Duet and SUSPECT). These resources will then be placed in the wider context of the applications and developments of protein modelling. Speakers include: Geoff Barton, Franca Fraternali, Julian Gough, Tim Hubbard, David Jones, Lawrence Kelley, Tony Andreeva, Bernardo Ochoa, Ian Sillitoe, Torsten Schwede and Janet Thornton. On the first day we will run a smaller introductory hands-on tutorial and workshop (7 December 2015) for biologists and clinicians less familiar with the field which will focus on sequence alignment (Geoff Barton, Dundee), structural families (Christine Orengo, UCL) and protein structure and variant prediction  (Mike Sternberg and Lawrence Kelley, Imperial). You can register for either or both days. 2015-12-07 09:00:00 UTC 2015-12-08 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • VIZBI

    9 - 11 March 2016

    VIZBI https://tess.elixir-europe.org/events/vizbi The 3rd EMBO Conference on Visualizing Biological Data (VIZBI 2016) - also the 7th international meeting on this topic - will be held 9–11 March 2016 at EMBL Heidelberg in Germany. VIZBI brings together scientists, illustrators, and designers actively using or developing computational visualization to study a diverse range of biological data. The conference features 21 invited talks that will review the state-of-the-art and challenges in visualizing data from genomes, transcripts, proteins, cells, organisms, and populations. Prior to the meeting (Tuesday, 8 March), there will also be tutorials on several visualization tools. All VIZBI 2016 participants have the opportunity to present a poster describing their work. Just before your poster session, you will be given 60 seconds and 2 PowerPoint slides to briefly introduce yourself and your poster to all VIZBI participants. 2016-03-09 09:00:00 UTC 2016-03-11 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • BioVis @ ISMB 2016

    8 July 2016

    BioVis @ ISMB 2016 https://tess.elixir-europe.org/events/biovis-ismb-2016 BioVis@ISMB2016 is co-located with ISMB 2016 and will be taking place on July 8 in Orlando, Florida at the Disney World Resort Swan and Dolphin hotel. The main ISMB 2016 conference will run from July 8 through July 12. As BioVis@ISMB is an ISMB Special Interest Group Meeting, registration for the meeting is managed through the ISMB conference. 2016-07-08 09:00:00 UTC 2016-07-08 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • New Scientist Live

    22 - 25 September 2016

    New Scientist Live https://tess.elixir-europe.org/events/new-scientist-live We will be showing our new BioBlox (www.bioblox.org) games based on protein docking in 2D and 3D https://live.newscientist.com/exhibitors/bioblox/ (stand #959) Teams involved include, at Goldsmiths, University of London: Pedro Quijada Leyton, Elio de Berardinis, Federico Soncini, Ciarán Wilson, Andy Thomason, Richard Leinfellner, William Latham, FFL; at Imperial College London: Prof. Michael Sternberg, Ioannis Filippis, Suhail Islam. We will also be showing our new platform to manipulate virtually DNA and RNA molecular strands (www.csynth.org); https://live.newscientist.com/…/weatherall-institute-of-mo…/ (stand #1058). Teams involved include, for Goldsmiths: Stephen Todd, Peter Todd, William Latham, Frederic Fol Leymarie, Andy Thomason; for Oxford: Jim Hughes, Stephen Taylor, Veronica Buckle, Bryony Graham et al.   2016-09-22 09:00:00 UTC 2016-09-25 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • New Scientist Live

    22 - 25 September 2016

    New Scientist Live https://tess.elixir-europe.org/events/new-scientist-live-c7fa44f8-818c-4cee-9aca-3bbe52244643 We will be showing our new BioBlox (www.bioblox.org) games based on protein docking in 2D and 3D https://live.newscientist.com/exhibitors/bioblox/ (stand #959) Teams involved include, at Goldsmiths, University of London: Pedro Quijada Leyton, Elio de Berardinis, Federico Soncini, Ciarán Wilson, Andy Thomason, Richard Leinfellner, William Latham, FFL; at Imperial College London: Prof. Michael Sternberg, Ioannis Filippis, Suhail Islam. We will also be showing our new platform to manipulate virtually DNA and RNA molecular strands (www.csynth.org); https://live.newscientist.com/…/weatherall-institute-of-mo…/ (stand #1058). Teams involved include, for Goldsmiths: Stephen Todd, Peter Todd, William Latham, Frederic Fol Leymarie, Andy Thomason; for Oxford: Jim Hughes, Stephen Taylor, Veronica Buckle, Bryony Graham et al.   2016-09-22 09:00:00 UTC 2016-09-25 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • BioVis @ IEEE VIS 2016

    23 October 2016

    BioVis @ IEEE VIS 2016 https://tess.elixir-europe.org/events/biovis-ieee-vis-2016 The BioVis meetings are intended to educate, inspire, and engage visualization researchers in problems in biological data visualization, as well as bioinformatics and biology researchers in state-of-the-art visualization research. 2016-10-23 09:00:00 UTC 2016-10-23 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • Data Visualisation for Biology: a practical workshop on design, techniques and tools

    30 January - 3 February 2017

    Data Visualisation for Biology: a practical workshop on design, techniques and tools https://tess.elixir-europe.org/events/data-visualisation-for-biology-a-practical-workshop-on-design-techniques-and-tools-b96f2cca-acf8-49dc-9b98-247bea1be401 *Application deadline:  Friday November 11 2016* As biological datasets increase in size and complexity, we are moving more and more from an hypothesis-driven research paradigm to a data-driven one. As a result, exploration of that data has become even more crucial than in the past. In this 5-day workshop, we will dive into the topic of biological data visualization and how it can be used to gain insight in and get a "feel" for a dataset, so that targeted analyses can be defined. We will start by covering theoretical questions like: What is data visualization? How do we perceive images? How can we visualise data in the best possible way? As the workshop continues, it will become more and more hands-on and interactive; a large part will be committed to creating visualisations using the P5 javascript library, based on biological data. In the workshop, we will focus on omics (e.g. genomics, transcriptomics) data rather than e.g. imaging data.  Audience This course is targeted at biologists who want to explore, and gain further insight, into their own data through the use of visualisation and design approaches.  Some prior experience in programming would be beneficial, but pre-reading and exercises will be sent out to all successful applicants prior to the start of the course.     Contact:  Johanna Langrish 2017-01-30 09:00:00 UTC 2017-02-03 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • Data Visualisation for Biology: a practical workshop on design, techniques and tools

    30 January - 3 February 2017

    Data Visualisation for Biology: a practical workshop on design, techniques and tools https://tess.elixir-europe.org/events/data-visualisation-for-biology-a-practical-workshop-on-design-techniques-and-tools-adf21e26-3045-4854-a98b-eff09861d8e5 *Application deadline:  Friday November 11 2016* As biological datasets increase in size and complexity, we are moving more and more from an hypothesis-driven research paradigm to a data-driven one. As a result, exploration of that data has become even more crucial than in the past. In this 5-day workshop, we will dive into the topic of biological data visualization and how it can be used to gain insight in and get a "feel" for a dataset, so that targeted analyses can be defined. We will start by covering theoretical questions like: What is data visualization? How do we perceive images? How can we visualise data in the best possible way? As the workshop continues, it will become more and more hands-on and interactive; a large part will be committed to creating visualisations using the P5 javascript library, based on biological data. In the workshop, we will focus on omics (e.g. genomics, transcriptomics) data rather than e.g. imaging data.  Audience This course is targeted at biologists who want to explore, and gain further insight, into their own data through the use of visualisation and design approaches.  Some prior experience in programming would be beneficial, but pre-reading and exercises will be sent out to all successful applicants prior to the start of the course.     Contact:  Johanna Langrish 2017-01-30 09:00:00 UTC 2017-02-03 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • RNA-seq, 1 hp

    13 - 16 March 2017

    Elixir node event
    RNA-seq, 1 hp https://tess.elixir-europe.org/events/rna-seq-1-hp-bb9f6240-741a-4ea8-aa48-deda7e1198b4 Course content This course will cover both theoretical and hands-on exposure to current topics in RNA-seq analysis. Lectures from experts in RNA-seq and biostatistics will cover a range of cutting-edge issues in RNA quality control, transcript assembly in model and non-model organisms, differential expression analysis and downstream analysis using other types of data. An extensive case study in the computer lab will familiarize you with concepts of mapping, quality control of your RNA-seq data, de novo assembly, assembly using a reference, differential expression analysis and downstream enrichment analysis. Topics covered will include: Gene and isoform detection using short RNA-seq reads Gene and isoform detection using long RNA-seq reads Gene and isoform detection combining RNA-seq data with other data sources Quality assessment of RNA-seq data Differential expression analysis using RNA-seq data on multiple cells Downstream analysis after identifying differentially expressed genes. 2017-03-13 09:00:00 UTC 2017-03-16 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • R Programming Foundations for Life Scientists, 2 hp

    27 March - 1 April 2017

    Elixir node event
    R Programming Foundations for Life Scientists, 2 hp https://tess.elixir-europe.org/events/r-programming-foundations-for-life-scientists-2-hp-56fa30d4-110b-45eb-a88c-682e65f58c51 Course content The course is addressed to life scientists with little or moderate experience in programming but enthusiastic about learning how to use R to make their work smoother and easier. The course covers fundamental concepts of programming and software design focusing on programming in R. We will go through various aspects of R scripting with some more attention paid to the parts useful for life scientists. After introductory lectures on good programming practices, basic software design theory and a brief overview of R, we will delve into programming. We start by learning how to use R as a simple calculator, what are variable types, how to use data structures, how to implement repeating actions with and without loops, how to take actions based on certain condition. We gradually proceed to loading data, importing data from common file formats, we do some basic matrix algebra; learn how to perform basic statistical tests and how to visualize results. We will also put stress on giving you tools to access help and information on R-related challenges and issues, we will spend some time on learning how to install external packages, how to find bugs and address common installation issues. We also mention some more advanced topics and tell you more about BioConductor that is an invaluable tool for a computational biologist. You will also learn how to document your work and how to generate automatic reports. We try to illustrate all these concepts with some real-life examples and interesting lab tasks. The course will be given by experienced computational biologists from SciLifeLab and Uppsala University. Dr. Marcin Kierczak responsible for the content of the course is an experienced R user/coder, who has previously developed R packages and has experience in teaching programming and R to different audiences. 2017-03-27 09:00:00 UTC 2017-04-01 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • 3rd BiVi Annual Meeting (2017)

    20 - 21 April 2017

    3rd BiVi Annual Meeting (2017) https://tess.elixir-europe.org/events/3rd-bivi-annual-meeting-2017 Keep in touch with what is happening within Bio-visualisation.  \n Connect with community of researchers from the UK and worldwide.  \n Get hands-on experience and training with the latest tools.  \n We are delighted to invite you to join us for our 3rd Annual Meeting on 20th-21st April. We have an exciting programme in historic Edinburgh with three thought provoking keynotes from highly regarded international researchers. Another highlight is a full day of workshop traning sessions from leading UK and international bio-visualisation researchers and developers. There are items of interest to biologists, bioinformaticians and bio-visualisation researchers and developers of all levels and interests. \n A series of shorter talks will focus on the latest in UK based bio-visualisation. A poster session and lightning talks will give us the chance to hear about other new and upcoming research in the field. We will round out the first day with dinner in the evening for all the delegates. Throughout the meeting there will be opportunites for discussions and making contact with others with a interest in bio-visualisation. \n 2017-04-20 09:00:00 UTC 2017-04-21 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • 3rd BiVi Annual Meeting (2017)

    20 - 21 April 2017

    3rd BiVi Annual Meeting (2017) https://tess.elixir-europe.org/events/3rd-bivi-annual-meeting-2017-4efea527-2add-48cd-8fe5-fd211183dba7 Keep in touch with what is happening within Bio-visualisation.  \n Connect with community of researchers from the UK and worldwide.  \n Get hands-on experience and training with the latest tools.  \n We are delighted to invite you to join us for our 3rd Annual Meeting on 20th-21st April. We have an exciting programme in historic Edinburgh with three thought provoking keynotes from highly regarded international researchers. Another highlight is a full day of workshop traning sessions from leading UK and international bio-visualisation researchers and developers. There are items of interest to biologists, bioinformaticians and bio-visualisation researchers and developers of all levels and interests. \n A series of shorter talks will focus on the latest in UK based bio-visualisation. A poster session and lightning talks will give us the chance to hear about other new and upcoming research in the field. We will round out the first day with dinner in the evening for all the delegates. Throughout the meeting there will be opportunites for discussions and making contact with others with a interest in bio-visualisation. \n 2017-04-20 09:00:00 UTC 2017-04-21 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • EuroVis 2017

    12 - 16 June 2017

    EuroVis 2017 https://tess.elixir-europe.org/events/eurovis-2017 In 2017, EuroVis will be organized in Barcelona. Hosted by the ViRVIGGroup of the Universitat Politécnica de Catalunya. This year will be the 19th edition. EuroVis is the annual Visualization Conference organized by the Eurographics Working Group on Data Visualization and supported by the IEEE Visualization and Graphics Technical Committee (IEEE VGTC). It has been a Eurographics and IEEE co-supported international visualization symposium held in Europe annually since 1999. Since 2012 EuroVis is a conference. The exciting and vibrant field of Visualization is an increasingly important research area due to its wide range of applications in many disciplines. In general, our ability to collect, store, and archive data vastly exceeds our ability derive useful knowledge and insight from it. This is a ubiquitous problem. Data visualization is key in gaining an understanding large, complex data sets by exploiting the human visual system. Data visualization leverages computer graphics in order to provide a visual overview, explore, analyze, and present phenomena which is often difficult to understand.  The objective of the EuroVis conference is to create and strengthen connections between visualization researchers and practitioners, to foster collaborations, and to draw more researchers in Europe to enter this rapidly growing area of research. EuroVis has an expanded scope to include all areas of visualization, and a steadily more wide-spread visibility that allows to achieve a more wide-spread impact. 2017-06-12 09:00:00 UTC 2017-06-16 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • EuroVis 2017

    12 - 16 June 2017

    EuroVis 2017 https://tess.elixir-europe.org/events/eurovis-2017-85c55144-1525-4f19-a929-d27e4d022353 In 2017, EuroVis will be organized in Barcelona. Hosted by the ViRVIGGroup of the Universitat Politécnica de Catalunya. This year will be the 19th edition. EuroVis is the annual Visualization Conference organized by the Eurographics Working Group on Data Visualization and supported by the IEEE Visualization and Graphics Technical Committee (IEEE VGTC). It has been a Eurographics and IEEE co-supported international visualization symposium held in Europe annually since 1999. Since 2012 EuroVis is a conference. The exciting and vibrant field of Visualization is an increasingly important research area due to its wide range of applications in many disciplines. In general, our ability to collect, store, and archive data vastly exceeds our ability derive useful knowledge and insight from it. This is a ubiquitous problem. Data visualization is key in gaining an understanding large, complex data sets by exploiting the human visual system. Data visualization leverages computer graphics in order to provide a visual overview, explore, analyze, and present phenomena which is often difficult to understand.  The objective of the EuroVis conference is to create and strengthen connections between visualization researchers and practitioners, to foster collaborations, and to draw more researchers in Europe to enter this rapidly growing area of research. EuroVis has an expanded scope to include all areas of visualization, and a steadily more wide-spread visibility that allows to achieve a more wide-spread impact. 2017-06-12 09:00:00 UTC 2017-06-16 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • VIZBI 2017

    14 - 16 June 2017

    VIZBI 2017 https://tess.elixir-europe.org/events/vizbi-2017 VIZBI 2017 features keynotes from Daniel Keim, Tamara Munzner, and Drew Berry, in addition to talks from 18 world-leading researchers showcasing visualizations transforming how life scientists view data, and driving key advances in molecular biology, systems biology, biomedical science, and ecology. The conference brings together a diverse community, including bioinformaticians, data scientists, computer scientists, and experimentalists, as well as medical illustrators, graphic designers, and graphic artists. VIZBI 2017 will be part of Vivid Sydney - a spectacular festival of light, music, and ideas - strong synergies between these events give extra incentive to make the trip to Sydney. All participants will have the opportunity to present a poster and lightning talk describing their work. Registration is now open. If you cannot join us in Sydney, you have the option of virtual registration, which allows participation via streaming video and chat. 2017-06-14 09:00:00 UTC 2017-06-16 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • VIZBI 2017

    14 - 16 June 2017

    VIZBI 2017 https://tess.elixir-europe.org/events/vizbi-2017-1ada1afd-2850-43c2-8458-e584670861d3 VIZBI 2017 features keynotes from Daniel Keim, Tamara Munzner, and Drew Berry, in addition to talks from 18 world-leading researchers showcasing visualizations transforming how life scientists view data, and driving key advances in molecular biology, systems biology, biomedical science, and ecology. The conference brings together a diverse community, including bioinformaticians, data scientists, computer scientists, and experimentalists, as well as medical illustrators, graphic designers, and graphic artists. VIZBI 2017 will be part of Vivid Sydney - a spectacular festival of light, music, and ideas - strong synergies between these events give extra incentive to make the trip to Sydney. All participants will have the opportunity to present a poster and lightning talk describing their work. Registration is now open. If you cannot join us in Sydney, you have the option of virtual registration, which allows participation via streaming video and chat. 2017-06-14 09:00:00 UTC 2017-06-16 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • BioVis @ ISMB

    24 July 2017

    BioVis @ ISMB https://tess.elixir-europe.org/events/biovis-ismb The rapidly expanding field of biology creates enormous challenges for data visualization techniques that enable researchers to gain insight from their large and highly complex data sets. The BioVis Interest Group organizes the interdisciplinary event BioVis, covering all aspects of visualization in biology. This symposium brings together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in problems in biological data visualization as well as bioinformatics and biology researchers in state-of-the-art visualization research. The symposium will be a one-day single-track event at ISMB. The event will feature keynote and invited talks, paper sessions, highlight talks, and posters/demos. Primers acting as tutorial introductions to visualization topics will be provided.   2017-07-24 09:00:00 UTC 2017-07-24 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • BioVis @ ISMB

    24 July 2017

    BioVis @ ISMB https://tess.elixir-europe.org/events/biovis-ismb-70f91491-8416-49eb-9a89-7bac11b9e337 The rapidly expanding field of biology creates enormous challenges for data visualization techniques that enable researchers to gain insight from their large and highly complex data sets. The BioVis Interest Group organizes the interdisciplinary event BioVis, covering all aspects of visualization in biology. This symposium brings together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in problems in biological data visualization as well as bioinformatics and biology researchers in state-of-the-art visualization research. The symposium will be a one-day single-track event at ISMB. The event will feature keynote and invited talks, paper sessions, highlight talks, and posters/demos. Primers acting as tutorial introductions to visualization topics will be provided.   2017-07-24 09:00:00 UTC 2017-07-24 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • BioVis@IEEE Vis

    29 September 2017

    BioVis@IEEE Vis https://tess.elixir-europe.org/events/biovis-ieee-vis The rapidly expanding field of biology creates enormous challenges for data visualization techniques that enable researchers to gain insight from their large and highly complex data sets. The BioVis Interest Group organizes the interdisciplinary event BioVis, covering all aspects of visualization in biology. This workshop brings together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in problems in biological data visualization as well as bioinformatics and biology researchers in state-of-the-art visualization research. We invite submissions of original research articles, poster submissions, as well as submissions for data visualization and redesign contests. Paper and Contest submissions can only be submitted to the BioVis workshop at VIS. 2017-09-29 09:00:00 UTC 2017-09-29 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • BioVis@IEEE Vis

    29 September 2017

    BioVis@IEEE Vis https://tess.elixir-europe.org/events/biovis-ieee-vis-2cf81050-96f3-4350-83c5-93a57ae078b8 The rapidly expanding field of biology creates enormous challenges for data visualization techniques that enable researchers to gain insight from their large and highly complex data sets. The BioVis Interest Group organizes the interdisciplinary event BioVis, covering all aspects of visualization in biology. This workshop brings together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in problems in biological data visualization as well as bioinformatics and biology researchers in state-of-the-art visualization research. We invite submissions of original research articles, poster submissions, as well as submissions for data visualization and redesign contests. Paper and Contest submissions can only be submitted to the BioVis workshop at VIS. 2017-09-29 09:00:00 UTC 2017-09-29 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • Quality Assurance and Quality Control in Metabolomics

    12 - 13 October 2017

    Birmingham, United Kingdom

    Elixir node event
    Quality Assurance and Quality Control in Metabolomics https://tess.elixir-europe.org/events/quality-assurance-and-quality-control-in-metabolomics-ea29a17f-d41e-4488-808b-b137b7c82b93 This 2-day course will provide a comprehensive theoretical overview and hands-on experience of the application of quality assurance (QA) and quality control (QC) in metabolomics. It will include both theoretical and practical components to provide hands-on experience of using the mass spectrometer (a maximum of 4 people working on the instrument in a session) and the analysis of data. Experts who have developed the application of QA and QC procedures within the field will lead the course. 2017-10-12 09:00:00 UTC 2017-10-13 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • NERC-MDIBL Environmental Genomics and Metabolomics 2018

    4 - 9 March 2018

    Birmingham, United Kingdom

    Elixir node event
    NERC-MDIBL Environmental Genomics and Metabolomics 2018 https://tess.elixir-europe.org/events/nerc-mdibl-environmental-genomics-and-metabolomics-2018 This NERC funded short course will provide a hands-on approach to guide genomics and metabolomics research applied to the environmental scientists. Participation in the course is open to everyone but priority is given to NERC-funded PhD students and early-career scientists. The course will include ~1.5 days generic environmental omics training and ~3.5 days specialized genomics or metabolomics training. Case studies using multi-omics data will be provided so that you gain practical experience of analyzing and interpreting multi-omics data. Distinguished visiting academics will provide keynote lectures on each day of the course to highlight environmental omics applictions that draw on the expertise of the guest faculty. 2018-03-04 09:00:00 UTC 2018-03-09 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT Genomics Metabolomics [] [] [] [] [] []
  • Tools for Reproducible Research

    22 - 24 March 2018

    Elixir node event
    Tools for Reproducible Research https://tess.elixir-europe.org/events/tools-for-reproducible-research #url https://www.scilifelab.se/events/reproducible-research-vt18/ #training Course leaders: Leif Wigge (leif.wigge@scilifelab.se) and Rasmus Ågren (rasmus.agren@scilifelab.se) Location: Air/Fire, Stockholm SciLifeLab National course open for PhD students (prioritized), postdocs, researchers and other employees within all Swedish universities with interest in making their computational analysis more reproducible.  Responsible teachers: Leif Wigge, Rasmus Ågren Contact information: leif.wigge@scilifelab.se and rasmus.agren@scilifelab.se Apply here: https://www.scilifelab.se/events/reproducible-research-vt18/   2018-03-22 09:00:00 UTC 2018-03-24 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • RNA-seq

    14 - 17 May 2018

    Elixir node event
    RNA-seq https://tess.elixir-europe.org/events/rna-seq Course information: https://www.scilifelab.se/events/rnaseqvt18/ Course leader Johan Reimegård (johan.reimegard@scilifelab.se) #training Course content This course will cover both theoretical and hands-on exposure to current topics in RNA-seq analysis. Lectures from experts in RNA-seq and biostatistics will cover a range of cutting-edge issues in RNA quality control, transcript assembly in model and non-model organisms, differential expression analysis and downstream analysis using other types of data. An extensive case study in the computer lab will familiarize you with concepts of mapping, quality control of your RNA-seq data, de novo assembly, assembly using a reference, differential expression analysis and downstream enrichment analysis. Topics covered will include: Gene and isoform detection using short RNA-seq reads Gene and isoform detection using long RNA-seq reads Gene and isoform detection combining RNA-seq data with other data sources Quality assessment of RNA-seq data Differential expression analysis using RNA-seq data on multiple cells Downstream analysis after identifying differentially expressed genes. Entry requirements Basic knowledge in linux is a requirement! We will not teach Linux at the course and you will have considerable trouble to follow the practical sessions if you are not reasonably used to work in a linux environment. Be able to bring your own laptop for the practical computational exercises. If you don’t have a laptop to bring please contact education@scilifelab.uu.se before you register. Some programming/scripting experience is desirable, but not required. Experience working on the SNIC center Uppmax is desirable, but not required. Participants of the SciLifeLab Course “Introduction to Bioinformatics using NGS data” (or alike) are most welcome to apply, but this course is not required. Some overlap with this course is expected, but the workshops will be considerably more detailed on the covered topics. Due to space constraints for the computer exercises, there are a maximum number of allowed participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Date and time 2017-11-07 - 2017-11-09 Location Husargatan 3, Uppsala Important dates Application open: June 19 Application deadline: September 28 Confirmation to accepted students: October 9 Responsible teachers: Johan Reimegård If you don’t receive information according to the dates above, contact education@scilifelab.uu.se Course fee A course fee of 1300 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.     2018-05-14 09:00:00 UTC 2018-05-17 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Introduction to Genome Annotation

    15 - 18 May 2018

    Elixir node event
    Introduction to Genome Annotation https://tess.elixir-europe.org/events/introduction-to-genome-annotation Course Information: https://www.scilifelab.se/events/geneeann-vt18/ Course leader Henrik Lantz (henrik.lantz@nbis.se) #training Apply here: https://docs.google.com/forms/d/e/1FAIpQLSeOLov4kGj8t50KZSS7Tsc2TSuuj91ZY-E33Mw263pfBaXMsQ/viewform  Course content Genome annotation is the process in which loci of interest in a genome are identified, both in structure and function. The structural part includes identifying the number and size of exons and introns, size of UTRs, and number of isoforms. The functional annotation, in turn, focuses on inferring the biological role of different transcripts. The course is aimed at researchers that are involved in on-going or upcoming genome projects and wish to deepen their understanding of the various forms of data and computational steps required to achieve a comprehensive annotation. The focus of the course will be on non-model eukaryote organisms, and in particular the structural annotation of protein coding genes. We will use de novo gene finders, protein alignments and RNA-seq data to infer the structure of genes, and show how to combine these different lines of evidence to get the most stable and informative annotation. We will also infer the function of these genes using similarity to known proteins as well as the presence of functional domains. Topics covered will include: ·       Project planning ·       Gene finders ·       Protein alignment ·       RNA-seq assembly ·       Combined structural annotation using Maker2 ·       Functional annotation ·       Procaryote annotation ·       The NBIS annotation service Entry requirements Participants must be comfortable navigating a linux shell and execute programs from the command line. Without this knowledge, it will be impossible to participate in the computer exercises. Previous experience from working with NGS data (genome assembly, transcriptome assembly, SNP calling) is a plus. Applicants are also encouraged to bring their own laptops, but there will be computers to use for participants unable to do so. Due to space constraints for the computer exercises, there are a maximum number of allowed participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course. 2018-05-15 09:00:00 UTC 2018-05-18 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Single cell RNA sequencing data analysis

    21 - 24 May 2018

    Elixir node event
    Single cell RNA sequencing data analysis https://tess.elixir-europe.org/events/single-cell-rna-sequencing-data-analysis-2986aebb-b31b-499d-9bd0-e7cc04658a51 #url https://www.scilifelab.se/events/scRNAseq-VT18/ National course open for PhD students, postdocs, researchers and other employees in need of single cell RNA-seq data analysis skills within all Swedish universities Course name: Single cell RNA sequencing data analysis Course dates: 2018-05-21 to 2018-05-23 Course location: SciLifeLab, Tomtebodavägen 23A, 171 65 Solna Important dates Application opens: February 1 Application closes: April 23 Confirmation to accepted students: April 27 Responsible teachers: Åsa Björklund If you do not receive information according to the above dates please contact: asa.bjorklund@scilifelab.se Course fee A course fee* of 1700 SEK will be invoiced to accepted participants. This includes lunches, coffee and course dinner.. *Please note that NBIS cannot invoice individuals Course content This course will cover the basic steps in single cell RNAseq (scRNAseq) processing and data analysis. Topics covered will include: An overview of the current scRNAseq techniques Basic overview of pipelines for processing raw reads into expression values Quality control of scRNAseq data Dimensionality reduction and clustering techniques Data normalization Differential gene expression for scRNAseq data Examples on how to use these tools in a research project. Entry requirements Required for being able to follow the course and complete the computer exercises Basic knowledge in Linux is a requirement. We will not teach Linux at the course and you may have considerable trouble to follow the practical sessions if you are not reasonably used to work in a Linux environment. Be able to bring your own laptop with R installed for the practical computational exercises. Instructions on installation will be sent by email to accepted participants. Some programming/scripting experience is required (preferably in R). Desirable: Experience working on the SNIC center Uppmax is desirable, but not required. We encourage accepted participants to do an Uppmax tutorial before the course. Previous experience with RNA-seq analysis and/or participation in NGS/RNA-seq course is an advantage. Due to limited space the course can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Link to application: https://goo.gl/forms/89JPQcm0j7zKtjLN2 2018-05-21 09:00:00 UTC 2018-05-24 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Introduction to Bioinformatics using NGS data

    21 - 26 May 2018

    Elixir node event
    Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/introduction-to-bioinformatics-using-ngs-data-8ba319ee-3569-4b1f-839d-1f2cbc483a10 Course Information: https://www.scilifelab.se/events/ngsdatavt18lkp/ #training Course leader: Manfred Grabherr, manfred.grabherr@scilifelab.se and Malin Larsson, malin.larsson@scilifelab.se Course content The course will provide an entry-level introduction to a wide range of analytical techniques for massively parallel sequencing, including basic Linux commands. We will pair lectures on the theory of analysis algorithms with practical computational exercises demonstrating the use of common tools for analyzing data from each of several common sequencing study designs. Topics covered will include: Basic Linux usage NGS read-to-reference alignment (genomic and RNA-Seq) Variant calling in populations De novo assembly of RNA-sequence data Reference-guided RNA-Seq expression analysis Analysis techniques covered will focus mostly on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data. Entry requirements A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable To get the maximum benefit from the course we would like you to Have relevant previous experience in sequencing or analysis Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing Be able to bring your own laptop for the practical computational exercises It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Important dates Application open: August 1 Application deadline: October 7 Confirmation to accepted students: October 23 Responsible teachers: Manfred Grabherr If you don’t receive information according to the dates above, contact education@scilifelab.uu.se Course fee A course fee of 1800 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.   2018-05-21 09:00:00 UTC 2018-05-26 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • EuroVis 2018

    4 - 8 June 2018

    EuroVis 2018 https://tess.elixir-europe.org/events/eurovis-2018 EuroVis 2018, hosted by the Masaryk University in Brno, Czech Republic, is the 20th anniversary of annual visualization gathering organized by the Eurographics Working Group on Data Visualization and supported by the IEEE Visualization and Graphics Technical Committee (IEEE VGTC). EuroVis has been a Eurographics and IEEE co-supported international visualization symposium held in Europe annually since 1999. EuroVis has been a conference since 2012. The organizational team at the Masaryk University is looking forward to welcome the researchers from the field of data visualization, covering also many interdisciplinary applications. Data visualization is key in gaining an understanding of large, complex data sets by exploiting the human visual system. Data visualization leverages computer graphics in order to provide a visual overview, explore, analyze, and present phenomena which are often difficult to understand. The objective of EuroVis is to foster greater exchange between visualization researchers and practitioners, and to draw more researchers and industry partners in Europe to enter this rapidly growing area of research. EuroVis has an expanded scope to include all areas of visualization, and a steadily more wide-spread visibility that achieves a more wide-spread impact. 2018-06-04 09:00:00 UTC 2018-06-08 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • MolVA 2018

    4 June 2018

    MolVA 2018 https://tess.elixir-europe.org/events/molva-2018 Workshop on Molecular Graphics and Visual Analysis of Molecular Data (MolVA, co-located with EuroVis 2018), June 4, 2018, Brno, Czech Republic Molecular visualization is one of the oldest branches of scientific visualization, which has been developing for over 50 years. Due to the continuous advances in both computational biology and computer graphics techniques, molecular graphics and visualization are still very active areas of research. Not only the ever-increasing dataset sizes yield a constant challenge for visual analysis, but also new technologies like advances in web-based graphics or augmented and virtual reality open new possibilities. In this half-day workshop, which is held for the first time in conjunction with EuroVis, we would like to initiate a multidisciplinary meeting which brings visualization researchers together working with molecular data. Whereas molecular graphics is an established topic since many years, the hybrid-dimensional visual analysis of molecular structures is still a quite new research field with a lot of potential. We would like to encourage submissions especially using new technologies, such as immersive analytics-related approaches. We invite short papers as well as full papers (2-4 pages for short and up to 8 pages for full papers, both with an additional page reserved for references). All papers will undergo a single-stage, double-blind peer review process. Accepted papers will be published in the EG digital library. The workshop will be held in Brno, Czech Republic, June 4th, 2018 as part of EuroVis 2018. Suggested topics include, but are not limited to: Molecular Graphics Visual Analysis of Molecular Data (e.g., molecular structures, biological networks and pathways, or omics data) Visualization of Dynamic Molecular Data Visualization of Large Molecular Systems Web-based Molecular Graphics and Visualization Immersive Analytics approaches using, e.g., VR/AR technologies More info: http://decibel.fi.muni.cz/~xbyska/molva/ Important Dates Paper Submission Deadline:    March 5, 2018 Notification of Acceptance:    April 10, 2018 Camera-ready Deadline:    April 20, 2018 Workshop Date:        June 4, 2018 Submission Please submit your full paper via PCS (Deadline: March 5, 2018): https://new.precisionconference.com/molva18a/ Please follow the EG guidelines for writing the paper. More info and templates you will find here: http://www.eurovis2018.org/public/download/EuroVis2018FullPapers_latex2e.zip Organizers and Contact Jan Byska, University of Bergen, Norway Michael Krone, University of Stuttgart, Germany Björn Sommer, University of Konstanz If you have any question, please contact us: molva.eurovis@gmail.com   2018-06-04 09:00:00 UTC 2018-06-04 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • EuroVis 2018

    4 - 8 June 2018

    EuroVis 2018 https://tess.elixir-europe.org/events/eurovis-2018-1b387fa7-5770-4c1b-b831-dc310a22a321 EuroVis 2018, hosted by the Masaryk University in Brno, Czech Republic, is the 20th anniversary of annual visualization gathering organized by the Eurographics Working Group on Data Visualization and supported by the IEEE Visualization and Graphics Technical Committee (IEEE VGTC). EuroVis has been a Eurographics and IEEE co-supported international visualization symposium held in Europe annually since 1999. EuroVis has been a conference since 2012. The organizational team at the Masaryk University is looking forward to welcome the researchers from the field of data visualization, covering also many interdisciplinary applications. Data visualization is key in gaining an understanding of large, complex data sets by exploiting the human visual system. Data visualization leverages computer graphics in order to provide a visual overview, explore, analyze, and present phenomena which are often difficult to understand. The objective of EuroVis is to foster greater exchange between visualization researchers and practitioners, and to draw more researchers and industry partners in Europe to enter this rapidly growing area of research. EuroVis has an expanded scope to include all areas of visualization, and a steadily more wide-spread visibility that achieves a more wide-spread impact. 2018-06-04 09:00:00 UTC 2018-06-08 00:00:00 UTC [] [] [] workshops_and_courses [] []
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