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Content provider: Birmingham Metabolomics Tra...  or NBIS  or VIB Conferences 

  • Advances in Cell Engineerign, Imaging and Screening

    17 - 18 November 2016

    Leuven, Belgium

    Elixir node event
    Advances in Cell Engineerign, Imaging and Screening https://tess.elixir-europe.org/events/advances-in-cell-engineerign-imaging-and-screening Advances in Cell Engineering, Imaging and Screening A VIB Tools & Technologies Conference EARLY BIRD DEADLINE: OCTOBER 6, 2016 VIB’s Tools and Technologies meetings provide a forum for top academic speakers and scientists from both established and emerging companies to present their latest scientific achievements and exciting technological solutions. The first edition of Advances in Cell Engineering, Imaging and Screening will bring together some of the most highly regarded Academics and Companies in the field. The conference will focus on novel technologies through presentations in several sessions: New imaging and microscopy tools Super-resolution Imaging IPS and cell reprogramming 3D cell culture and organoids Cell manipulation In vivo cell-based assays Cytometry High Content Screening. In addition to a great scientific and technology program, the conference will provide ample opportunities to network during the breaks, poster sessions, the conference dinner @ 'The Faculty Club' and our ‘Meet the Expert’ session! Meet the Expert session with: ‘Prof. Christine Mummery - Leiden University Medical Center, NL’ We offer all junior researchers the opportunity to join our ‘Meet the Expert' session with Prof. Christine Mummery. During an informal round table discussion on the 17th of November, PhD students and postdocs will have the exclusive opportunity to ask any question/advise related to their research and careers. If you are interested in joining the session, then send an e-mail to conferences@vib.be. Seating is very limited so make sure to reserve a spot soon. 2016-11-17 09:00:00 UTC 2016-11-18 18:00:00 UTC VIB Conferences Kinepolis Leuven, Leuven, Belgium Kinepolis Leuven Leuven Vlaanderen Belgium 3000 Proteomics Data visualisation Biology Microbiology Genomics Physiology Systems biology Immunology [] Merck Pall Life Sciences Thermofisher Scientific VyCap Zeiss Alvéole Analisis BD Bioké Hamamatsu JSR Life Sciences Leica Lonza Molecular devices Westbuirg [] meetings_and_conferencesworkshops_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 [] [] [] [] []
  • Revolutionizing Next-Generation Sequencing (2nd edition)

    20 - 21 March 2017

    Antwerpen, Belgium

    Elixir node event
    Revolutionizing Next-Generation Sequencing (2nd edition) https://tess.elixir-europe.org/events/revolutionizing-next-generation-sequencing-2nd-edition Revolutionizing Next-Generation Sequencing (2nd edition) A VIB Tools & Technologies Conference Enabled by better cost-performance curves and novel technology developments, Next-Generation Sequencing technologies keep on pushing the boundaries of our scientific knowledge. The NGS-field is still expanding and to take advantage of new opportunities offered by these technologies in life sciences, VIB Conferences will host the second edition of Revolutionizing Next-Generation Sequencing: Tools and Technologies. After a sold-out 2015 edition, RNGS17 will look at emerging tools and approaches for: Large-scale Sequencing Applications for Current and Emerging Next-Generation Sequencing Platforms Single-Cell Genomics Epigenetics Next-gen Transcriptomics technologies Ultra-long reads and Assembly Computational genomics and data analysis In addition to a great scientific and technology program, the conference will provide ample opportunities to network during the breaks, poster sessions, the conference dinner and our ‘Meet the Expert’ session! You can find more info about the sold out first edition in our event archive. 2017-03-20 08:45:00 UTC 2017-03-21 17:45:00 UTC VIB Conferences Koningin Astridplein 20, 20, Koningin Astridplein, Antwerpen, Belgium Koningin Astridplein 20, 20, Koningin Astridplein Antwerpen Anwerpen Belgium 2018 Epigenomics VIB www.vibconferences.be conferences@vib.be Bluebee Covaris Perkin Elmer SeqLL BD Bioké Diagenode Labcyte Multiplicom Takara Westburg To see all our sponsors please visit www.vibconferences.be PhD'sAcademicsPost-DocsIndustry meetings_and_conferences first_come_first_served Structural genomicsPreclinical and clinical studiesclinical sequencingPopulation geneticsSingle Cell GenomicsDNA-seqSequencingApplied NGSEpigenomicsGenome structureGenome MappingTranscriptomicsData Analysis
  • 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 [] [] [] [] []
  • At The Forefront Of Plant Research

    15 - 16 June 2017

    Gent, Belgium

    Elixir node event
    At The Forefront Of Plant Research https://tess.elixir-europe.org/events/at-the-forefront-of-plant-research Understanding and exploiting plant life lies at the heart of human civilization. Not only do we rely on plants to feed a growing world population and to improve our standard of living, plants also play a pivotal role in providing a significant portion of our energy needs, and in fulfilling our demand for renewable industrial resources. It is expected that technological advances will further boost crop productivity and quality in a wider range of applications. In addition, new technologies will enable the development of agricultural practices that are in better harmony with the natural environment. The genomics revolution has been steering plant life sciences for more than a decade now. For that reason it is good to reflect and look ahead to which new opportunities are on the horizon. The aim of this conference is to unite leaders from a wide range of pioneering research topics, to give us a glimpse of where plant science will lead us to in the coming decade. 2017-06-15 08:00:00 UTC 2017-06-16 18:00:00 UTC VIB Conferences NV Zebrastraat, 32, Zebrastraat, Gent, Belgium NV Zebrastraat, 32, Zebrastraat Gent Oost-Vlaanderen Belgium 9000 Plant biology VIB conferences@vib.be [] Life Science Researchers 250 meetings_and_conferences [] plantbiologygenomics
  • 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 [] [] [] [] [] []
  • Next-Generation Antibodies and Protein Analysis (2nd edition)

    16 - 17 October 2017

    Gent, Belgium

    Elixir node event
    Next-Generation Antibodies and Protein Analysis (2nd edition) https://tess.elixir-europe.org/events/next-generation-antibodies-and-protein-analysis-2nd-edition Next-Generation Antibodies and Protein Analysis (2nd Edition) A VIB TOOLS & TECHNOLOGIES CONFERENCE The Next Generation Antibodies and Protein Analysis: Tools and Technologies meeting (NGAPA) in June 2015 was a great success and we are pleased to announce the 2nd edition in October, 2017. The symposium will bring together some of the most highly regarded Academics and Companies in the world with novel technologies in several sessions, with topics focused on: - Proteomics - Protein Modifications - Single Domain and Recombinant Antibody tools - Next-Generation Affinity Reagents - Interactomics - Bio-sensing and molecular interactions - Single-Cell technologies - Protein design Catalyzed by VIB’s Technology Scouting team, the Tools and Technologies meetings focus on the front end of innovation and bring together key innovators in selected life sciences research fields. The Next-Generation Antibodies and Protein Analysis conference is set to make another world class meeting, bringing together an exciting selection of top speakers and newly emerged companies. In addition to great scientific and technology program, the conference will provide ample networking opportunities. 2017-10-16 09:00:00 UTC 2017-10-17 17:00:00 UTC VIB Gent ICC, Gent, Belgium Gent ICC Gent Oost-Vlaanderen Belgium 9000 Protein interactions Proteomics Protein modifications Protein folding, stability and design [] info@vibconferences.be Absolute Antibody PerkinElmer Abcam BioConnect BioRadGenscriptMerck Macs Miltenyi Biotec ThermoFisher PhD studentsindustryAcademicsPost-Docs meetings_and_conferencesreceptions_and_networking first_come_first_served protein sequence analysisProtein identificationProteinsantibodiesinteractomicsSingle Cell technologies
  • 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 [] [] [] [] [] []
  • Applied Bioinformatics in Life Sciences (2nd edition)

    8 - 9 March 2018

    Leuven, Belgium

    Elixir node event
    Applied Bioinformatics in Life Sciences (2nd edition) https://tess.elixir-europe.org/events/applied-bioinformatics-in-life-sciences-2nd-edition Registration is now open! As an integral part of biological research, the field of bioinformatics brings forth innovative computational approaches leading to high-impact results in an increasingly data-dense environment. After a sold-out first edition in March 2016, this second edition will feature recent developments in bioinformatics research, and highlight the power of computational biology in the fields of medical, agricultural, and biotechnology research. Renowned speakers will present how bioinformatics is applied broadly in life sciences, and shed light on the future perspectives of their research. During four plenary sessions, the speakers will focus on the topics: Medical Integrative Omics Proteomics and Metabolomics Structural Bioinformatics Systems Biology ​Conference attendees will have ample networking opportunities besides an exciting scientific program. Find out more about the first edition 'ABLS' Poster information: Format: A0 (841 x 1189 mm / 33.1 x 46.8 in), portrait orientation 2018-03-08 08:45:00 UTC 2018-03-09 17:30:00 UTC VIB Conference series Iers college, 1, Janseniusstraat, Leuven, Belgium Iers college, 1, Janseniusstraat Leuven Vlaams-Brabant Belgium 3000 VIB Practical questions: VIB conferences team +32 9 244 66 11 conferences@vib.be [] PhDAcademicsIndustry 250 meetings_and_conferences first_come_first_served ProteomicsMetabolomicsbioinformaticsSystems biologyProteinsEpigenomicscellular signalingMass spectrometry datamass spectrometry
  • 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 [] [] [] [] []
  • Medical Biotechnology

    24 - 25 May 2018

    Gent, Belgium

    Elixir node event
    Medical Biotechnology https://tess.elixir-europe.org/events/medical-biotechnology “New research issues in the life sciences require new research tools,” said Nico Callewaert of the VIB-UGent Center for Medical Biotechnology and organizing committee member of this conference. “We are pushing back the limits of bio-analytical and bioengineering tools to arrive at a new technological approach to drug development, diagnostics, vaccines, therapies, etc.” With this conference on Medical Biotechnology VIB will bring together experts in the field to discuss the new developments and future challenges in this field. During four plenary sessions the following topics will be covered: • biopharmaceutical technology; • targeted delivery; • diagnostics & biomarkers; • vaccines. Registration is now open! 2018-05-24 08:45:00 UTC 2018-05-25 18:00:00 UTC VIB Conference Series Universiteit Gent - Aula, 9, Voldersstraat, Gent, Belgium Universiteit Gent - Aula, 9, Voldersstraat Gent Oost-Vlaanderen Belgium 9000 [] Practical questions: VIB conferences team +32 9 244 66 11 or conferences@vib.be [] PhDAcademicsIndustry 250 meetings_and_conferences first_come_first_served medical biomarkers diagnosticsvaccine developmentbiopharmaceutical technologymedical biotechnolgyantiviral immunityviral growth and purificationnext-generation biologicstherapeutic applicationdrug discoverypersonalized medicinebiomoleculartherapeutic antibodiesbiobettersdiagnostic toolsvaccinesdiagnostics & biomarkerstargeted therapeuticstargeted deliveryBiotherapeuticsBiopharmaceuticalsbiopharma
  • RaukR, Advanced R for Bioinformatics, Summer course

    10 - 22 June 2018

    Elixir node event
    RaukR, Advanced R for Bioinformatics, Summer course https://tess.elixir-europe.org/events/advanced-r-for-bioinformatics-summer-school #training #url: https://www.scilifelab.se/events/raukr-advanced-r-for-bioinformatics-summer-school/ #url: https://nbisweden.github.io/workshop-RaukR-1806/  International course. The course is open for researchers at university or in industry such as PhD students, postdocs, group leaders, core facility staff and analysts. Course leaders: Marcin Kierczak (marcin.kierczak@scilifelab.se), Sebastian Dilorenzo (sebastian.dilorenzo@nbis.se) Course description Join us in medieval Visby this June to improve your R skills and have a nice time! In Life Science and Bioinformatics, R is increasingly being used to transform and analyse data, perform statistical analysis and produce publication-ready visualizations. This Summer course will focus on advanced R functionality, to increase the participants skillset and understanding of what is possible to do today. You are very welcome to apply or see the homepage for more information. Please, help us spread the word to interested participants! Guest speakers Martin Morgan (Director at Bioconductor) Paula Moraga (Lancaster Univ., RLadies) Yhui Xie (RStudio) Course content Reproducibility with R Writing R packages R scripts S3, S4 and Reference Classes Code debugging and optimization R markdown tidyverse Bioconductor ggplot2 Interactive plots Statistics in R Machine Learning Shiny web applications Working with maps Area specific workshops (RNAseq, spatial stats etc) Working with your own dataset Course fee Academic: 8500 SEK (Includes participation in all official activities and events, course materials, breakfast, lunch and accommodations). Participants from outside of academia should contact us for a fee quote. The fee does not include travel costs. Important dates  Application open: March 17 Application deadline: April 15 Notification of acceptance/decline: April 25 2018-06-10 09:00:00 UTC 2018-06-22 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Advanced Python programming

    11 - 16 June 2018

    Elixir node event
    Advanced Python programming https://tess.elixir-europe.org/events/advanced-python-programming #training More information will follow Course leader: Sergiu Netotea (sergiu.netotea@scilifelab.se) 2018-06-11 09:00:00 UTC 2018-06-16 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Metabolomics: Understanding Metabolism in the 21st Century

    23 July - 17 August 2018

    Birmingham, United Kingdom

    Elixir node event
    Metabolomics: Understanding Metabolism in the 21st Century https://tess.elixir-europe.org/events/metabolomics-understanding-metabolism-in-the-21st-century Metabolomics is an emerging field that aims to measure the complement of metabolites (the metabolome) in living organisms. The metabolome represents the downstream effect of an organism’s genome and its interaction with the environment. Metabolomics has a wide application area across the medical and biological sciences. The course provides an introduction to metabolomics, describes the tools and techniques we use to study the metabolome and explains why we want to study it. By the end of the course you will understand how metabolomics can revolutionise our understanding of metabolism. 2018-07-23 09:00:00 UTC 2018-08-17 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Introduction to Bioinformatics using NGS data

    10 - 15 September 2018

    Elixir node event
    Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/introduction-to-bioinformatics-using-ngs-data-5ae594b9-4fa3-4e1e-addd-ec9cc2b6a98b #training More information will follow Course leader: Manfred Grabherr, manfred.grabherr@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. 2018-09-10 09:00:00 UTC 2018-09-15 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • 4th Plant Protease and Programmed Cell Death Symposium

    11 - 13 September 2018

    Gent, Belgium

    Elixir node event
    4th Plant Protease and Programmed Cell Death Symposium https://tess.elixir-europe.org/events/4th-plant-protease-and-programmed-cell-death-symposium After three successful conferences on Plant Proteases and Programmed Cell Death organized in Hemavan, Sweden (2011); Barcelona, Spain (2013); and Oxford, UK (2016), it is our pleasure to host the fourth meeting in the beautiful medieval town of Ghent, Belgium. The roles of proteases in cell death, immunity, and developmental processes in plants have received increasing attention over the past years. On the one hand, proteases exert a key regulatory level of posttranslational modification on their substrates. On the other hand, proteolytic cascades are involved in household functions, as well as responsible for point-of-no-return decisions during developmentally or environmentally controlled programmed cell death. Despite their importance, however, we still know little about the functions and mode-of-actions of individual plant proteases. Over the past years, several research groups have tackled the functional characterization of plant proteases from different angles. Some laboratories are advancing technology development, others focus on biological processes that depend on protease activities, while again others elucidate the biochemistry of specific protease families. The aim of our meeting is to bring researchers of these different research directions together to discuss the latest developments and concepts in the field of plant proteases and programmed cell death. 2018-09-11 15:00:00 UTC 2018-09-13 22:00:00 UTC VIB Conferences Het Pand, 1, Onderbergen, Gent, Belgium Het Pand, 1, Onderbergen Gent Oost-Vlaanderen Belgium Plant biology [] Moritz Nowack 0032 9 331 38 00 moritz.nowack@vib.be [] [] [] [] plant proteaseplant cell deathplantsprotease
  • Structural Dynamics in Cellular Communication (2nd edition)

    20 - 21 September 2018

    Brussel, Belgium

    Elixir node event
    Structural Dynamics in Cellular Communication (2nd edition) https://tess.elixir-europe.org/events/structural-dynamics-in-cellular-communication-2nd-edition After a successful first edition in February 2015, with a great audience and speakers such as Nobel Prize winner Ada Yonath, we are honored to announce a second edition. This conference will feature current developments in protein science with plenary sessions focusing on: • macromolecular machines • in situ structural biology • structural engineering & drug discovery • protein function/dynamics In addition to the scientific program, conference attendees will have ample networking opportunities during breaks, reception, conference dinner and guided walk in Brussels. 2018-09-20 09:00:00 UTC 2018-09-21 17:00:00 UTC VIB Conferences Paleis der Academiën - Palais des Académies - Academy Palace, 1, Hertogstraat, Brussel, Belgium Paleis der Academiën - Palais des Académies - Academy Palace, 1, Hertogstraat Brussel Belgium [] VIB Conferences +32 9 244 66 11 conferences@vib.be [] [] meetings_and_conferences [] macromolecular machinesstructural biologybiologydrug discoverystructural engineering protein function/dynamics
  • Elixir-EXCELERATE Train-the-Trainer course

    9 - 12 October 2018

    Elixir node event
    Elixir-EXCELERATE Train-the-Trainer course https://tess.elixir-europe.org/events/elixir-excelerate-train-the-trainer-course #training ELIXIR-EXCELERATE, in collaboration with ELIXIR Sweden and ELIXIR-IIB, is pleased to announce a Train the Trainer (TtT) event. Course information/Course webpage: https://elixir-iib-training.github.io/website/2018/10/09/train-the-trainer-stockholm.html  Application form: https://docs.google.com/forms/d/e/1FAIpQLSc0KwSjcBJ6wemxCBhgDrfg4OxccFbbDM_ZA-0Ui4jEe_eV1Q/viewform  Important dates Course date: 9-11 October, 2018 We will accept a maximum of 20 participants. Priority will be given to candidates from ELIXIR Sweden and other ELIXIR nodes. Notifications of acceptance will be sent shortly after the application, which will remain open until we reach 20 participants. Venue Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden Room: Air Fee There is no course attendance fee. The participants will need to bear their travel, hotel (if any) and meal costs. Candidates from ELIXIR nodes might apply for an ELIXIR-EXCELERATE TtT Exchange Programme Travel Grant when they fill their application form. Instructors Allegra Via (Training Coordinator ELIXIR-IIB, IBPM-CNR) Jessica Lindvall (Training Coordinator ELIXIR-SE, NBIS) Local organisers Jessica Lindvall, NBIS (National Bioinformatics Infrastructure Sweden), Elixir-SE Description The course is made up of four sessions, covering: Learning principles and how they apply to training and teaching Teaching techniques that can be used to enhance learner engagement and participation Assessment and feedback in training and teaching Lesson, course, and materials design Application form Target Audience Whoever is interested in becoming a teacher or a better one. If you have questions like the following ones, this course may be very helpful to you. How learning works? How can I use learning principles and theories to improve my teaching? How can I make my teaching more engaging and effective? How should I adjust my teaching to different types of learners? How can I help slow learners? How can I assess whether my students are actually understanding my lessons? Are they actually learning? What is the best balance between theory and practice? How can I best assess whether learning is occurring and/or has occurred? What works in a classroom and what doesn’t? How can I become a better teacher? Etc. Learning Objectives: To get acquainted with Learning principles and how they apply to training To be able to select and utilise training techniques that can be used to enhance learner engagement and participation To learn how to use assessment and feedback in training To learn about session, course, and materials design Learning Outcomes: Learners can name learning principles that a good teacher/instructor should have in mind Learners can describe at least three training techniques, drawing on learning principles Learners can design a training session and a course Learners can develop assessment questionnaires Learners can enumerate types of materials needed for each part of a training session or course Preliminary Programme TimeActivity DAY 1 10.00 - 10.30Introductions, who is who and what we need to achieve 10.30 - 12.30Session 1: Review of learning principles and how they apply to training and teaching 12.30 - 13.30Lunch time 13.30 - 14.30Cont. Session 1 14.30 - 17.00Session 2: Training techniques that can be used to enhance learner engagement and participation DAY 2 09.00 - 11.30Cont. Session 2 11.30 - 12.30Lunch time 12.30 - 15.30Session 3: Session, course, and materials design 15.30 - 17.00Session 4: Assessment and feedback in training DAY 3 09.00 - 11.30Cont. Session 4 11.30 - 12.00Wrap-up 2018-10-09 09:00:00 UTC 2018-10-12 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • ChIP-seq data analysis

    7 - 10 November 2018

    Elixir node event
    ChIP-seq data analysis https://tess.elixir-europe.org/events/chip-seq-data-analysis-adf544b3-77df-4f8d-9bf8-b0446bbff0fa Course name: ChIP-seq data analysis Course dates: 2018-11-07 and 2018-11-09 Course location: SciLifeLab, Tomtebodavägen 23A, 171 65 Solna, Room Fire ------------------------------------------------ National course open for PhD students, postdocs, researchers and other employees in need of ChIP-seq data analyses skills within all Swedish universities Important dates Application opens: now https://docs.google.com/forms/d/e/1FAIpQLSfJR1YbBeKqDUFbDDxAEVZh-h-je_4Ve4I9iVRRs7dsANCPGg/viewform Application closes: 2018-09-28 Confirmation to accepted students: 2018-10-06 Responsible teachers: Agata Smialowska, Olga Dethlefsen If you do not receive information according to the above dates please contact agata.smialowska@nbis.se, olga.dethlefsen@nbis.se Course fee A course fee* of 1700 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks. *Please note that NBIS cannot invoice individuals Course content This course will introduce the best practice bioinformatics methods for processing and analyses of ChIP-seq data via a series of lectures, group work and computer practicals. Topics covered will include: ●Quality controls of raw sequencing reads ●Reads trimming and filtering ●Alignment to the reference genome ●Peak-independent quality metrics ●Peak calling ●Peak-dependent quality metrics and visualization ●Differential binding analysis ●Functional analysis, incl. finding nearest genes, exons and custom features, obtaining enriched Gene Ontology terms and pathways Entry requirements Required for being able to follow the course and complete the computer exercises ●Basic knowledge in Linux ●Ability to bring your own laptop with R installed for the practical exercises ●Programming/scripting experience, preferably in R Desirable ●Experience working on the SNIC center Uppmax or another HPC. We encourage participants to run Uppmax tutorial before the course ●Previous experience with NGS data analyses ●Completing NBIS courses “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists” 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. 2018-11-07 09:00:00 UTC 2018-11-10 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • R Programming Foundations for Life Scientists

    12 - 17 November 2018

    Elixir node event
    R Programming Foundations for Life Scientists https://tess.elixir-europe.org/events/r-programming-foundations-for-life-scientists #training More information will follow Course leader: Marcin Kierczak (marcin.kierczak@scilifelab.se) and Sebastian DiLorenzo (sebastian.dilorenzo@nbis.se) Course description 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. Course literature We recommend the following books for the course: N. Matloff, “The Art of R Programming”   Book   Free PDF R.I. Kabacoff, “R in Action”   Book/Ebook and preview   38% discount code: ria38 Entry requirements Good general computer literacy is expected, but no previous experience in programming or R is required. You are expected to know basic concepts in mathematics and statistics, but the emphasis on the course is to learn how to use R. Participants are expected to use their own computers with pre-installed R and R Studio (detailed instructions will be given upon acceptance). 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. 2018-11-12 09:00:00 UTC 2018-11-17 00:00:00 UTC Software engineering [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Introduction to Bioinformatics using NGS data

    12 - 17 November 2018

    Elixir node event
    Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/introduction-to-bioinformatics-using-ngs-data-d4329625-5393-441f-a409-91037a6d81de Course leader: Manfred Grabherr, manfred.grabherr@scilifelab.se and Jeanette Tångrot (jeanette.tangrot@nbis.se) and Nina Norgren (nina.norgren@scilifelab.se) Location: room NA340, Naturvetarhuset, Umeå universitet 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. Apply here: https://fm.webforum.com/scilifelab/form.asp?sid=583883780 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. For more information and application form, please visit https://www.scilifelab.se/events/introduction-to-bioinformatics-using-ngs-data-umea/ 2018-11-12 09:00:00 UTC 2018-11-17 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Biostatistics

    13 - 15 November 2018

    Elixir node event
    Biostatistics https://tess.elixir-europe.org/events/biostatistics More information will follow 2018-11-13 09:00:00 UTC 2018-11-15 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • RNA-seq

    14 - 17 November 2018

    Elixir node event
    RNA-seq https://tess.elixir-europe.org/events/rna-seq-715ffd57-3ca8-4948-a1e7-10e47853d649 Course information: https://www.scilifelab.se/events/rna-seq-data-analysis/ Course leader: Johan Reimegård (johan.reimegard@scilifelab.se) Local Course leaders: Jeanette Tångrot (jeanette.tangrot@nbis.se) and Nina Norgren (nina.norgren@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. A selection of tutorials 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: RNA seq introduction RNA seq transcript assembly and annotation RNA seq read mapping programs RNA seq QC analysis Differential expression analysis Gene set enrichment analysis 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. Experience working in R and some programming/scripting experience is desirable, but not required. Experience working on the SNIC center Uppmax is desirable, but not required. Experience working with NGS data analysis is desirable. 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. 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. 2018-11-14 09:00:00 UTC 2018-11-17 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • International Meeting on Optical Biosensors

    15 - 17 November 2018

    Ghent, Belgium

    Elixir node event
    International Meeting on Optical Biosensors https://tess.elixir-europe.org/events/international-meeting-on-optical-biosensors Biological processes show extreme complexity orchestrated both in space and time. To face this complexity, it has been necessary, as pointed out by R.Y. Tsien in his lecture "Unlocking Cell Secrets with Light Beams and Molecular Spies" (Heineken Prize for Biochemistry and Biophysics, 2002), to develop fluorescent spies in order to analyze, quantify in real time and decrypt very sophisticated cellular mechanisms. The recent explosion of fluorescent biosensors development opens a new field of investigation by allowing the analysis of extremely specific biological events at the level of cellular organelles, individual cells, tissues and even entire living organisms in physiological and pathological conditions. The development and the use of these tools require solving a number of conceptual, experimental and technological problems concerning both the biosensors themselves and the tools to follow them. Equally important, a range of new developments including optogenetic and optochemical tools allow systematic perturbation of biochemical processes while they are read out by optical biosensors. The purpose of this conference is to gather and consolidate the expertise in the field of biosensors and to promote the reflection and the exchange of information so as to accelerate the development of these new dynamic imaging approaches in all areas of biology and biomedical sciences. • Early Bird: 2 October 2018 • Late Registration: 31 October 2018 • Abstract deadline: 30 June 2018 2018-11-15 09:00:00 UTC 2018-11-17 17:00:00 UTC VIB Conferences VIB-UGent Center for Inflammation Research, 'Fiers-Schell-Van Montagu' building, Ghent, Belgium VIB-UGent Center for Inflammation Research, 'Fiers-Schell-Van Montagu' building Ghent Belgium 9052 Imaging [] Practical questions: VIB conferences team +32 9 244 66 11 conferences@vib.be [] [] meetings_and_conferencesreceptions_and_networking [] biosensorsoptical biosensorsImaging
  • Python Programming with Application to Bioinformatics

    19 - 24 November 2018

    Elixir node event
    Python Programming with Application to Bioinformatics https://tess.elixir-europe.org/events/python-programming-with-application-to-bioinformatics Course name: Python programming with applications to bioinformatics Course dates: 2018-11-19 to 2018-11-23 Course location: SciLifeLab Uppsala, Entrance C11, BMC,, Husargatan 3, 752 37 Uppsala, Sverige National course open for PhD students, postdocs, researchers and other employees in need of fundamental Python skills within all Swedish universities Important dates Application opens: August 21 Application closes: October 11 Confirmation to accepted students: October 16 Responsible teacher: Nina Norgren If you do not receive information according to the above dates please contact: Nina Norgren (nina.norgren@scilifelab.se) Link to application https://goo.gl/forms/yf4fL6xgZynCgiAU2 Course fee A course fee* of 2000 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks, and course dinner *Please note that NBIS cannot invoice individuals Course content This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs. Course content ●Core concepts about Python syntax: Data types, blocks and indentation, variable scoping, iteration, functions, methods and arguments ●Different ways to control program flow using loops and conditional tests ●Regular expressions and pattern matching ●Writing functions and best-practice ways of making them usable ●Reading from and writing to files ●Code packaging and Python libraries ●How to work with biological data using external libraries. Learning objectives ●Edit and run Python code ●Write file-processing python programs that produce output to the terminal and/or external files. ●Create stand-alone python programs to process biological data ●Know how to develop your skills in Python after the course (including debugging) Format Presentations and demonstrations. Practical exercises (either in the lab with assistants or on your own). Prior to the course, you can read a companion book “Programming Python”, or “Learning Python”. Such a book will also prove useful for your programming tasks, after the course is over. It is however not required, and material will be presented in class. Entry requirements The course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). A very basic knowledge of UNIX would be an advantage, such as navigating through folders and issuing commands at a shell prompt. We will not teach Unix in detail: Other course are available at SciLifeLab for it. Bring your own laptop with python installed for the practical exercises. Due to limited space the course can accommodate maximum of 20 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. 2018-11-19 09:00:00 UTC 2018-11-24 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • De Novo Genome Assembly

    20 - 23 November 2018

    Elixir node event
    De Novo Genome Assembly https://tess.elixir-europe.org/events/de-novo-genome-assembly Course name: De Novo Genome assembly Course dates: 2018-11-20 to 2018-11-22 Course location: Husargatan 3, Uppsala National course open for PhD students, postdocs, researchers and other employees in need of genome assembly skills within all Swedish universities. The course is run by the SciLifeLab bioinformatics platform NBIS (https://www.nbis.se). Important dates Application closes: October 15 Confirmation to accepted students: October 22 Link to application https://goo.gl/forms/Oins4D9QZVoncbGy1 Responsible teachers: Henrik Lantz If you do not receive information according to the above dates please contact: henrik.lantz@nbis.se Course fee A course fee* of 1700 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks. *Please note that NBIS cannot invoice individuals Course content The course is mostly aimed at researchers getting into their first de novo genome assembly project, but will also include information of use for the more experienced researcher. We will cover assembly of both prokaryotes and eukaryotes and spend a lot of time on learning how to run the analyses in hands-on computer exercises. Applicants will be taken through all steps of a genome assembly project, from the quality assessment of data, through assembly, to validation of assemblies. After this course, the students will be well aware of common practices in genome assembly projects and will know how to avoid common pitfalls. Topics covered will include: ●Different sequencing technologies and their use in genome assembly, including Illumina, PacBio, Oxford Nanopore, 10X Genomics, and Hi-C data ●Quality assessment of data ●Data filtering including Quality based cleaning and adapter trimming ●Assembly of genomes including overview of commonly used programs ●Assembly validation and polishing ●Contamination analyses Entry requirements This is an advanced course. Participants must be comfortable navigating a linux shell and executing 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 is beneficial. Applicants are encouraged to bring their own laptops, but there will be computers to use for participants unable to do so. Due to limited space the course can accommodate a maximum of 14 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. 2018-11-20 09:00:00 UTC 2018-11-23 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
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