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  • Data Carpentry Workshop 2016

    18 - 19 October 2016

    Norwich, United Kingdom

    Data Carpentry Workshop 2016 https://tess.elixir-europe.org/events/data-carpentry-workshop Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. 2016-10-18 08:30:00 UTC 2016-10-19 17:30:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom Bioinformatics Earlham Institute training@earlham.ac.uk [] Researchers workshops_and_courses first_come_first_served Data carpentry
  • Multiple Sequence Alignment with Jalview and Protein Structure and Function Modelling

    14 - 15 May 2018

    Liverpool, United Kingdom

    Elixir node event
    Multiple Sequence Alignment with Jalview and Protein Structure and Function Modelling https://tess.elixir-europe.org/events/multiple-sequence-alignment-with-jalview-and-protein-structure-and-function Date: Monday 14th to Tuesday 15th May 2018 Time: 9.00 to 17.00 Location: MSTC, Sherrington Building, University of Liverpool, L69 3BX Overview This two day hands-on training course is aimed at students and researchers who want to gain practical understanding of the tools and approaches for protein sequence, structure and function prediction and analysis. In day 1, participants will be introduced to Jalview - a free desktop application for the visualisation and comparative analysis of protein, DNA and RNA sequences. Jalview can integrate data from Ensembl, Uniprot, PDBe, Rfam and Pfam, and can access a range of tools for multiple sequence alignment, conservation analysis and secondary structure and disorder prediction, including the widely used JPred4. On the second day, participants will learn to use Jalview’s 3D structure visualisation capabilities in conjunction with UCSF Chimera, and take a whistle-stop tour of the methodologies and tools for prediction and analysis of Protein 3D structure and function. Participants are encouraged to bring their own protein analysis problems and time will be reserved at the end of day 2 for discussion. Register using the link on the Jalview website: http://www.jalview.org/training/training-courses/Multiple-Sequence-Alignment-with-Jalview-and-Protein-Structure-and Day 1: Multiple Sequence Alignment and Analysis with Jalview Workshop trainers: Dr Jim Procter and Dr Suzanne Duce 9 9.15 Introduction to the Workshop 9.15 10.30 Session 1.Loading sequences, structures and alignments with Jalview Coffee break 11 12.30 Session 2. Multiple alignment Creation and Alignment Reliability Lunch 1.30 3pm Session 3. Phylogenetic trees and subfamily analysis of Proteins and CDS Coffee break 3.30 5pm Session 4. Protein secondary structure and disorder prediction, and working with annotation Day 2: Protein Structure Analysis and Modelling Workshop trainers: Dr Jim Procter and Dr Dan Rigden 9 9.15 Introduction to Workshop Day 2 9.15 9.30 Introduction to Protein 3D Structure 9.30 10 Viewing and Comparing 3D structures with Jalview and UCSF Chimera 10 10.30 Mapping sequence conservation to Biological Assemblies with Jalview Coffee Break 11 12.30 Functional analysis of Protein Structures Lunch 1.30 2.30 Homology modelling and model quality evaluation 2.30 3.15 Ab initio models and searching for fold matches 3.15 3.30 Wrap up: Function Analysis and 3D models Coffee Break 4pm 5pm Analyse your own protein sequences and structures. 2018-05-14 09:00:00 UTC 2018-05-15 17:00:00 UTC Dr Jim Procter and Dr Dan Rigden MSTC, Sherrington Building, University of Liverpool, Liverpool, United Kingdom MSTC, Sherrington Building, University of Liverpool Liverpool Merseyside United Kingdom L69 3BX University of Liverpool Dr Jim Procter and Dr Suzanne Duce, School of Life Sciences, University of Dundee, Dundee University of Dundee PhD studentspostdoctoral researchersprinciple investigatorsLife Science Researchersbioinformaticians 45 workshops_and_courses registration_of_interest Jalviewmultiple sequence alignmentMSAprotein sequence protein structure protein predictionHomology modellingAb initio modelsChimerasubfamily analysisPhylogenetic treesProtein secondary structureUniversity of DundeeUniversity of Liverpool
  • Single-Cell RNAseq

    3 - 7 December 2018

    Norwich, United Kingdom

    Single-Cell RNAseq https://tess.elixir-europe.org/events/single-cell-rnaseq-workshop The course provides an introduction to Single Cell Genomics. It covers several aspects such as the experimental design, cell sorting and processing for production of quality samples for sequencing, generation of sequencing data, assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variants at the single cell level. 2018-12-03 09:00:00 UTC 2018-12-07 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ Cell biology RNA-Seq [] training@earlham.ac.uk [] PhD studentspost-docsWet-lab Researchers workshops_and_courses [] []
  • CyVerse UK RNASeq Workshop

    10 - 12 December 2018

    Norwich, United Kingdom

    CyVerse UK RNASeq Workshop https://tess.elixir-europe.org/events/cyverse-uk-rnaseq-workshop This meeting is focused on researchers who are either at the beginning of their studies or have moved onto a new subject area and will be analysing RNAseq expression data as part of their studies. This workshop is designed for non-bioinformatic experts and will be run at a level appropriate for wet-lab researchers without previous bioinformatics experience. We will provide hands-on sessions that will describe the use of software tools that can interrogate RNAseq data and the biological relevance of these tools. The workshop will also demonstrate different ways to visualise RNAseq data. Prior to the workshop we will provide an example dataset that will be analysed as part of the workshop. This hands-on training will be useful for the analysis of delegates’ own data. In addition we include a session on Open Data and data reuse strategies that can benefit your research. We are also offering a optional one-day Genomics Data Carpentry (Monday December 10) for researchers who have limited or no previous command-line experience. This optional section will introduce you to analysing data in R, and better prepare you for future analyses. The cost of this additional session is £20 to cover food, refreshments and administration. 2018-12-10 09:00:00 UTC 2018-12-12 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ RNA-Seq [] training@earlham.ac.uk [] PhD Studentspost-docs workshops_and_courses first_come_first_served []
  • Introduction to Python for Biologists

    12 - 16 August 2019

    Liverpool, United Kingdom

    Introduction to Python for Biologists https://tess.elixir-europe.org/events/introduction-to-python-for-biologists-965f36b3-e040-43cd-bb06-f4e5e3cc588e Registration fee: £500 Places: 15 (first come, first served) Application deadline: 14th June 2019 DESCRIPTION Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Python education in a self-directed way. The instructor of the workshop is the Founder of Python for Biologists, Dr. Martin Jones. Format The workshop will take place over 5 days. Each day will consist of 2 half-day sessions, each consisting of a ~1 hour lecture followed by 2 hours of practical exercises. It is important that attendees attend each session as they will use examples and exercises that build on the materials from previous sessions. For more information and a detailed syllabus please see the following link: https://pythonforbiologists.com/introduction-to-python-for-biologists Who should attend This workshop is aimed at all researchers and technical workers with a background in biology who want to learn programming. The syllabus has been planned with complete beginners in mind. Requirements Attendees will require a level of biological and bioinformatics background so they can appreciate the examples and exercises (i.e. they should know what a protein accession number, BLAST report, and FASTA sequence is). Attendees will require the ability to us a text editor (e.g. nano, vim, or gedit). No previous programming knowledge is required. Attendees will use their own laptops during the workshop. Instructions for any software to be installed will be sent out prior to the course. If you are not sure if this course is suitable for you please do not hesitate to contact Dr Martin Jones (martin@pythonforbiologists.com) Please fill in the following form (https://forms.gle/mkjiASxS7sKBxeGo7) if you would like to register for the Introduction to Python for Biologists workshop. Applicants will be asked to pay a registration fee of £500. After the application deadline (14th of June) or when all places are fill applicants will be asked to pay for the workshop. Once your fee is paid your place on the course will be confirmed. 2019-08-12 09:00:00 UTC 2019-08-16 17:00:00 UTC Centre for Genomic Research, University of Liverpool (https://www.liverpool.ac.uk/genomic-research/) 126 Mount Pleasant, 126, Mount Pleasant, Liverpool, United Kingdom 126 Mount Pleasant, 126, Mount Pleasant Liverpool Merseyside United Kingdom L3 5SR University of Liverpool [] [] 15 workshops_and_courses [] pythonbioinformaticsprogrammingintrobeginner
  • Software Carpentry

    21 - 22 January 2020

    Norwich, United Kingdom

    Software Carpentry https://tess.elixir-europe.org/events/software-carpentry-e28d91b4-59e7-47d7-a7f0-54b3d09e0172 Our goal is to help scientists become more productive by teaching them basic computing skills like program design, version control, testing and task automation. In this two-day bootcamp, short tutorials will alternate with hands-on practical exercises. Participants will be encouraged both to help one another, and to apply what they have learned to their own research problems during and between sessions. 2020-01-21 09:00:00 UTC 2020-01-22 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ Earlham Institute training@earlham.ac.uk [] PhD studentspost-docspostgrad workshops_and_courses first_come_first_served SoftwareCarpentrypythonUnix Shell
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