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  • Biological data analysis using InterMine

    26 November 2015

    Cambridge, United Kingdom

    Elixir node event
    Biological data analysis using InterMine https://tess.elixir-europe.org/events/biological-data-analysis-using-intermine [InterMine](http://intermine.org/) is a freely available data warehouse and analysis software system that has been used to create a suite of databases for the analysis of large and complex biological data sets. InterMine-based data analysis platforms are available for many organisms including [mouse](http://www.mousemine.org/mousemine/begin.do), [rat](http://ratmine.mcw.edu/ratmine/begin.do), [budding yeast](http://yeastmine.yeastgenome.org/yeastmine/begin.do), [plants](https://apps.araport.org/thalemine/begin.do), [nematodes](http://www.wormbase.org/tools/wormmine/begin.do), [fly](http://www.flymine.org/), [zebrafish](http://www.zebrafishmine.org/) and more recently [human](http://www.humanmine.org/). The InterMine web interface offers sophisticated query and visualisation tools, as well as comprehensive web services for bioinformaticians. Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression. We have recently re-designed the InterMine interface to provide a more intuitive user-experience. This workshop will provide an overview of key features of the new interface and how this can be used to interrogate genomic and proteomic data. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to Book or register Interest by linking [here](http://marstons.bio.cam.ac.uk/course-booking/?CourseID=Biological%20data%20analysis%20using%20InterMine_bioinfo-intermine_26.11.2015_1539952&CourseName=Biological%20data%20analysis%20using%20InterMine&CourseDate=26.11.2015&CourseDuration=0.5&EventID=1539952).'' 2015-11-26 09:30:00 UTC 2015-11-26 12:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] The course is aimed at bench biologists who need to analyse their own data against large biological datasetsor who need to search against several biological datasets to gain knowledge of a gene/gene setbiological process or function. The course may also be of interest to bioinformaticians who wish to familiarise themselves with the InterMine suite of databasesalthough the webservices will not be covered in detail.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Biological data analysis using InterMine

    27 October 2017

    Cambridge, United Kingdom

    Elixir node event
    Biological data analysis using InterMine https://tess.elixir-europe.org/events/biological-data-analysis-using-intermine-a237eb77-8aca-4dd0-bf8c-0a47c9295e4d [InterMine](http://intermine.org/) is a freely available data integration and analysis system that has been used to create a suite of databases for the analysis of large and complex biological data sets. InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants, nematodes, fly, zebrafish and more recently human. The InterMine web interface offers sophisticated query and visualisation tools, as well as comprehensive web services for bioinformaticians. Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression. Part 1 (2.5 - 3 hours) will introduce participants to all aspects of the user interface, starting with some simple exercises and building up to more complex analysis encompassing several analysis tools and comparative analysis across organisms. No previous experience is necessary for this part of the workshop. Part 2 (1 hour) will focus on the InterMine API and introduce running InterMine searches through Python and Perl scripts. While complete beginners are welcome, some basic knowledge of perl, and/or python would be an advantage. The InterMine R package will also be introduced. Those not interested in this part of the workshop are welcome to leave or there will be a more advanced exercise using the web interface available as an alternative. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to Book or register Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=1572573&amp;course-title=Biological%20data%20analysis%20using%20InterMine).'' 2017-10-27 08:30:00 UTC 2017-10-27 12:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] The course is aimed at <b>bench biologists and bioinformaticians</b> who need to analyse their own data against large biological datasetsor who need to search against several biological datasets to gain knowledge of a gene/gene setbiological process or function. The exercises will mainly use the flyhuman and mouse databasesbut the course is applicable to anyone working with data for which an InterMine database is available. See www.intermine.org for a comprehensive list of InterMine databases.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Biological data analysis using InterMine (User Interface)

    19 June 2019

    Cambridge, United Kingdom

    Elixir node event
    Biological data analysis using InterMine (User Interface) https://tess.elixir-europe.org/events/biological-data-analysis-using-intermine-98ca2f5d-2b72-48e4-bd7b-463d61ab6d2b [InterMine](http://intermine.org/) is a freely available data integration and analysis system that has been used to create a suite of databases for the analysis of large and complex biological data sets. InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants, nematodes, fly, zebrafish and more recently human. See [here](http://intermine.org/) for a comprehensive list of InterMine databases. The InterMine web interface offers sophisticated query and visualisation tools, as well as comprehensive web services for bioinformaticians. Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression. This course will focus on the InterMine web interface and will introduce participants to all aspects of the user interface, starting with some simple exercises and building up to more complex analysis encompassing several analysis tools and comparative analysis across organisms. The exercises will mainly use the fly, human and mouse databases, but the course is applicable to anyone working with data for which an InterMine database is available. This event is organised alongside a half day course on Biological data analysis using the InterMine API. More information on this event are available [here](https://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-intermineAPI). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to Book or register Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2874533&amp;course-title=Biological%20data%20analysis%20using%20InterMine).'' 2019-06-19 08:30:00 UTC 2019-06-19 11:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] The course is aimed at <b>bench biologists and bioinformaticians</b> who need to analyse their own data against large biological datasetsor who need to search against several biological datasets to gain knowledge of a gene/gene setbiological process or function.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • IAFIG-RMS: Bioimage analysis with Python

    9 - 13 December 2019

    Cambridge, United Kingdom

    Elixir node event
    IAFIG-RMS: Bioimage analysis with Python https://tess.elixir-europe.org/events/iafig-rms-bioimage-analysis-with-python THIS EVENT IS NOW FULLY BOOKED! The aim of this 5 days course is to develop motivated participants toward becoming independent BioImage Analysts in an imaging facility or research role. Participants will be taught theory and algorithms relating to bioimage analysis using Python as the primary coding language. Lectures will focus on image analysis theory and applications. Topics to be covered include: Image Analysis and image processing, Python and Jupyter notebooks, Visualisation, Fiji to Python, Segmentation, Omero and Python, Image Registration, Colocalisation, Time-series analysis, Tracking, Machine Learning, and Applied Machine Learning. The bulk of the practical work will focus on Python and how to code algorithms and handle data using Python. Fiji will be used as a tool to facilitate image analysis. Omero will be described and used for some interactive coding challenges. Research spotlight talks will demonstrate research of instructors/scientists using taught techniques in the wild. This event is organized in collaboration with the [Image Analysis Focused Interest Group](http://iafig-rms.org/) and is sponsored by the [Royal Microscopical Society](https://www.rms.org.uk/). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3129158&amp;course-title=BioImage%20analysis%20with%20Python).'' 2019-12-09 09:30:00 UTC 2019-12-13 17:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Data visualisation Data mining Biological imaging Bioinformatics University of Cambridge Bioinformatics Training [] Cell BiologistsBiophysicistsBioImage Analysts with some experience of basic microscopy image analysisThis course may be of interest to physical scientists looking to develop their knowledge of Python coding in the context of bioimage analysisThis course is appropriate for researchers who are relatively proficient with computers but maybe not had the time or resources available to become programmers.The course is open to Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals<span style="color:#FF0000">Please note that all participants attending this course will be charged a registration fee. <span style="color:#0000FF"> Members of Industry to pay 575.00 GBP. </span style> <span style="color:#0000FF">All Members of the University of CambridgeAffiliated Institutions and other academic participants from External Institutions and Charitable Organizations to pay 250.00 GBP. </span style> <span style="color:#FF0000">A booking will only be approved and confirmed once the fee has been paid in full.</span style> workshops_and_courses [] HDRUK
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