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Deputy Director of Department
Deputy Director of National Reference Center
Deputy Head of Facility
Director of Center
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Software Carpentry

Scientific Programming in Python

© Research

Course

Bacterial strain nomenclatures applied to international epidemiological surveillance: A Theoretical and Hands-on Course

Team: Biodiversity and Epidemiology of Bacterial Pathogens

Member: Sylvain Brisse

Scientific Fields

Diseases

Organisms

Applications

Technique

Starting Date

29

Oct 2018

Ending Date

30

Oct 2018

Time

10:00:00

25 Rue du Dr Roux, 75015 Paris, France

Address

Building: Building 23

Location

2018-10-29 10:00:00 2018-10-30 17:00:00 Europe/Paris Bacterial strain nomenclatures applied to international epidemiological surveillance: A Theoretical and Hands-on Course This two-day course will provide participants both theory and hands-on practical exercises on bacterial strain nomenclatures using the core genome MLST concept. Focus will be put on the BIGSdb software tool and database and […] 25 Rue du Dr Roux, 75015 Paris, France Sylvain Brisse sylvain.brisse@pasteur.fr

This two-day course will provide participants both theory and hands-on practical exercises on bacterial strain nomenclatures using the core genome MLST concept. Focus will be put on the BIGSdb software tool and database and its interface with other molecular epidemiology software including BioNumerics. The cgMLST approach and in particular, cgMLST schemes for Listeria and Campylobacter public health surveillance, will be used in exercises.

The overall objective of the course is to create a distributed community of curators of cgMLST nomenclature databases that will be dedicated to implement genomic epidemiological surveillance of bacterial pathogens using a unified nomenclature of alleles and bacterial genotypes.

The priority focus of the course will be Listeria and Campylobacter, although the concepts and tools that will be presented may be applicable to other bacterial pathogens such as E. coli or Salmonella.

****

This course is organized with support from :
* Institut Pasteur
* Institut Français de Bioinformatique
* Pulse-Net International
* Association of Public Health Laboratories

Faculty:
* Sylvain Brisse, Institut Pasteur
* Joao Carriço: University of Lisbon, Portugal
* Keith Jolley, Oxford University, UK
* Martin Maiden, Oxford University, UK
* Hannes Pouseele: Applied-Maths, Belgium

Location

Location: 25 Rue du Dr Roux, 75015 Paris, France

Published on: 22 Aug 2018 • Modified on: 25 Oct 2018

(function($) { /* * render_map * * This function will render a Google Map onto the selected jQuery element * * @type function * @date 8/11/2013 * @since 4.3.0 * * @param $el (jQuery element) * @return n/a */ function render_map( $el ) { var MY_MAPTYPE_ID = 'custom_style'; var featureOpts = [{"stylers":[{"hue":"#0088ff"}]}]; var styledMapOptions = { name: 'Custom Style' }; var customMapType = new google.maps.StyledMapType(featureOpts, styledMapOptions); // var var $markers = $el.find('.marker'); // vars var args = { zoom : 16, scrollwheel : false, center : new google.maps.LatLng(0, 0), mapTypeId : google.maps.MapTypeId.ROADMAP, mapTypeId : MY_MAPTYPE_ID }; // create map var map = new google.maps.Map( $el[0], args); map.mapTypes.set(MY_MAPTYPE_ID, customMapType); // add a markers reference map.markers = []; // add markers $markers.each(function(){ add_marker( $(this), map ); }); // center map center_map( map ); } /* * add_marker * * This function will add a marker to the selected Google Map * * @type function * @date 8/11/2013 * @since 4.3.0 * * @param $marker (jQuery element) * @param map (Google Map object) * @return n/a */ function add_marker( $marker, map ) { // var var latlng = new google.maps.LatLng( $marker.attr('data-lat'), $marker.attr('data-lng') ); //var image = 'https://research.pasteur.fr/wp-content/themes/biologyx2/images/logomap.png'; var myIcon = new google.maps.MarkerImage('https://research.pasteur.fr/wp-content/themes/biologyx2/images/map-pin.png', null, null, null, new google.maps.Size(32,32)); // create marker var marker = new google.maps.Marker({ position : latlng, map : map, icon : myIcon }); // add to array map.markers.push( marker ); // if marker contains HTML, add it to an infoWindow if( $marker.html() ) { // create info window var infowindow = new google.maps.InfoWindow({ content : $marker.html() }); // show info window when marker is clicked google.maps.event.addListener(marker, 'click', function() { infowindow.open( map, marker ); }); } } /* * center_map * * This function will center the map, showing all markers attached to this map * * @type function * @date 8/11/2013 * @since 4.3.0 * * @param map (Google Map object) * @return n/a */ function center_map( map ) { // vars var bounds = new google.maps.LatLngBounds(); // loop through all markers and create bounds $.each( map.markers, function( i, marker ){ var latlng = new google.maps.LatLng( marker.position.lat(), marker.position.lng() ); bounds.extend( latlng ); }); // only 1 marker? if( map.markers.length == 1 ) { // set center of map map.setCenter( bounds.getCenter() ); map.setZoom( 15 ); } else { // fit to bounds map.fitBounds( bounds ); } } /* * document ready * * This function will render each map when the document is ready (page has loaded) * * @type function * @date 8/11/2013 * @since 5.0.0 * * @param n/a * @return n/a */ $(document).ready(function(){ $('.acf-map').each(function(){ render_map( $(this) ); }); }); })(jQuery);