{"action":"created","comment":{"url":"https://api.github.com/repos/openmicroscopy/ome-help/pulls/comments/48018189","id":48018189,"diff_hunk":"@@ -0,0 +1,806 @@\n+---\n+layout: default\n+title: Using OMERO for Facility Managers\n+menu-id: l1-workflow2\n+pdfs:\n+    - facility-manager.pdf\n+description: Descriptions of common workflows for Facility Managers and links to useful sections of User Help and Developer documentation.\n+version:\n+    - yes\n+---\n+<div class=\"page-navigation\">\n+<h2>Contents</h2>\n+<p>\n+<a href=\"#introduction\">Introduction</a><br />\n+<a href=\"#using\">Using OMERO</a><br />\n+<a href=\"#permissions\">Permissions on OMERO</a><br />\n+<a href=\"#access\">Access control, authentication, user accounts</a><br />\n+<a href=\"#manage\">Managing Groups</a><br />\n+<a href=\"#import\">Importing</a><br />\n+<a href=\"#data\">Data structure</a><br />\n+<a href=\"#measure\">Measurement and analysis</a><br />\n+<a href=\"#disk\">Disk usage</a><br />\n+<a href=\"#email\">Emailing users</a><br />\n+<a href=\"#upgrade\">Upgrading</a><br />\n+<a href=\"#publish\">Using OMERO for publication</a><br />\n+<a href=\"#training\">Getting users started</a>\n+</p>\n+</div><!-- End Page Navigation -->\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div>\n+</div>\n+\n+<h2><a class=\"anchor\" id=\"introduction\"></a>Introduction</h2>\n+\n+<p>This section brings together descriptions of common workflows for Facility Managers and links to useful sections of User Help and technical documentation.</p>\n+\n+<h2><a class=\"anchor\" id=\"install\"></a>Installation and configuration</h2>\n+\n+<p>Documentation covering the installation and configuration of the OMERO server is in the <a href=\"http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/index.html\" target=\"_blank\" class=\"external-url\">System Administrator</a> documentation on the main OME website.</p>\n+\n+<h2>Specifications for hardware</h2>\n+\n+<p>This is a frequently asked question, and the simplistic (if slightly unhelpful) answer is the best you can manage.</p>\n+\n+<p>Apart from basic CPU number, speed and physical disk size, there are a number of other issues to be taken into account, including the nature of the storage being used for the data, the connection type, and the speed of the network used to access the server.</p>\n+\n+<p>Examples of system specifications and set-ups for production OMERO servers have kindly been provided by a number of institutes to serve as illustrations of working systems. These are shown in the <a href=\"http://www.openmicroscopy.org/site/support/omero5.2-staging/sysadmins/server-setup-examples.html\" target=\"_blank\" class=\"external-url\">Example production server set-ups</a> page on the OME website.</p>\n+\n+<p class=\"top_link\"><a href=\"#top\"><img src=\"images/back_to_top.png\" alt=\"Image for link to top of page\" style=\"float: right;\"/></a></p>\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+<h2><a class=\"anchor\" id=\"using\"></a>Using OMERO</h2>\n+\n+<p>Details on downloading the OMERO clients and accessing the OMERO server are in <a href=\"http://help.openmicroscopy.org/getting-started-5.html\" target=\"_blank\" class=\"external-url\">Getting Started with OMERO.insight</a> in User Help.</p>\n+\n+<p>Details on accessing OMERO with the OMERO.web client are in the <a href=\"http://help.openmicroscopy.org/web-client.html\" target=\"_blank\" class=\"external-url\">Using the OMERO.web Client</a> section of User Help.</p>\n+\n+<p>Details of the command line interface <a href=\"http://www.openmicroscopy.org/site/support/omero5.2/users/cli/index.html\" target=\"_blank\" class=\"external-url\">OMERO.cli</a> are in the OME documentation.</p>\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+<h2><a class=\"anchor\" id=\"permissions\"></a>Permissions on OMERO</h2>\n+\n+<p>There are three levels of user permission in OMERO, Administrator, Group Owner and Member. Each level of permission allows different actions to be performed on a user's own, or other user's data, and certain administrative tasks.</p>\n+\n+<p>In brief, and practically speaking, Administrators can do anything they like to any user's data, in any group (except annotate in Private groups) and Group Owners can do anything to any user's data in the groups they own.</p>\n+\n+<p>Full details of the permissions for each level of user are shown in the <a href=\"http://help.openmicroscopy.org/sharing-data.html#roles\" target=\"_blank\" class=\"external-url\">User Roles</a> table in the Sharing data section of User Help.</p>\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+<h2><a class=\"anchor\" id=\"access\"></a>Access control, authentication, user accounts</h2>\n+\n+<p>The recommended way to control access to the OMERO server is to configure integration with your institute's authentication system (most commonly LDAP).</p>\n+\n+<p>See the documentation for <a href=\"http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-ldap.html\" target=\"_blank\" class=\"external-url\">LDAP configuration</a> for details. Instructions for using Active Directory included on this page.</p>\n+\n+<p>Using LDAP authentication means new user accounts are created, and the user placed in the default group, the first time a user logs in, substantially reducing the administration load. Any change in the LDAP password by the user will then be reflected in the OMERO login.</p>\n+\n+<p>With LDAP authentication configured, an administrator can still create new accounts for non-LDAP users. In general, OMERO.web offers the best interface for administrative tasks.</p>\n+\n+<p class=\"top_link\"><a href=\"#top\"><img src=\"images/back_to_top.png\" alt=\"Image for link to top of page\" style=\"float: right;\"/></a></p>\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+<h2><a class=\"anchor\" id=\"other\"></a>Users from other institutions</h2>\n+\n+<p>It is recommended to adopt a policy where users who do not have LDAP logins, such as external collaborators, must apply for guest accounts at the host institute if they wish to access the OMERO server.</p>\n+\n+<p>This ensures that the identities of such users are correctly verified, they sign up to the standard terms and conditions of use agreements of the host institute, and the burden of authentication security such as reminders of regular password changes does not fall on the OMERO server administrator.</p>\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+<h2><a class=\"anchor\" id=\"manage\"></a>Managing Groups</h2>\n+\n+<p>Group structures and permissions are completely flexible in OMERO, so it is worthwhile taking some time to draw up a policy for the structure and naming of groups on your OMERO server that will meet the requirements of your facility.</p>\n+\n+<p>In Biology institutes, groups generally reflect the laboratory structure of the institute, with groups for each lab, groups containing members from different labs for cross-lab collaborative projects, and groups for cross-facility and inter-institution collaboration.</p>\n+\n+<p>PIs or laboratory leaders are usually made Group Owners of their lab groups, which enables them to add new members to their groups and import and manage data for users who are members of their groups. Groups may have more than one owner. The permissions for these groups are most commonly set as Read-Annotate, although Read-Write might be more appropriate in some cases.</p>\n+\n+<p>Administrators and Group Owners can change group permissions between Private, Read-Only and Read-Annotate. Only Administrators can change a group to Read-Write. Full details of permissions can be seen in the <a href=\"http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/server-permissions.html\" target=\"_blank\" class=\"external-url\">System Administrator documentation</a>.</p>\n+\n+<div class=\"note\">\n+<p class=\"note-title\">Note</p>\n+<p class=\"note-text\">If permissions are reduced to Private when one member has created output from another member's image in the group using a script, e.g. made a projection, the permissions change will fail.</p>\n+</div><!-- End note -->\n+\n+<p class=\"top_link\"><a href=\"#top\"><img src=\"images/back_to_top.png\" alt=\"Image for link to top of page\" style=\"float: right;\"/></a></p>\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+<h2><a class=\"anchor\" id=\"default\"></a>Default groups</h2>\n+\n+<p>Most facilities use a default group that a new user is automatically allocated to when they first log on and create an account using the LDAP or similar authentication system, or when an account is created for them by the Admin. Typically this group would be Private.</p>\n+\n+<p>If the user is also made a member of their lab or other groups, they can set any group as their default group. This group will be then shown in the data tree each time they log in.</p>\n+\n+<p>For details on how users can change their default group see Changing your default group in the <a href=\"http://help.openmicroscopy.org/sharing-data.html#default\" target=\"_blank\" class=\"external-url\">Sharing Data</a> section of User Help.</p>\n+\n+<p>Administrators can set or change the default group for a user through the Admin tab in OMERO.web or the Administration tab in OMERO.insight.</p>\n+\n+<div class=\"note\">\n+<p class=\"note-title\">Note</p>\n+<p class=\"note-text\">Although the Administration functions are shown for both OMERO.web and OMERO.insight, the OMERO.web Admin tools are recommended for ease of use over the OMERO.insight Administration tools.</p>\n+</div><!-- End note -->\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+<h3>OMERO.web</h3>\n+\n+<ol>\n+\n+<li>\n+\n+<p>Click on <span class=\"bold\">Admin</span> in the top toolbar.</p>\n+\n+<p>In the <span class=\"bold\">Users</span> tab, find user by filtering.</p>\n+\n+<p>Click on the <span class=\"bold\">Edit</span> button.</p>\n+\n+<p>Select the new default group from the drop-down list.</p>\n+\n+<p>Click <span class=\"bold\">Save</span> to save the new default group.</p>\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+<img alt=\"../images/facilityManagerDefaultWeb.jpg\" class=\"align-center\" src=\"images/facilityManagerDefaultWeb.jpg\" style=\"width: 100%;\" />\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+</li>\n+\n+</ol>\n+\n+<p class=\"top_link\"><a href=\"#top\"><img src=\"images/back_to_top.png\" alt=\"Image for link to top of page\" style=\"float: right;\"/></a></p>\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+<h3>OMERO.insight</h3>\n+\n+<ol>\n+\n+<li>\n+\n+<p>Select the <span class=\"bold\">Administrator</span> tab in the left hand pane.</p>\n+\n+<p>Select a group of which the user is already a member.</p>\n+\n+<p>Select the user from the group members.</p>\n+\n+<p>In the right-hand pane, select the new default group from the drop-down list.</p>\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+<img alt=\"../images/facilityManagerDefaultInsight.jpg\" class=\"align-center\" src=\"images/facilityManagerDefaultInsight.jpg\" style=\"width: 100%;\" />\n+\n+</li>\n+\n+</ol>\n+\n+<p class=\"top_link\"><a href=\"#top\"><img src=\"images/back_to_top.png\" alt=\"Image for link to top of page\" style=\"float: right;\"/></a></p>\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+<h2><a class=\"anchor\" id=\"new\"></a>Creating groups and users</h2>\n+\n+<div class=\"line-block\">\n+<div class=\"line\"><br /></div> <!-- end #line -->\n+</div> <!-- end #line-block -->\n+\n+<h3>OMERO.web</h3>\n+\n+<ol>\n+\n+<li>\n+<p class=\"first\">Click on <span class=\"bold\">Admin</span> in the top toolbar.</p>\n+\n+<p>Click on the <span class=\"bold\">Groups</span> tab.</p>\n+\n+<p>Click on the <span class=\"bold\">Add new Group</span> button.</p>\n+\n+<p>Fill in the details.</p>\n+\n+<p>Add group owners and members.</p>\n+\n+<p>Click to select the permissions level.</p>\n+\n+<p>Click <span class=\"bold\">Save</span> to save the new group.</p>","path":"facility-manager.html","position":235,"original_position":235,"commit_id":"344af2237e69e558ab1fdaef6daedbd0e72690f8","original_commit_id":"344af2237e69e558ab1fdaef6daedbd0e72690f8","user":{"login":"hflynn","id":2368904,"avatar_url":"https://avatars.githubusercontent.com/u/2368904?v=3","gravatar_id":"","url":"https://api.github.com/users/hflynn","html_url":"https://github.com/hflynn","followers_url":"https://api.github.com/users/hflynn/followers","following_url":"https://api.github.com/users/hflynn/following{/other_user}","gists_url":"https://api.github.com/users/hflynn/gists{/gist_id}","starred_url":"https://api.github.com/users/hflynn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hflynn/subscriptions","organizations_url":"https://api.github.com/users/hflynn/orgs","repos_url":"https://api.github.com/users/hflynn/repos","events_url":"https://api.github.com/users/hflynn/events{/privacy}","received_events_url":"https://api.github.com/users/hflynn/received_events","type":"User","site_admin":false},"body":"Another 'click save to save' instance. ","created_at":"2015-12-18T11:50:41Z","updated_at":"2015-12-18T11:50:41Z","html_url":"https://github.com/openmicroscopy/ome-help/pull/138#discussion_r48018189","pull_request_url":"https://api.github.com/repos/openmicroscopy/ome-help/pulls/138","_links":{"self":{"href":"https://api.github.com/repos/openmicroscopy/ome-help/pulls/comments/48018189"},"html":{"href":"https://github.com/openmicroscopy/ome-help/pull/138#discussion_r48018189"},"pull_request":{"href":"https://api.github.com/repos/openmicroscopy/ome-help/pulls/138"}}},"pull_request":{"url":"https://api.github.com/repos/openmicroscopy/ome-help/pulls/138","id":53671225,"html_url":"https://github.com/openmicroscopy/ome-help/pull/138","diff_url":"https://github.com/openmicroscopy/ome-help/pull/138.diff","patch_url":"https://github.com/openmicroscopy/ome-help/pull/138.patch","issue_url":"https://api.github.com/repos/openmicroscopy/ome-help/issues/138","number":138,"state":"open","locked":false,"title":"Facility manager section","user":{"login":"gusferguson","id":1552703,"avatar_url":"https://avatars.githubusercontent.com/u/1552703?v=3","gravatar_id":"","url":"https://api.github.com/users/gusferguson","html_url":"https://github.com/gusferguson","followers_url":"https://api.github.com/users/gusferguson/followers","following_url":"https://api.github.com/users/gusferguson/following{/other_user}","gists_url":"https://api.github.com/users/gusferguson/gists{/gist_id}","starred_url":"https://api.github.com/users/gusferguson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gusferguson/subscriptions","organizations_url":"https://api.github.com/users/gusferguson/orgs","repos_url":"https://api.github.com/users/gusferguson/repos","events_url":"https://api.github.com/users/gusferguson/events{/privacy}","received_events_url":"https://api.github.com/users/gusferguson/received_events","type":"User","site_admin":false},"body":"New section aimed at Facility Managers. 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