nitrc:User Guide - Overall Administration

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Contents 1 Admin Overview 1.1 Misc. Tool/Resource Information 1.2 Tool Admin 1.3 Group Members 1.4 Pending Requests 1.5 Edit Roles 2 Edit Public Info 3 Manage Images 4 Custom Tool Menu Entries 5 Tool/Resource History 6 Stats 7 Tool/Resource Associations

Admin Overview

The Tool/Resource Admin page presents you with Misc. Tool/Resource Information, Attribute List Classification, Tool Admin, Group Members, Pending Requests, and Edit Roles.

Misc. Tool/Resource Information

This shows the public description of the tool/resource and the location of the tool/resource home page, which other users can access from your Tool/Resource Summary page. The description and home page link can be modified through the Admin Edit Public Info page. When you first register your tool/resource, the home page link is set to your Tool/Resource Summary page. If you have an external Web site, you should provide that link. Go to the Edit Public Info page to change the home page location.

Download Nightly SCM Tree Snapshot: The "Download Your Nightly SCM Tree Snapshot" link allows you to download the nightly compressed collection of source code files for your tool/resource.

Attribute List Classification: One way NITRC users find tools/resources that fit their needs is to browse by or narrow search results down to desired attributes. If you want NITRC users to find your tool/resource, you must classify it in the Attribute List. Click the Attribute List Classification "Edit" link to modify your current attribute selections. You want to select as many specific attributes that are applicable as possible. The more applicable attributes you select, the more likely your tool/resource will be found by a user browsing or searching by attribute. After you submit the selections you will be returned to the Tool/Resource Admin page.

Javascript Enabled: NITRC shows your current classification followed by a section for adding attributes to your classification. You may remove attributes from your classification and the "Current Selections" section by clicking the in front of the attribute. To add attributes to your classification, click the appropriate parent attribute in the selection list of the "Make Additional Selections" section. If the parent attribute has sub-attributes, another selection list will be displayed to the right of the first. Click on an applicable sub-attribute to select it. If that attribute has sub-attributes another selection box will be displayed to the right of the last. This continues for each sub-attribute until you reach the end of a branch. You should select the most specific attributes from the selection list that apply for your tool/resource. Simultaneous classification with a specific attribute and a parent attribute will result in only the more specific attribute being accepted. Click the "Add to Selection" button to add the selected attribute to the "Current Selections" section. When you are finished adding or removing selections, click the "Save Changes" button to store you classification.

Note: If you need help in understanding what a particular attribute is, click on the attribute name in the "Current Selections" section or select the attribute and click on the "View in Glossary" button in the "Make Additional Selections" section. This will bring up the definition of the attribute.

Javascript Disabled: NITRC shows several sections, one for each parent attribute. For each of these sections (for each parent attribute) 15 drop down selection boxes are shown. You should select all the most specific attributes from the drop down selection boxes that apply for your tool/resource. Simultaneous classification with a specific attribute and a parent attribute will result in only the more specific attribute being accepted. If the parent attribute does not apply to your tool/resource, then leave "None Selected" for all the selections below the parent attribute. When you have finished making all the applicable selections for your tool/resource, click the "Update All Attribute Changes" button to save your attribute list classification.

Note: If you need help in understanding what a particular attribute is, click the Glossary link in the footer, find the attribute in the glossary, and review its definition.

Google Analytics ID: If you wish to use Google Analytics to track access to your tool/resource pages and files, simply enter your Google Analytics ID in the box, and then click the "Update" button to save your entry.

Note: It can take up to 24 hours for tracking data to appear in your Google Analytics dashboard.

Tool Admin

This section provides links to the administration pages for the tool/resource functions.

Group Members

This displays the names of the members participating in the development of the tool/resource or those willing to be a reference for the tool/resource. Here, as the tool/resource administrator, you may add members, modify member roles, or send a message to all tool/resource members.

Add Member: There are several ways for you to add members to your tool/resource group.

1. To add one member, enter the user's NITRC login name into the box provided below the list of current members, select a role, and click the "Add User" button.
2. To add members by e-mail address, click the "Add Members By Email Address" link. Here you may enter e-mail addresses for current NITRC users and those individuals who may not yet use NITRC. NITRC users with e-mail address that match those you submitted will automatically be made members of your tool/resource group. An invitation will be sent to e-mail addresses that do not match current NITRC users. The invitation allows a recipient to register with NITRC and automatically become a member of your tool/resource group upon successful registration, or a recipient can log into NITRC with an existing login and automatically become a member of your tool/resource group upon successful login. You can remove membership invitations at any time. The system will automatically expire membership invitations after one month.
3. To add members from a list of current NITRC users, click the "Add Users From List" link. Check the box for the users you want to add to your tool/resource group. Click the "Finish" button when you have selected all the users.

Delete Member: To remove a member, click the "Remove" button to the right of the name. You will not be asked to confirm this deletion.

Update User Role: To change a member’s role, select a new role next to the member’s name and click the "Update" button. (Note: Every tool/resource must have an administrator, so you may not change the role of a lone administrator.)

Update Observer Permissions: To change permissions to areas of your tool/resource that are generally open to all users, click the "Edit Observer" button. You will be presented with a page that allows you to modify access by an observer. This is where you may make your tool/resource private, rather than public (set by default). This is also where you set permissions for your source code access and access to individual forums, trackers, task subprojects, and file packages.

Email Members: To e-mail all members of your tool/resource, click on the "Email All Members" link. This is a "mailto:" link that has a comma-separated list of registered e-mail addresses for all of your tool/resource members.

Pending Requests

This section displays the names of users who have requested to join your tool/resource group on NITRC. You may reject the request by clicking the "Reject" button to the right of the user’s name, or accept the request by selecting a role for the user and clicking the "Accept" button.

Edit Roles

Certain permissions for user roles may be edited by selecting a role and clicking the "Edit Role" button. You may then change the name of the role and set permissions for the file release system, the source code repository, the document manager, forum management (as well as permissions for individual forums), tracker management (as well as permissions for individual trackers), and task management (as well as permissions for individual task subprojects). You may also set tool/resource-wide administrative permissions.

New roles can also be created. Click the "Add Role" link to create a new role. You must enter a name for the role and define the permissions for that role. Roles may be created, but cannot be deleted. All roles inherit the observer permissions as minimums.

Edit Public Info

Click the "Edit Public Info" link at the top of the Tool/Resource Administration page. This page enables you to change the basic information and functionality available for your tool/resource. You may modify the following information:

Descriptive Tool/Resource Name: The name of your tool/resource as it appears on NITRC.

Tool/Resource Visibility: Select "Public" if you want your tool/resource visible to all NITRC users; select "Private" is you want your tool/resource only visible to its members.

Short Description: A brief description of your tool/resource that appears at the top of your tool/resource Summary page.

Organization: The organization (such as Johns Hopkins University, UCSD, or Neuroinformatics Research Group) that supports your tool/resource. This information is displayed in a box on the right side of your tool/resource Summary page.

Center: The research center or institute (such as Motefiore Institute, CIRM, or Center for Systems Biology) that supports your tool/resource. This information is displayed in a box on the right side of your tool/resource Summary page.

Funding Source: A list of your funding sources and/or acknowledgments. This information is displayed in a box on the right side of your tool/resource Summary page.

Note: Special markup is allowed for funding sources. A WYSIWYG editor is provided to make this easier for commonly used markup, but you may directly enter the special markup in the box. To edit the source code directly, click the "BBCode" button in the WYSIWYG editor. Special markup for funding sources: Math commands can be used in your funding source. Simply embed your LaTeX math commands between [tex] and [/tex] tags. BBCode, Bulletin Board Code, can be used in your funding source. Refer to http://en.wikipedia.org/wiki/BBCode for BBCode tags. A useful tag for funding source is the URL tag. You may enter the source in the suggested format and link to that source's external Web site: [url=<URL starting with http://, https://, or ftp://>]<funding source name>[/url] URLs starting with http://, https://, or ftp:// can be used in funding source and will be clickable. E-mail addresses can be used in your funding source and will be clickable.

Note: If you choose "Quote" for the style in the WYSIWYG editor, the editor assumes a new paragraph when you press "Enter" on your keyboard and a new box is created. To stay in the same box and move to the next line, press "Shift" and "Enter" on your keyboard.

Homepage Link: A link to your tool/resource’s home page, accessible by following the "Home Page" link in the box on the right side of your tool/resource Summary page. The home page link is initially set to your Summary page. If you have an external Web site, you should provide that home page link here.

Active Features: A list of the tool/resource-specific functionality available in NITRC. You may activate or deactivate these built-in NITRC functions for your tool/resource. Most of these functions are accessed by users through your tool/resource menu. The available NITRC built-in functions are:

• Mailing Lists: If checked, your tool/resource menu will have a "Mailing Lists" link. You can create mailing lists that any NITRC user can subscribe to. You can also create private mailing lists that only your members may subscribe to.

• Surveys: If checked, your tool/resource menu will have a "Surveys" link. You can create surveys to poll NITRC users for information.

• Forums: If checked, your tool/resource menu will have a "Forums" link. Three discussion forums are automatically created for your tool/resource, and you can create other discussion forums as desired. Each forum can be open to all NITRC users or restricted to your members.

• Task Manager: If checked, your tool/resource menu will have a "Tasks" link. You can manage work that needs to be done for your tool/resource similar to MS Project.

• Source Code Repository (SCM): If checked, your tool/resource menu will have a "Source Code" link. You may use NITRC as your version control repository for all your source code.

• News: If checked, your tool/resource menu will have a "News" link. You can post news bulletins that will be displayed on your Summary page. These bulletins may also be selected by the NITRC news team for display on the NITRC Home page.

• Doc Manager: If checked, your tool/resource menu will have a "Docs" link. You and members of your tool/resource can upload documents that all NITRC users can view.

• Tracker: If checked, your tool/resource menu will have a "Tracker" link. You can manage items that need to be tracked, like bugs or feature requests for your tool/resource. All NITRC users can view these items, but only registered users can submit items and comment on them. Only designated members of your tool/resource can modify tracking information.

• File Release System (FRS): If checked, your tool/resource menu will have a "Downloads" link. You can upload software that other NITRC users can download and use.

• Statistics: If checked, your Summary page will display your tool/resource activity percentile and a link to view some statistics. The activity percentile shows how active your tool/resource has been in comparison to other tools/resources for the current week. The Statistics page shows activity graphs for your tool/resource, including opened and closed tracker items, posted forum messages, submitted documents, opened and closed tasks, and downloads. If unchecked, the activity percentile and statistics link will not be shown on your tool/resource Summary page, but activity will be tracked. Administrators can access statistics through the Admin Stats menu link.

Note: The Most Active All Time and Most Active This Week lists include tools/resources that do not have the "Use Statistics" box checked, as these metrics have a site-wide perspective.

• One Click Backup: If checked, NITRC will create a nightly backup of your tool/resource. You must set up a virtual machine to upload and view a backup of your tool/resource.

• CVS 2 Tracker: (Only displayed if CVS was chosen for source control management at registration.) If checked, NITRC will look to link your CVS log messages to Trackers and Tasks when files are committed to your CVS repository. If your CVS log message contains text in the form [#NNN] for Tracker (for example, [#54] or [#243]) and [TNNN] for Tasks (for example, [T68] or [T132]), the message will be shown on the Tracker or Task Detail page with links to the involved files.

• MediaWiki Plugin: If checked, your tool/resource menu will have a "MediaWiki" link. You can provide wiki pages that all NITRC users can view and your members can contribute to. You can also create private wiki pages that only members can view and edit.

In addition to the built-in NITRC functions, you may link to your own tool/resource functions. Click "External Links" to get a page where can enter the URLs for your external functions. Refer to the Custom Tool Menu Entries section in this User Guide for more information on that page.

New Document Submissions: The e-mail addresses of those who will review all new document submissions for your tool/resource. Multiple addresses must be separated by a comma.

Manage Images

The Image feature is an important publicity tool. You can build branding awareness by uploading your laboratory logo or your tool/resource logo. You can also post images of your software in action, highlighting features you believe will most interest potential users.

Existing Images: Any images that you have already uploaded are displayed in this section. If an image has been made the default image, it is highlighted by a red box and the "Make Default" checkbox is checked. The default image is displayed on your Tool/Resource Summary page. If you would like set or change the default image, check the "Make Default" box for the image that you want displayed on the Summary page, and click the "Update" button. If you do not want any of your uploaded images displayed on your Summary page, then make sure all the "Make Default" boxes are unchecked.

An image description is not required, but may be useful. Users access your uploaded images by clicking on the default image displayed on your Tool/Resource Summary page. The description is displayed below any image that they enlarge. If you would like to change the description of an image, make the change to the "Description" field, and then click the "Update" button.

If you would like to delete an image, make sure you check the "I'm Sure" box, and then click the "Delete" button.

Add New Image: You may add a maximum of six images. In order to add a new image, either enter the file location or click the "Browse" button to select the file. The file must be a GIF, JPEG, or PNG that is no larger than 500kb. We suggest that the image has a resolution between 150x150 pixels and 640x480 pixels. You may enter a description for the image, and you may set it as the default image if you want it displayed on your Tool/Resource Summary page. Click the "Add" button to upload the image.

Custom Tool Menu Entries

This page allows you to create new items in the menu for your tool/resource that will link to the page you specify here.

Required Fields—indicated by a red asterisk (*)

Suggested Name: You first need to provide a name for your new menu item. If you want to replace one of the built-in NITRC functions (like Forums or Tracker), then you would select the appropriate "Suggested Name" and leave the "Custom Name" field blank. This will ensure uniformity across the NITRC tools/resources.

Note: If you have not already turned off the built-in NITRC functionality that you are replacing, the name will appear twice in your tool/resource menu. You should go to the Edit Public Info page to remove the built-in NITRC function from your tool/resource menu.

Custom Name: (Only required if "Custom Name" is selected for "Suggested Name"—indicated by a double red asterisk (**).) If you want to add a link to an external page or specific pages in NITRC, then you would select "Custom Name" and enter an appropriate menu name in the "Custom Name" field. For example, you may want users to have easy access to a contact person for your tool/resource, so you may enter "Contact Us" for the "Custom Name."

Link URL: Once you have given a name to the menu item, you must provide the link for the page. Enter the full URL beginning with http://, https://, ftp://, or mailto:.

If you would like the NITRC banner and menu system available when the page is displayed, check the box under "Display with NITRC Menu"; otherwise, leave the box unchecked, and your browser window will only display your page. Click the "Add" button to insert your new menu item, allowing users to access your page from the tool/resource menu.

Custom menu items with standard names appear alphabetically with the other standard features for your tool/resource. Custom menu items with non-standard names appear below all the standard menu items. These non-standard items can be ordered as you like within the custom menu section. Simply click the arrow to the left of the item on the Custom Tool Menu Entries page to change its placement in the tool/resource menu.

The Custom Tool Menu Entries page also allows you to update and delete custom menu entries that have already been created for your tool/resource. You may change the menu name (either selecting a "Suggested Name" or entering a "Custom Name"), update the URL, and check or uncheck the box under "Display with NITRC Menu." Click the "Update/Refresh" button to save your changes. If you would like to remove the custom entry from your tool/resource menu, check the box next to "I'm sure" and click the "Delete" button. (Note: If you would like to remove a built-in NITRC function from your tool/resource menu, click on the "Edit Public Info" link at the top of the page.) Clicking the "Cancel" button will take you to the Admin page.

Tool/Resource History

This page presents a history of the tool/resource, indicating dates for major changes such as adding or removing members, modifying public information, changing Attribute List attributes, etc.

Stats

The Stats page provides reports and graphs of statistical information for your tool/resource.

Reports:

• File Release Download Report: This report shows the total downloads, unique IP addresses and unique users for each package, release, and file for your tool/resource.
  • Generate CSV Download Report: You may generate a file with raw data for each download associated with your tool/resource. The data generated includes the date of download, package name, release name, file name, and IP address for the user who downloaded the file. If you have required the collection of user contact information in order to download a release, the e-mail address, login name, and name of the user are also included. (You indicate that contact information is required on download when you create the release, and you can also change this indication by editing the release.) To generate the file, enter the date range of interest and click the "Submit" button.
• Monitored Items Report: This report shows the number of users monitoring the news, forums, file packages, and trackers for your tool/resource.

Recent Activity: Statistical information that can be graphed for your tool/resource includes opened and closed tracker items, posted forum messages, submitted documents, opened and closed tasks, and downloads. To view a graph, select a component of interest (under "Areas": tracker, forums, docs, tasks, or downloads), the type of plot (daily, weekly, or monthly), and start and end months, and then click the "Refresh" button.

Tool/Resource Associations

With tool/resource associations, you can show relationships between your tool/resource and other public tools/resources hosted on NITRC. Associations help users understand if a particular tool/resource is a subproject, dependency, and/or plugin of another tool/resource. An association may also show that a tool/resource interacts well with another tool/resource or has been created by the same developers as another tool/resource.

Add New Tool/Resource Associations: You may declare your relationship to another tool/resource by adding a new association. This association is displayed on your Tool/Resource Summary page, and on the associated Tool/Resource Summary page if approved by its administrator. Association types include:

• is a plugin for (is a plugin for another tool/resource)
• can be extended by (has a plugin that is another tool/resource)
• is part of (is a subpart of another tool/resource)
• has subpart (has a subpart that is another tool/resource)
• build requires (needs another tool/resource for its build)
• is required to build (is needed by another tool/resource to build that tool/resource)
• execution requires (needs another tool/resource to run it)
• is required to run (is needed by another tool/resource to run that tool/resource)
• works well with (interacts with another tool/resource)
• is from the makers of (has the same developers as another tool/resource)

Note: Associations are the result of some level of developer-to-developer interactions that provide unique interoperable functionality.

Select an association type and the associated public tool/resource. (Both fields are required as indicated by the red asterisk (*).) Click the "Add" button. This association will now appear on your Tool/Resource Summary page and below in the Edit Existing Tool/Resource Associations section. The association will also appear in the Approve Tool/Resource Associations section for the other tool/resource.

Note: If your tool/resource is private, the association will not be visible to anyone who is not a member of your tool/resource, including the other tool/resource's administrator.

Edit Existing Tool/Resource Associations: Any associations that you have already added are displayed in this section. If you want to change the association type or associated tool/resource, make the appropriate selection, and then click the "Update/Refresh" button. This new association will now be displayed on your Tool/Resource Summary page. The association will be displayed on the associated Tool/Resource Summary page if approved by its administrator.

You may delete an existing tool/resource association. Make sure you check the "I'm Sure" box, and then click the "Delete" button. The association will be removed from the Tool/Resource Summary page(s).

Approve Tool/Resource Associations: When another tool/resource claims a relationship with your tool/resource, that tool/resource will be listed here. The association type and tool/resource name are shown along with the association status. The association status includes:

• Approved/Displayed (association shown on your Tool/Resource Summary page)
• Rejected/Hidden (association not shown on your Tool/Resource Summary page)

Note: The association will still be shown on the Tool/Resource Summary page of the tool/resource that added the association even if you hide the association on your Tool/Resource Summary page.

To change the status, make your selection and click the "Update/Refresh" button.

You may also easily send a message to the associated tool/resource administrator. Simply click the link "Email <tool/resource> admin" to get the Send Message page. Enter your subject and message, and then click the "Send Message" button.