Administration of SEEK
Here are described some basic administration tasks you may want to do after installing SEEK. All admin tasks can be found in the Admin area, by selecting the Account tab, and then selecting Server Administration. Many of the settings have a description of what they do and are not covered here.
Creating a Project and Institution
Before you can add items, such as Data files or Models, to SEEK, you need to create the first Project and Institution and add yourself to them.
You can first create your Project and Institution from the Common Tasks in the admin area.
Once these have been created, you need to link the Project to the Institution, by navigating to the Project show page and clicking the Project administration button. From this page you can select one or more Institutions for this Project, and then saving by clicking the Update button at the bottom of the form.
You can add yourself to the Project and Institution you have created, by navigating to your profile, selecting Person administration, and then selecting the Project/Institution pair from the list, and clicking the Update button at the bottom of the form.
Note that, Projects can be associated with multiple Institutions, and People can belong to multiple Project/Institution pairs. When selecting multiple items from the lists you need to hold CTRL as you select them.
By default email is disabled, but if you are able to you can configure it to enable SEEK to send emails - such are emails about changes within your project, notification emails, feedback emails and notifications about errors. You can configure email under Admin->Configuration->Enable/disable features. Part way down that page there is a checkbox “Email enabled” that you should select. This reveals some SMTP settings that you need to fill out. Any that are not needed can be left blank. The meaning of the settings are:
- Address - the address (name or IP address) of the SMTP server used to deliver outgoing mail
- Port - the port that your mail server receives mail
- Domain - if you need to specify a HELO domain, you can do it here.
- Authentication - if your mail server requires authentication, you need to specify the authentication type here. This can be plain (will send the password in the clear), login (will send password Base64 encoded) or in rare cases cram_md5
- Auto STARTTLS enabled - enable this is your mail server requires Tranport Layer Security, and you get STARTTLS errors when testing your configuration
- User name - if your mail server requires authentication, set the username in this setting.
- Password - if your mail server requires authentication, set the password in this setting
There is a box beneath here that you can use to test your settings. Also, if you wish to receive emails about errors that occur - then you can check the box for Exception notification enabled, and supply a list of email addresses below (comma or space seperated).
BioPortal is a service used in SEEK for supporting and searching ontologies, which we communicate with via its API. However, the API requires an api-key that we are unable to distribute with SEEK. To be able to link organisms with NCBI terms, or search for organisms when defining new ones, an api-key has to be setup. We also have future plans for more widespread uses of ontologies - such as for the Assay and Technology types, and for tagging with semantic terms.
To get an api-key you first need to register with BioPortal at https://bioportal.bioontology.org/accounts/new, and once registered and logged in your api-key should be shown under Account details. More information is available at https://www.bioontology.org/wiki/index.php/BioPortal_REST_services.
In SEEK, you apply the BioPortal api-key under the Admin->Configuration->Settings.
Configuring DOI and PubMed search
To be able to support adding publications using a PubMed ID or DOI to your SEEK installation, you need to do 2 things.
- For PubMed you simply need to add your email address under Admin->Configuration->Settings
- For DOI - you need to register your email address with CrossRef at https://www.crossref.org/requestaccount/ and then provide that email to SEEK under Admin->Configuration->Settings
Configuring Session Store Timeout
The timeout period is set to 1 hour by default. This means that a user may be logged out after 1 hour, if they haven’t selected “Remember Me” when logging in, and could lead to lost information if spending a long time filling out a form.
Usually, 1 hour is sufficient, but the timeout can be updated under Admin->Configuration->Settings.