Administration tasks

1. Logging in

You need to log in to MISO LIMS in order to make changes to any LIMS entities. Logging in lets MISO record any changes you make on entities you have access to.

If you are a new user and have not been given a username and password, you will first need to get a username and password by following the steps in the Adding Users section.

Try to log in now:

  1. Click on http://miso.gsi.oicr.on.ca.
  2. Enter your username (e.g. jdoe) and password and click the Login button.

If all goes well, you should see the MISO Dashboard and see a message at the top right: "Logged in as: jdoe".

In order to perform the tasks in this section you must be a MISO admin. Contact your MISO administrator to gain admin status.

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2. Adding Users

The method of adding users varies by MISO installation.

If you were able to log in at the beginning of this tutorial using a user name and/or password you chose, you can add new users.

  1. On the left hand menu under the User Administration section, click Users.
  2. Click the Add button at the top left of the table.
  3. Enter the new user's login name (all one word), email, and a password.
  4. Click Save in the top right corner.

If you were able to log in at the beginning of this tutorial using a user name and password that you use for other services at your institute, users cannot be manually added by administrators. Users must be added by IT; once added, users can log in to MISO using their existing credentials (LDAP or Active Directory).

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3. Adding new instruments

New sequencing machines must be added to MISO so that MISO can be made aware of the runs that use them.

3.1 Add a new model of sequencer

If MISO does not yet have this type of sequencer in the database, you will need to email gsi@oicr.on.ca or file a JIRA ticket in GSI Common to put the new model into MISO before you can add a new sequencer of that model.

  1. Please email gsi@oicr.on.ca or file a JIRA ticket in GSI Common to add the new sequencer model to MISO. Include the following information:
    • Sequencer manufacturer (Platform)
    • Model
    • Standard read lengths you anticipate using for sequencing (e.g. 1x250, 2x126)

3.1 Add a new sequencer

  1. Click Instruments in the Instrument Runs section of the menu on the left.
  2. Ensure that the Sequencer tab is selected.
  3. Click the Add link in the top left corner.
  4. Fill in the fields of the new row that is inserted at the top of the table:
    • Instrument Name: enter the instrument name (case-sensitive)
    • Platform: select a platform from the dropdown menu
    • Serial Number: enter the serial number (case-sensitive)
    • Date Commissioned: enter the date that the instrument was first put into use
  5. Click Add to save the new sequencer.

3.2 Set up MISO to be aware of aware of the sequencer's output

  1. Please email gsi@oicr.on.ca or file a JIRA ticket in GSI Common. Give the name of the new sequencing machine and indicate that you would like them to add the sequencing machine's output folder to Run Scanner's configuration file.

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4. Creating project and monthly reports

If you require a report, please email gsi@oicr.on.ca or file a JIRA ticket in GSI Common for assistance.

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