Project Coordinator tasks

Print the worksheet for this section here: Project coordination Worksheet.

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 contact your MISO administrator to get a username and password.

Try to log in now:

  1. Click on https://misodev.pmgenomics.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".

top

2. Creating projects

A Project contains information about a set of Studies that may comprise many different Samples, Experiments and Runs. Samples are attached to Projects and they are often processed into Libraries and then Library Aliquots, which are then Pooled and sequenced. This part of the workshop details creating a new project.

Projects represent a sequencing effort toward a particular goal, usually led by a particular group or principal investigator. For example, the PCSI project is sequencing pancreatic tumors, references, cell lines and xenografts as part of the International Cancer Genome Consortium, and the FFPER project sequences samples from a bio-bank with a number of different preparations and treatments in order to determine the impact of each on data quality.

In this workshop, you will make your own project where you will create samples, libraries and other entities.

Most pages have a "Quick Help" tab at the top right under the Save button where you can find basic information about the current page.

2.1 Creating a new project

To create a new project:

  1. After logging in, click the Projects link under Preparation in the menu on the left side of the screen.
  2. Click the Add button at the top left corner. The Create Project page will display with a number of fields that you can fill in.
  3. Ignore Project ID and Name, since they are set by MISO once the Project is saved.

  4. Enter a unique Alias. The alias is a name, chosen by us, that is associated with a project. e.g. Do It 4 Science (be creative!). Record this alias in your worksheet.

  5. Enter a Short Name for your project. The short name should be 2-5 letters and/or numbers in all CAPS and related to the project alias. e.g. DI4S. This short name will be used to automatically generate sample and library names. Record the short name in your worksheet.

  6. In the Description field, enter MISO training workshop [Date]
  7. For the Progress field, choose Active
  8. Select the Reference Genome GRCh38. This should be the primary species that will be sequenced in the course of the project. Xenografts count as human.
  9. Select the Pipeline Default. This value identifies the analysis pipeline to put sample data through after sequencing
  10. Click the Save button at the upper right.
  11. MISO will generate an ID and name for the project. The name will be 'PRO' followed by the ID (e.g. "PRO123"). Record this name in your worksheet.

2.2 Projects List

  1. Click again on the Projects link under Preparation in the menu on the left side of the screen. You will see a list of all of the projects in MISO.
  2. Find the project you just created in the list. You can sort by any column in the table by clicking the column header. You can also search for your project by name, alias, short name, or description by typing text into the Search box at the top right and pressing the Enter key on your keyboard.
  3. Click on the link in the Project Name, Short Name or Alias column (they all go to the same page).

2.3 Edit Project page

The Edit Project page is used for viewing basic information about a project as well as all of the entities associated with that project, such as the samples, libraries, pools, and runs.

Once you create different entities for your project like samples, libraries, library aliquots, pools, and runs, you can view and search them on this page. Each section can be expanded by clicking on its name or the arrow next to it. The tables under each section can be sorted by clicking the column header or searched using the field in the upper right.

2.3.1 Add Project Files

In the Project Files section, you can attach any necessary documents to the project (e.g. Project Information form, REB).

  1. On the Edit Project page, click the Project Files header to expand the section.
  2. Click the Upload button at the top left of the table.
  3. In the dialog, click the Browse… button.
  4. Select a document or image that is appropriate for your study
  5. Choose a category for the attachment
  6. Click the Upload button

top

3. Configuring sub-projects

Samples in a project can be assigned a sub-project designation. The sub-project is primarily a label for human use. Sub-projects are an optional feature - a project is not required to have sub-projects.

  1. On the left hand menu in the Misc section, click Subprojects.
  2. Click the Add button at the top left of the table.
  3. Enter quantity 1 and click Create.
    • Select the main Project from the drop-down
    • Fill in the alias and description.
    • Select the priority from the drop-down. This will cause high-priority items to display priority messages in the MISO interface.
    • Select GRCh38 from the Reference Genome dropdown
  4. Click Save in the top right corner of the page.

Once a subproject is set up, it can be selected when creating Samples.

Now that your project has been created, continue to make your first samples.

< Working with Tables Home Samples >