Using the System¶
The experiment design and sample management features of Mastr-MS are accessed through a web browser.
The preferred way to create users is to have the user request an account. This can be done from the Login screen.
When someone requests an account, they are added to the Pending user
list, and the registration contact is e-mailed. This e-mail address is
configured with the
REGISTRATION_TO_EMAIL setting (see
Django Settings File).
The user can then be enabled by the “Admin Requests” screen.
User management is described in the Admin screencast: Accepting/Rejecting users.
An administrator user can also create users through the Users section of the Django Admin interface (see Administration). When using this interface, be careful to ensure that the username and e-mail address are the same, and all users are at least members of the User group.
Users can have different roles which determine what they can see and change in the system.
- Administrators can do see all data and perform any action in the Mastr-MS system. Such users also have permission to edit objects in the Django Admin (see Administration).
- Node Reps can edit the list of nodes and organisations. They can also grant user account requests and edit users in their node.
- Mastr Administrators can edit users and edit all aspects of projects and experiments.
- Project Leaders can edit users and edit all aspects of projects and experiments.
- Mastr Staff can edit all aspects of projects and experiments.
If users do not have any of these roles, then they are considered to be Clients. Clients can only download experiment files.
Nodes are a way of managing groups of users and directing quote requests to the correct group.
Users can view and answer quote requests sent to their node.
The list of nodes can be edited through the Admin → Node Management screen.
The pre-configured nodes can be deleted and replaced with one or more nodes specific to your site.
Experiments are grouped in Projects which have a designated client user, as well as optional project manager users.
Rule generators control the addition of QC, blank and sweep components to experiment runs.
These components can be added at the beginning, end, or for every n samples.
If the Apply Sweep Rule option is ticked for the rule generator, the run builder will add a sweep component after each sample unless it is a blank or sweep.
Rule generators cannot be changed once in use, in order not to corrupt previously run experiments. You can however clone rule generators or create new versions. Unwanted rule generators can be disabled.
At least one rule generator must exist before a run can be created.
An experiment run requires information about the samples that will constitute that run. Samples are typically generated from sample classes or imported from CSV files.
Runs are created by selecting a set of samples and clicking Add Selected Samples to Run. Previously created runs can also be cloned into new runs.
Once you are happy with the run parameters and samples, you can start the run by clicking the Generate Worklist button.
This will display a CSV worklist in a new browser window. The worklist can then be copied and pasted into the lab instrument software.
One important thing to note is that any web browser popup blocker must be disabled for the Mastr-MS web site.
Otherwise you will not be able to see CSV worklists, which are opened in a new window.
Most new web browsers have popup blockers enabled by default, but certain web addresses can be excluded from blocking.
After generating the worklist, the run is maked as “In Progress”.
The Mastr-MS data sync client periodically uploads new data found on the lab machine into the data management system. The data sync client is told by the Mastr-MS server which filenames to look for.
Once the samples data files are uploaded, the client marks that sample as complete. The percentage of complete samples is shown in the progress bar on the Runs page.
When all samples in a run are completed, the run is marked as complete.
Getting the data¶
Sample data can be seen from the Files page of the experiment. PBQCs, QCs and sweeps can be downloaded from the Runs page.
To download the data files, expand the Files tree and click the filename.
Importing metadata from file¶
Run and sample data can be imported from a CSV file. CSV files can
be created with a text editor or spreadsheet program and usually end
with the file extension
Sample CSV Import¶
To import samples, first create a CSV file which looks something like this:
Label,Weight,Comment smplbla,1.234,Comment about the sample smplblb,2.345,Another sample
Click the Upload CSV file button on the Samples page, then choose the file.
If you would like to update existing samples, first download the
sample CSV file (which contains an
ID column), edit the fields,
then upload it again.
Completed Run Sample Data Import¶
If you have sample data on the lab machine which was not created through a worklist designed in Mastr-MS, and would like to add it to the data management system, you can import it from the Runs page.
Set up a CSV file with a single column
Filename and list the
filenames for the run.
Then click the Capture Completed External Run button and upload this file. You also need to specify a name for this run and which machine the data is on.