ProteinCenter User Manual
Table of Contents

Chapter 22. μLIMS

Table of Contents

22.1. Editing link & text annotation
22.2. Permissions

The μLIMS page (pronounced micro LIMS) contains the annotation and hyperlinks you might have for an entire dataset. It also contains dataset properties, permissions and import summary.

The page enables you to put your dataset into context by adding information like:

Click the μLIMS tab on the WorkBench to manually switch to the page. Also, when selecting a new dataset, ProteinCenter will automatically change to the μLIMS page. See below for an example of the page layout.

  1. Link section

  2. Text section

  3. Edit mode button

  4. General information

  5. Permissions

  6. Quantitation name mappings

  7. Import summary

The information in sections 1 and 2 can be edited as described below. Some information (e.g. parts of search summary from a search engine result file) is automatically extracted from imported files into these sections. Section 4 contains information about when and by whom the dataset or category was created. The import summary in section 5 is displayed for datasets. For a detailed description of the import summary, see Chapter 21, Import.

Figure 22.1. The μLIMS page in view mode

The μLIMS page in view mode

22.1. Editing link & text annotation

To enter annotation edit mode, click the Edit mode button shown in section 3 of Figure 22.1, “The μLIMS page in view mode”. Below is an example layout of the annotation view, ready to be edited.

  1. Link section

  2. Text section

  3. View mode button

  4. Save button

  5. Add link button

  6. Add text button

The link section consists of three columns, namely Tag, Link and URI. The first two are the ones you see in the two columns in section 1 on Figure 22.1, “The μLIMS page in view mode”. URI is short for Uniform Resource Identifier and is a standardized (RFC2396) way of representing resource addresses. If this sounds a bit technical, don't worry. Basically you can use this field to create a hyperlink that points to an external resource like an internet web page or a file on a shared drive. The Tag is optional.

Below are some examples of typical use.

  • ftp://ftp.example.com/example.txt

  • http://www.example.com/example.txt

  • mailto:example@example.com

The text section is a bit more simple, only containing the columns Tag and Text. Again Tag is optional but if filled out, will be displayed as a header for the text. The Text field contents does not have to conform to any special format, but can contain free text.

The 'X' buttons in the left side of section 1 and 2 removes the individual entries in these sections.

Figure 22.2. The μLIMS page in edit mode

The μLIMS page in edit mode

The button panel on the lower part of the page is mainly used to handle creation and storage of annotation. The first, however, is merely to switch back to view mode. Please remember to store any changes first!. To store any changes, simply press the floppy-like icon numbered 4 in the above figure. Lastly, the two buttons numbered 5 and 6 in the figure will create a new link item or text item, respectively.

22.2. Permissions

Note

For ordinary users the Permissions section will only be shown if the user has the Grant role (see Section 32.2.3.1, “Roles” ) and if the user is the owner of the selected category or dataset. Users with the Admin role or with the Manager role will be allowed to view and change permissions of every user's categories and datasets.

The possibility to set permissions on your data is a powerful feature of ProteinCenter. Imagine you are working on some data and you want only a handful of people to be able to see that data. Maybe you are working closely with a few colleagues and you want them to be able to make changes to your project? The permissions section allows you just that, to discriminate access to your data on a per user level.

So what are the permissions that can be set? Well, there are just four: create, read, change and delete. Their precise meaning is listed here:

  1. Create: Denotes if a user is allow to create datasets and categories here. This can only be set for categories because you cannot create a dataset or a category IN a dataset. Thus when a dataset is selected this permission cannot be set.

  2. Read: Denotes if a user is allowed to view this dataset or category. If granted, a user can look at a dataset and copy data from it but not change or delete it.

  3. Change: Denotes if a user is allowed to modify this dataset or category. If granted, a user is allowed to cluster a dataset or delete data from it. He cannot however delete the dataset itself. For a category this gives a user the permission to change it's name and annotation.

  4. Delete: Denotes if a user is allowed to delete this dataset or category. If granted, a user can delete a dataset but it does not mean that he can change it. Note: deleting a category also removes its contents; therefore a category can only be deleted if the user has the right to delete every category/dataset contained within it.

It is important to understand that these permissions do not overlap! This means that having permission to change or delete a dataset does not imply having the permission to see the dataset!

Category and dataset permissions can be set explicitly on a dataset or category or be inherited from a parent category. They can also be set through the Everyone role or even as a combination of these. All this might sound a bit complicated so to use this feature efficiently it is important to know the precise meaning of the symbols used. Below these symbols are shown, followed by an explanation for each.

  • Granted on selected category/dataset

  • Denied on selected category/dataset

  • Granted on a parent category/dataset or by role

  • Denied on a parent category/dataset or by role

  • Granted by ownership

  • Not relevant for selection

With the meaning of these symbols in mind, try to study the example screen shot of the permissions matrix below.

Figure 22.3. The μLIMS permissions section

The μLIMS permissions section

The example shows the Everyone role along with three user ids. The Everyone role is a simple way of granting (or revoking) rights to all users of your ProteinCenter installation. In this example, everyone has create and read access to the category in question. The green arrows pointing downwards denote that the permission is inherited, i.e. it is set on a parent category.

The check marks for the owner, user1, are all disabled because they cannot be changed. The owner of a category or dataset always has the entire range of permissions.

Also, the example shows that user2 has been granted both create, read and change permissions explicitly (the boxes are checked) but inherits the revoked delete permission.

Finally, user3 simply inherits all permissions so that he has create and read permissions, but not change and delete.

Note

When deleting a category or dataset, special rules apply! The first step of a deletion is moving the item in question into the Recycle Bin. If the item being deleted inherits from it's parent category, that it may not be seen (i.e. read permission is denied), this must be enforced also when located in the Recycle Bin. For this reason any permissions that are implicit at the time of deletion, are made explicit.