ProteinCenter User Manual
Table of Contents

Chapter 9. The Workspace

Table of Contents

9.1. Description of the Workspace
9.1.1. Workspace controls
9.1.2. Folder tree
9.1.3. How to merge datasets
9.1.4. Searching the workspace

The workspace is the control center of datasets, where the user is allowed to create folders within categories to organize data from different projects, much like working with folders in a file system.

The folder structure is used to select data for general analysis or for comparing different datasets.

9.1. Description of the Workspace

The workspace contains three components.

  1. A toolbar with control buttons for manipulation of folders and categories

  2. A tree structure which holds the datasets.

Figure 9.1. The Workspace

The Workspace

A category is a holder for folders and other categories, whereas a folder corresponds directly to a dataset. Folders can not contain other folders, which means that they will always be leafs in the workspace tree. The number of unique proteins in each folder is displayed in parenthesis after the folder name.

9.1.1. Workspace controls

At the top of the workspace a number of buttons makes it possible to create new categories or folders, delete existing ones or place folders into other categories.

  1. Create category - Create a new category

  2. Delete folder/category - Delete a folder or category (along with any sub folder/category)

  3. Cut a folder/category - Cut a folder or category (to move it to another location in the tree)

  4. Paste folder/category - Paste a folder or category to move it to another category

  5. Rename folder/category - Rename a an existing folder or category

  6. Merge folders - Merge two or more folders into a single folder.

  7. Compare folders - Creates a compare folder for the selected datasets.

Note that these operations require that the user has the appropriate permissions to perform them. The permissions for a category or a data folder can be seen in the Permissions section on the μLIMS page - See Section 22.2, “Permissions”.

9.1.2. Folder tree

The branches of the tree are categories marked by the icon. They are used to organize the sets of proteins in descriptive categories.

There are three main branches in the folder tree:

  1. DataSets - Datasets as organized by the user during analysis

  2. Incoming - The system places new datasets that have been imported externally (if integrated with other systems), here. Also, if a category is not selected when saving contents from the basket or lookup, the data is put here. It is then recommended to move these datasets to a location in the DataSets category - for more details on importing datasets see Chapter 21, Import

  3. Recycle Bin - When deleting folders/categories, from either of the two above mentioned categories, they are actually put here. From here they can be restored (by moving them back into DataSets) or permanently deleted by repeating the delete action.

The data can be organized in multiple levels, making it possible to have a well structured organization of the data. Folder names and the organization are decided by the user.

The actual protein data are added to the folders ( icon) as leafs of the tree. To select a dataset simply click a folders name, and the µLIMS page will appear in the data view to the right. Depending on the pane selected from here, you will see a list of proteins (the Proteins pane), experimental data (Protein Data pane) etc.

9.1.2.1. Creating new folders (datasets)

Since folders and datasets are tightly connected, new folders cannot be created explicitly by the users. New folders are created during import or when using the save icon (located at the lower left of the data view) to save datasets from the basket, the lookup or the dataset view.

  1. Save - Save the data to a new folder

  2. Delete - Delete proteins selected with the checkbox

  3. Check all - Selects all proteins in the current view

  4. Uncheck all - Unselects all proteins in the current view

Of course the Delete operation require that user has the permissions to delete entries in the dataset.

9.1.2.2. Renaming a category

To rename a category follow these steps

  1. Select the category (by clicking it's name)

  2. Click the rename button in the workspace controls

  3. Type the new name and press return

  4. The category has been renamed

Folders can be renamed in the exact same way.

9.1.3. How to merge datasets

Datasets can be merged together in a three step process.

All supplementary data types represented in any datasets (e.g. AQR, GD#, GI#) are preserved in the merged dataset, along with corresponding values attached to the experimental data of either of the old datasets.

In cases where the individual datasets are clustered, this clustering is not transferred to the new merged dataset.

In the given example we want to merge two datasets named Dataset1 and Dataset2.

Step 1. Click the folder icon on each of the datasets that are to be merged. When clicked, a green check mark appears on the folder icon.

Step 2. Select the category in which the merged dataset should be placed.

Step 3. Click the Merge folder icon in the workspace controls. All folders with the green check mark will be merged

Now the merged dataset appears in the folder.

Remember to consider whether the generic fields of supplementary data are consistent in the datasets that are merged - i.e. does e.g. the GS1 column contain the same type of data.

Multiple folders may also be analyzed simultaneously in a comparative analysis - see Chapter 19, Dataset comparison for more details.

9.1.4. Searching the workspace

Over time many datasets may be accumulated and it might be difficult to find older data that you want to look at. Using the Search Workspace functionality, you can find categories and datasets by entering criteria like owner, creation date and annotations.

To search the workspace, do as follows (you can see the corresponding GUI location on the image below)

Please note that all criteria are optional but to get a meaningful result, you must select one or more of them.

  1. Activate the workspace search by clicking the magnifier glass, the button will stay depressed while the function is active

  2. Select an owner by choosing from the drop down list or start writing in the text box and matches will be suggested

  3. Select creation date by manually entering the dates or selecting from the calendars (click the calendar icons)

  4. Select annotation tag/value by choosing from the drop down lists or start writing in the text boxes and matches will be suggested

  5. Press Show to display the result

After changing a criteria, the number of results matching that specific criteria will be displayed immediately. This helps in adjusting the criteria to get the desired results. The overall match result is shown below the criteria section.

The result of the applied criteria will be shown as a filtered version of the workspace tree. Any categories/folders matching all criteria will be shown in bold. These can be manipulated exactly as were they located by normal navigation in the workspace tree.

To close the workspace search functionality, simply click the magnifier glass icon once more or click the red close button in the top left part of the workpsace search window.