ProteinCenter User Manual
Table of Contents

Chapter 5. Overview of the interface

Table of Contents

5.1. Browsing the interface
5.2. The Navigation Menu
5.3. The Lookup, Workspace, Basket switchboard
5.4. General utilities
5.4.1. Status field
5.4.2. Status bar menu
5.4.3. Paging functionality
5.4.4. Sorting columns
5.4.5. Selecting which columns to display
5.4.6. Mouse-over information

In this chapter the functionalities for the main data views of the workbench are described.

After logging in to ProteinCenter through the login menu, the main interface is shown. The different components of the interface are described here.

5.1. Browsing the interface

ProteinCenter is a web based application. This means that all the data storage, and most of the data processing is done on a server. All you need to access this server is a web browser. No installation is required at the client machines. When using the application you should keep in mind that requests are sent to the server and results are delivered back to the client browser. A few types of requests take significant time for the server to execute, but most responses are fairly quick. Time consuming requests include importing data, loading data, clustering data, calculating statistics and reporting data. Depending on the size of the dataset, these tasks can take several minutes. When the server is executing a task, do not send new requests by clicking the interface again. It will only delay the response further. Also, when navigating the application, you MUST use only the buttons, panes, and links in the application itself. Using the browser navigation such as ‘Back’, ‘Forward’ or ‘Refresh’ will not give sensible results. Likewise, bookmarks to ProteinCenter pages (other than the login page), do not make sense. Finally you should always remember to log out of the application if you are not using it. The ProteinCenter license typically restricts the number of users, so logging out will allow other users to access ProteinCenter. Simply press the logout link in the upper right corner of the interface before closing the window or navigating to another page. Should you close the browser without loggin out, your session will still be active for up to 20 minutes.

Different browsers handle session information differently therefore you may experience undesired behavior in the following cases:

  • Opening a new Internet Explorer window using FileNewWindow (Ctrl + n) from an already opened ProteinCenter instance.

  • Using more than one FireFox browser window at a time to view the ProteinCenter interface.

Please note that this list is not exhaustive.

5.2. The Navigation Menu

At the top of the main view is the navigation menu which allows navigation in major and minor modules.

Major modules include:

  1. Workbench

  2. Administration module (only visible for users with administrator privileges) - see Chapter 32, Administrative Settings

    Figure 5.1. The Navigation menu - major modules in the top line and minor in the lower line

    The Navigation menu - major modules in the top line and minor in the lower line

    For each major module, there is a number of minor modules. For the Workbench these include:

  3. Import - a module for import of data - see Chapter 21, Import

  4. μLIMS - contains information about the dataset Chapter 22, μLIMS

  5. Peptides - a display of imported peptides - see Chapter 12, Peptides view

  6. Protein Data - a display of imported experimental data - see Chapter 13, Protein data view

  7. Proteins - a display for lists of proteins - see Chapter 14, Proteins view

  8. Genes - a display for lists of genes - see Chapter 15, Genes View

  9. Clusters - a display for clustered proteins - see Chapter 16, Clusters View

  10. Profiling - a module for grouping proteins based on their supplementary data - see Chapter 17, Profiling View

  11. Heat Maps - a module for generating heat map images for proteins based on their supplementary data - see Chapter 18, Heat Maps view

  12. ProteinCard - display of information for an individual protein - see Chapter 10, The ProteinCard

  13. Statistics - module for statistical summary of protein datasets - see Chapter 25, Statistics

  14. Report - a module for creating reports - see Chapter 24, Reports

  15. Export - a module for export of data -see Chapter 23, Export

5.3. The Lookup, Workspace, Basket switchboard

The left part of the interface contains a switchboard, which allows you to swich between an overview of all datasets in the system, a set of selected proteins of interest, and a utility to search for proteins in the system:

Figure 5.2. The switchboard for switching between the three ways of working with data.

The switchboard for switching between the three ways of working with data.

  1. The workspace in which datasets are stored in folders - see Chapter 9, The Workspace

  2. The Basket which allows you to maintain a set of interesting proteins while analysing datasets - see Chapter 8, The Protein Basket

  3. The Lookup - lookup of protein keys and tryptic peptides - See Chapter 7, The Lookup

5.4. General utilities

Across the platform a number of general utilities are available.

5.4.1. Status field

ProteinCenter will display status messages in the upper left corner just below the ProteinCenter logo

Figure 5.3. The status field

The status field

In this case the status field simply welcomes the user 'Manual' to the system.

5.4.2. Status bar menu

The right part of the status bar contains a simple menu

Figure 5.4. The status bar menu

The status bar menu

Options in the status bar.

5.4.2.1. Settings

In this section, it is explained how to configure what type of protein key to display with each protein. This setting can be made on a per-user level.

5.4.2.1.1. How to choose a preferred type of protein keys

ProteinCenter™ provides the possibility of choosing which type of protein keys to display. To display the settings page, click the link on the status bar menu

Figure 5.5. The Settings page

The Settings page

  1. Drag and drop the list entries to reorder them

    • UniProt identifiers = Swiss-Prot/Trembl accession codes (Swiss-Prot accessions are automatically preferred over Trembl accessions)

    • GI = NCBI GIs

    • IPI = IPI identifiers

    • ENSEMBL = Ensembl keys

    • SGD = SGD keys

    • FB = FlyBase keys

    • TAIR = TAIR keys

    • PLASMO = PlasmoDB keys

    • TRITRYP = TriTrypDB keys

    • PSE = Pseudomonas Genome Database keys

    • CMR = Comprehensive Microbial Resource keys

    • STRING = STRING DB keys

    • TBLIST = TubercuList keys

  2. Click Update to save the preference. The new order will be effective at the next logon.

In the given example, GI is the preferred keys, and if no live GI key exists for the given protein, an IPI key is shown and if no live IPIs exists, then a UniProt identifier will be shown and so on. Finally TubercuList keys are the least preferred types of keys in this example and will only be preferred for a protein if it does not have any of the other keys.

In the ProteinCard all keys that exists for a protein are shown as described in Section 10.2.1, “Keys details”.

Currently, all entries in ProteinCenter contain at least one of these types of keys.

In cases where no live protein key exists for the preferred type, the secondly most preferred type is shown etc. In the example above, this means that if only outdated GI accession codes exists for the protein record, a live IPI key will still be preferred.

Note, that the imported accession key is always preserved and can be found in the experimental data view.

5.4.2.2. About

Clicking this link will display an about box containing version info and license agreement.

Figure 5.6. The About box

The About box

To view more details about the current data release click the Data Release date link. Doing so will open a new window displaying some basic protein sequence and annotation counts.

Figure 5.7. The Data Release Statistics page

The Data Release Statistics page

5.4.2.3. Help (Context sensitive online help)

For every component in the interface, there is a context sensitive online help.

Follow this example to access the online help.

  1. In the top right of the interface click Help

  2. The cursor changes and a question mark icon appears

  3. Now press any component of the interface for which help is wanted. In this example we press the Lookup tab

  4. Now the online help appears - in this case Chapter 7, The Lookup

  5. Use the PDF version link to obtain a printable version of the complete user manual

  6. Click Prev to go to previous chapter

  7. Click Next to go to next chapter

  8. Use the Table of Contents to jump directly to specific sections of the chapters

  9. Below the table of contents, you will find the help for the first section of the given chapter

5.4.3. Paging functionality

At the top of the list views (Protein Data, Proteins, Clusters, Basket, etc), there is a toolbar for paging the dataset contents.

Figure 5.8. The paging functionality

The paging functionality

  1. Go to a specific page

  2. Set page size (number of entries displayed on each page)

  3. The records shown and the total number of entries in the set.

Note, that even though it is possible to set a very large page size this may slow down the system considerably.

5.4.4. Sorting columns

Most columns can be sorted. Clicking the column header will make this column the primary sorting column. The previous sorting is taken into account when doing a subsequent sorting and thereby it becomes possible to sort by multiple columns.

After a sort, a small blue arrow appears next to the column header and indicates whether the data has been sorted ascending or descending

Numbers are sorted numerically, while text and alphanumerics are sorted alphabetically.

The default sorting order is ascending. The sorting order is reversed by clicking once more on the underlined heading.

When sorting by multiple columns, the order in which the user sorts individual columns should start with the least important column and end with the most important column (i.e. the column selected last will be the primary column in the sort).

5.4.5. Selecting which columns to display

By default most of the information contained in a dataset is displayed in the relevant view.

For the Peptides, Protein Data, Proteins and Clusters view you can, however, choose which columns you want to see.

Right click anywhere on the table header to display the selection menu and then click any single item to show/hide the corresponding column. See the example below.

Your choices will be remembered per view while logged in.

Figure 5.9. The column selection drop-down menu

The column selection drop-down menu

5.4.6. Mouse-over information

In ProteinCenter most column names are abbreviated in order to fit many columns on the screen. Most column names (and icons) are supplied with mouse-over information which gives a more detailed description of the column (or icon). Just point to the column (or icon) and the information will be displayed. Likewise, in cases where a text has been truncated to fit on the interface, mouse-over will display the full text. As an example, most protein descriptions will not fit in the description column of the Proteins view. Switching to the ProtienCard is not necessary to view the complete description - just use the mouse-over.