WebProjectManager^TM

WebProjectManager organizes projects, and the data contained within them, for easier access to project information. WebProjectManager lists the various projects, their owners and descriptions, and allows users to filter this list by searching the project list for any of those three fields. WebProjectManager is used to display summary reports of the projects, edit project descriptions, delete projects, and incrementally add new sequence data to existing projects.

Projects that have been created with stackPACK v2.1 should be converted if users wish to have access to these projects on stackPACK v2.2 - this enables the user to continue data processing, output and analysis on a project created with stackPACK v2.1. Project conversion is performed from the command line with stack_ProjectManager.

Filtering the Project List
The project list can be filtered by searching by project name, owner or description, as specified below:

• Using the pop-up list, select the type of project information (name, owner or description) to be searched.
• Enter the text used as a filter in the text box.
• Click on the "Search" button in order to filter the list.
• NOTE:
  • Sequential filtering with multiple searches is not possible.
  • Wildcards (e.g., *) may not be used.
  • All or part of a term may be entered -- partial matches are allowed. (e.g., project owner liza will find projects where the owner is liza or liza@egenetics.com)
  • Searches are case-insensitive.

Summary Reports

• Clicking on the project name generates a summary report for that specific project.
• A window similar to the following is displayed:

• Linked Clusters: Singletons and multi-sequence clusters joined by virtue of shared cloneID.
  • Total number of linked clusters (ln#) formed due to clonelinking.
  • Number of sequences found in linked clusters.
  • Number of singletons found in linked clusters.
  • Number of multi-sequence clusters found in linked clusters.
• Multi-sequence Clusters: Sequences grouped together into clusters.
  • Total number of multi-sequence clusters.
  • Number of sequences in multi-sequence clusters.
  • Number of multi-sequence clusters found in linked clusters.
  • Number of multi-sequence clusters not found in linked clusters.
• Singletons: Sequences that could not be grouped into clusters with other sequences.
  • Total number of singletons
  • Sequences in singletons - always n/a.
  • Number of singletons found in linked clusters.
  • Number of singletons not found in linked clusters.

Note: Old clusters that are no longer active due to the incremental addition of sequence data to existing clusters will not be listed in the summary report. These clusters can be viewed in WebProbe.

Navigating the Summary Report:

• Clicking on the total number of linked clusters (22 in the above example) takes the user to an itemized list of the linked clusters for the specified project.
  • Clicking on a linked cluster accession number takes the user to that linked cluster's Consensus View.
• Clicking on the total number of multi-sequence clusters (268 in the above example) takes the user to a list of total multi-sequence clusters in the specified project.
  • Clicking on a cluster accession number takes the user to that cluster's Consensus View. If the cluster contains more than one contig, all consensus sequences from all contigs will be concatenated in this single view.
• Clicking on the total number of singletons link (1714 in the above example) takes the user to a list of total singletons in the specified project.
  • Clicking on a singleton accession number takes the user to the singleton sequence.

Long summary lists will be split into multiple pages. To view the following page, simply click the "Next" link at the bottom of the screen. In cases of very long lists, click on the "(+10)" link to move 10 pages forward. Similarly "Previous" and "-10" can be used to move backward in the list.

Editing Projects

• The project description may be edited by ticking the box next to the relevant project name, then clicking on the "Edit_Description" option at the top or bottom of the screen.
• A window similar to the following is displayed:
  
  

  

• Existing text may be changed and additional descriptive information may be entered. Clicking on the "Save_Project" button brings back the full project list, with the edited description, within the Web Project Manager.

Adding Data to Existing Projects

• Existing projects may be updated with the incremental addition of new sequence data by ticking the box next to the relevant project name, and by clicking on the "Add_Sequences" button at the top or bottom of the screen.
• A window similar to the following is displayed:
  
  

  

• Description: Enter additional descriptive information in the text box.
• Data Format: Select the appropriate data format from the pop-up box. StackPACK accepts any of the listed formats.
• Upon clicking on the "Next" button, a window similar to the following is displayed.
  
  

  

• Data File:
  • Name of the input data file. In the case of PHRED format, you will be prompted to enter both a data and quality file.
  • PHRED quality scores may not be added to converted projects that have been created with stackPACK v2.1.
  • Use the browse option to specify the name and location of the input file(s). If the browse option is not used, it must be ensured that the exact drive and full path is specified.
  • Every EST or mRNA sequence must have a unique accession number (per project) in order for all the data to be processed.
  • If the file contains two or more sequences with the same accession number, the program will only process the first sequence. The other duplicate(s) will not be imported or processed regardless of its primary sequence data.
• Upon clicking on the "Upload" button, the new data is submitted to the stackPACK processing pipeline and a window similar to the following is displayed.

Note: If the owner field of the existing project does not contain a valid e-mail address, an e-mail notification cannot be sent when the incremental addition completes.

Deleting Projects

• One or more projects may be selected for deletion by ticking the boxes next to the relevant project names, and then clicking on the "Delete_Project(s)" button at the top or bottom of the screen.
• A window similar to the following is displayed upon this selection.
  
  

  

• The program asks for confirmation of deletion and, upon clicking the "Delete" button, displays the full project list, without the deleted project(s), within the WebProjectManager window.