Overview of Help-Pages

Project Management

Introduction

The "Project Management" allows users to easily manage sequences, BED files, and results from all tasks of Genomatix main menu.
The project management page is available by selecting "Projects & Accounts -> Projects & Results" from the top menu of each task.

Job manager

Jobs that were started by the user in the background (e.g. with the email option set) and which are not yet completed are displayed in the table "Your currently running Jobs".

For each running job the following information is displayed:

• Job-ID
• task name
• parameters like sequence file used
• date when the job was started

The jobs can be killed by using the "Remove job" link in the last column.

Example project page

Here is an example project page with some explanations:

Explanations

The example shows a table with two projects (here called "MyProject" and "IGH_BCL-project"), each containing a sequences folder and a number of folders for results for the different tasks that were used (ElDorado, FrameWorker, MatInspector etc.).

• Clicking on a folder icon opens a folder (either the project (marked with the letter 'P') or the sequence/result folders) and lists its content dynamically.
• By default all results are stored in a project called "MyProject". You can create new projects with the buttons in the control sections (see below) and move results between projects.
• Using the check boxes next to the names you can select a whole sequence or results folder, or a single sequence, BED file or previously generated output file. This selection is valid for a number of tasks in the control section as described below.
• The HTML link next to the check box displays your previously uploaded sequence, a BED file or a generated output file.
• Date of generation of your output file is shown.
• On the Genomatix web server user generated files will be automatically deleted after a defined period of time. The remaining time until deletion of your output files is shown. However, you can protect selected files from automatic deletion.
• By using the icons on the right side you can manipulate your results:
  • Rename a project, a sequence, a BED file or a result:
    A window will pop up, where you can enter a new name for your project/sequence/BED file/result
  • Add a comment to a project, a sequence, a BED file or a result
    A window will pop up where you can enter your comment
  • Protect a sequence, BED file or result
    This will protect your sequence/result from automatic deletion (usually after 30 days), but you can still delete the file by using the delete option
  • Delete a project, a sequence, a BED file or result This will delete the whole project, the sequence or the result (after confirmation).
    Note: After deletion a file cannot be restored!
  • Edit a sequence
    Sequences that are uploaded on the Genomatix server can be edited via this option
  • Archive a project
    Projects can be downloaded as a compressed tar file (.tar.gz) via this option. A window will pop up where you can enter your email address to which a download link will be sent.
    NOTE: Gene2Promoter large scale and ElDorado results will not be archived. Furthermore, results containing Java Applet graphics won't contain them in the archived version.
• Jobs that are not yet completed are displayed above your results in the table "Your currently running Jobs" (only available on the Genomatix web server).
  • For each running job the following information is displayed: Job-ID, task name, sequence file used, date when the job was started.
  • The jobs can be killed by using the "Remove ..." link in the last column.

Control section

The following image shows the control section of the project management. Tasks like deletion and protection always refer to all selected sequences/results, i.e. all checked

• Create a new project:
  A window will pop up where you can enter the name of the new project. A new blue project folder will appear.
• Protect selected results and/or sequences from automatic deletion:
  After confirmation ALL selected sequences/results will be protected.
• Delete selected results and/or sequences:
  After confirmation ALL selected sequences/results will be deleted.
  Note: if you protected sequences/results before, they are only protected against automatic deletion; with this option they are deleted anyway and cannot be restored!
• Move selected results and/or sequences to:
  All selected sequences/results are moved to a different project, which is selected from a scroll down list.
• Copy selected sequences to:
  All selected sequences are copied to a different project, which is selected from a scroll down list.
• Sort all by:
  Sequences and results can be sorted by
  • name, ascending or descending
  • date, ascending or descending
  This option applies to ALL projects.
• Choose your default project:
  You can change the default project, i.e. the project where all newly uploaded sequences and newly generated results are automatically stored.
  The currently selected default project is also displayed on top of most Genomatix pages.