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This tutorial explain how to access data in openBIS instance for DynamiX project.

Access

Click http://dynamix.vital-it.ch/openbis to login into openBIS.
login: admin
password: ask Sebastian Maerkl <sebastian dot maerkl at gmail.com>

Browsing the chips

1. Click on the Browse chips link
2. Choose the chip. All chips have metadata, but for now only chip CHIP-EXP1 has also images uploaded.

3. Choose "Feature Category" from the "Choose heatmap kind" dropdown list:

4. Hold the mouse cursor over the well to see the category and other features of the chamber:

5. Click on the chamber to see the image series.
You can also click on the yORF to see all the metadata fetched from the yeastgenome.org database.

Finding the chamber

You can find a chamber by specifying its properties or the ORF metadata.

  • Click on the Search (http://dynamix.vital-it.ch/openbis/#action=WELL_SEARCH&experimentPermId=20101029155718464-4&isExactSearch=true&types=ORF&items=*) link.
    It may take a moment. You will see the first 50 chambers from all the chambers which have been ever measured.
  • Click on the "Filters" button at the bottom of the page. Now you can filter the chambers by:
    • chip name (corresponds to experiment number)
    • chamber quality
    • intensity change
    • localization change
    • ORF name ("Content" field), gene name ("Standard name") or its aliases. You can select several ORFs by separating their names with a space.
    • and much more

On the screenshot below you can see chambers where intensity was up and quality was good:

Settings

  • you can click on the column to sort all the rows by its content
  • after finding an interesting chamber click on the image to see the movie.
  • if you want to change the available filters click on the "Settings" button and select these columns which you want to filter in the second "Has Filter?" column.
  • you can change which columns are visible by clicking on "Settings" button and selecting the columns in the first "Visible?" column.

Metadata

Click on the Download all metadata link to fetch all the chips metadata.

You can also click on the "Export" button in any table in openBIS to save the table content in the file. The file can be opened later in Excel.

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