Sample Ranking in ISPyB - what is it and how does it help my experiment?

 

 

The objective of the ISPyB Sample Ranking feature is to provide a way to Rank individual samples that have been screened and characterised by DNA/EDNA in order to select the best ones for Data Collection.

 

Sample_Ranking_00.png (Sample_Ranking_00)

 

Step by Step guide

 

  1. Log-in to ISPYB at http://ispyb.esrf.fr/ with your proposal login and password
  2. Go to the Session tab (by clicking on the "Data collection" menu)
  3. Select a Session ("View last session" or "View all sessions" menu) or 
  4. Search for data collections ("Search data collection" menu) by Sample name or Protein Acronym.
  5. Select the data collections (screening samples) you want to rank (note that only data collections with successful indexing will be selectable)
  6. Rank Samples by clicking on the "Rank" button. The ranking tab will be displayed.
     

    copy2_of_copy_of_Sample_Ranking_01.jpg (Sample_Ranking_01)
     

  7. Ranking tab. Selected samples are ranked according to ranking criteria: Ranking resolution, Exposure Time, Mosaicity, Number of spots, Number of images.
    • Each cell contains the #rank and the value of the criterion for the given sample
    • Last column gives an overall ranking of the sample based on weighted criteria
    • Change the weight of each criteria by clicking on the combo box of the criterion and selecting a new number (0: ignored, 10: highest). You'll need to click on the "Rank" button to process the new ranking parameters
    • Sort samples by any of the criteria by clicking on the sort icon just left to the criterion column name
    • View the Comparison Chart tab by ticking the sample box (first column) and clicking on the "Chart" button.
    • Export samples to DNA for Data Collection by ticking the sample box (first column) and clicking on the "Export" button".

    copy3_of_copy2_of_copy_of_Sample_Ranking_02.jpg (Sample_Ranking_02)
     
  8. Sample Ranking Comparison Chart tab. Criteria ranking values of each selected sample are displayed in a radar chart. A point of the curve near the center means a low ranking while near the border means a high ranking for the criterion.
    • Draw a Sample chart by ticking the Sample box in the list
    • Moving the mouse over a graph highlights the sample in the list
    • Submit the selected samples by clicking on the "Submit" button (it will go back to the previous page) or "Cancel" your modifications

    Sample_Ranking_04.jpg (Sample_Ranking_04)
     
  9. Export samples to DNA for Data Collect. An xml file containing the samples you have selected is generated. Save it on disk. Then, in DNA, you will be able to import this file using the "Import Rank project" feature.

    Sample_Ranking_02_1.jpg (Sample_Ranking_02_1)