BatchKi User Manual

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User module

The user module in the Generic interface requires the following types of input data:

• A raw plate-reader data file representing either the reaction progress in enzyme assays, or single point (initial rate) assays.

  The plate-reader data file must be a ``plain text'' (ASCII) file, usually exported from the plate-reader control software.^4.1

  The ASCII plate-reader file should have one of the SoftMax formats (for example SoftMax ``Plate Format'' or ``Column Format''), with or without temperature readings included (ThermoMax). Alternately, the plate-reader file should have the BatchKi Universal format described in the separate Reference Manual.

• A spreadsheet file (for example, Excel spreadsheet) containing the plate layout. For an illustrative example, please examine the distributed example file [setup]/batchki/test-data/generic/layout.xls.

  The spreadsheet file should contain at least two grids of cells representing the wells on the given plate. For example, for a 96-well plate (8 rows, 12 columns) the spreadsheet will contain two $8\times12$ blocks of cells. In the first $8\times12$ block, we will have the concentrations of inhibitors; in the second $8\times12$ block, we will have the inhibitor labels.

With the above two types of data files in hand, we can proceed to submit the data for analysis by BatchKi. The user module in the Generic interface is best illustrated by way of an example.

Demonstration run

In the step-by-step instructions below, it is assumed that the BatchKi installation archive install-batchki.zip has been extracted in the directory [setup]. The extracted ZIP archive contains all required demonstration files.

1. Point a web browser to the BatchKi installation site, in this example http://www.biokin.com/batchki/.
2. Click on the link Data Submission Form
3. Click on the link Generic interactive interface
4. Under User Login, type the login name and password
5. From the main menu, select the radio button Compute inhibition constants from progress curves, then click on the Continue button.

   

6. From the drop down menu Settings, select Polynom (up to 2nd degree)
7. From the drop down menu Plate Format, select SoftMax
8. From the drop down menu Size/Rows, select 8
9. From the drop down menu Size/Cols, select 12

   

10. Click Submit button
11. Under the INHIBITOR heading, select CONCENTRATION ... uM (micromolar) from the drop down menu.
12. Under the ENZYME heading, select CONCENTRATION ... nM (nanomolar) from the drop down menu.
13. Under the SUBSTRATE heading, select CONCENTRATION ... uM (micromolar) from the drop down menu.
14. Open the test plate layout file in Excel:

    [setup]/batchki/test-data/generic/layout.xls

15. Highlight the eight rows and 12 columns under INHIBITOR CONCENTRATION (only the data, not the heading). Copy the data into the system clipboard (Ctrl+C).

    

16. Switch to BatchKi.
17. Paste the system clipboard (Ctrl+V) into the text area INHIBITOR CONCENTRATION.
18. Switch to the plate test plate layout file in Excel.
19. Highlight the eight rows and 12 columns under INHIBITOR I.D. (only the data, not the heading). Copy the data into the system clipboard (Ctrl+C).

    

20. Switch to BatchKi.
21. Paste the system clipboard (Ctrl+V) into the text area INHIBITOR I.D.

    

22. Under ENZYME CONCENTRATION, type or paste the single value 7
23. Under ENZYME I.D., type or paste the single value Prot-X
24. Under SUBSTRATE CONCENTRATION, type or paste the single value 500
25. Under SUBSTRATE I.D., type or paste the single value Pept-Y

    

26. Click Browse button next to the File label.
27. Navigate to the test data file: [setup]/batchki/test-data/generic/reader/plate-01.txt

    

28. Click Submit button. After approximately 2-3 seconds, the browser will display a page with the heading "BatchKi Results". Click on the link Administrator_..._index.html. This will open a new browser window.
29. Navigate in the output files freshly generated by BatchKi. Check to make sure that no error messages are displayed on the main output page.

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biokin.com/batchki/manual/user/html/node9.html
Petr Kuzmic | Jul 12 2008