Step 4

Collect Your Experimental Data

After completing Step 3, describing the experimental protocol in ProcessDB, you are now ready to enter experimental data into the program, so that ultimately you will be able to compare your hypothesis quantitatively with your experimental data (Steps 5 and 6). Some users, especially those on Experimental Teams, will want to enter experimental data first. That's fine too. Each experiment can be linked to as many measurements and experimental data sets as needed. Here in Step 4 you will learn how to import data from an Excel file into ProcessDB, or to manually insert data. Both formats will consist of two columns where the first column is the time the datum was collected and the second column is the data value.

Detailed step-by-step instructions for entering or uploading experimental data into ProcessDB

1. Everything ProcessDB needs to know about an experiment can easily be entered in an Experiment file.
2. There are two kinds of information you need to enter: experimental protocols (see Step 3), and experimental data.
3. You can enter either protocols or data first, or you can work on both at the same time. Different users have different preferences. This page explains how to enter experimental data.
4. If you have already created an Experiment file, open it by double-clicking it in the Experiments tab of the database pane. This will allow you to pick up where you left off last time you worked with this Experiment.
5. If you are starting a new experiment, look closely at the Experiments tab of the ProcessDB database pane. Just below the tab is a toolbar with three tools:
   1. New Experiment tool. The icon is a blue lab notebook with a + in the upper right of the icon.
   2. Delete Experiment tool. The icon is an X.
   3. Search Box. Used to search through your entire list of experiments to find the one you want.
6. Click the New Experiment icon.
7. Enter a descriptive name for your experiment in the dialog that appears. The name should be chosen so you and your colleagues will recognize this experiment in a list of experiments. An example might be "Subject ID Meal study - control"
8. Click OK
9. Your Experiment file will be created and displayed so that you can begin to work with it. Notice your experiment is also highlighted in the Experiments tab of the database pane.
10. Three items of information are filled in automatically
    1. Experiment ID. This is a unique number assigned to this experiment. Many of us find that the easiest way to search for a particular Experiment is to write its Experiment ID in our lab notebook and enter it in the Search box.
    2. Name. This is the name you entered in the dialog box. You can always edit this name by double-clicking it.
    3. Date. This is the date you created the Experiment file.
11. The Description field defaults to {Unspecified}. You can double-click to edit this field with a short description.
12. If you want to annotate this experiment with more detailed notes, you can right click the Experiment in the Experiments tab of the database pane and select Experiment Notes. A Notes window appears.
    1. Enter any text you find useful and click OK.
    2. Some items that different experimental biologists like to enter here are
       1. Date the experimental data were collected
       2. Names of spreadsheets or other data files connected with this experiment
       3. Cross-references to pages of your lab notebook
       4. Textual description of your experimental protocol (What?, Where?, How much?, and When?)
    3. Notes are not processed by ProcessDB; they are for your convenience only.
    4. Click OK to close your Experiment Notes
    5. If you entered text, in Description or Experiment Notes, you should save it to the ProcessDB database by clicking File/Save on the main ProcessDB Menu or the Save icon on the main ProcessDB toolbar at the top of the screen.
    6. Click Yes to verify. A progress bar will show your information being saved to the ProcessDB server.
13. Below the Description field in your Experiment file you will see four tabs:
    1. State protocols
    2. Process protocols
    3. Tracer protocols
    4. Experimental measurements and data
14. Click the Experimental measurements and data tab
15. The tab will open showing three areas. You will work with these areas in order:
    1. Experimental measurements made during this experiment
    2. Data Sets
    3. Experimental Data
16. Experimental measurements are the names of the variables you measured in this experiment. Examples might be "plasma insulin" or "cytosolic cAMP" or "NEFA palmitate d31 (umol/kgBW)" or "Golgi fluorescence", or "membrane potential (mV)." Some of us like to include measurement units in the measurement name. This helps the modeling team when they need to link the measurements to the model variables. ProcessDB can accommodate as many measurements as you have. After you have created a measurement name it can be edited by double clicking it in the Experimental Measurements panel.
17. Data Sets are the names of specific instances of a measurement. They identify the subject, or the animal, or the dish of cells. Examples might be "Subject ID - control", or "Mean data n=12 - during exercise", or "Fig.4 PMID", or "squid giant axon 1DEC1951", or "HeLa cells 01JUN2046"
18. Experimental Data are (time, value) pairs like 10 1.23, or -1 0.987 or 0 1.00. Use the time units (e.g. seconds, minutes, hours, etc.) that you want to see on output graphs.
19. At the bottom of the "Experimental measurements made during this experiment" panel you will see a + icon and a - icon.
20. Click the + icon to add a measurement to your experiment.
21. Click the dropdown list labeled "Measurement:"
    1. You can scroll through the alphabetical list to see if the measurement you want has been created previously. If so, select it and click OK.
    2. If you don't see exactly what you want, go back to the top of the list and select "Add new measurement".
    3. Enter the measurement name you want (with measurement units if desired)(recommended) and click OK. Click OK again and your new measurement name will be added to your experiment with its own unique ID.
22. Click the measurement name for which you want to enter or upload experimental data. The measurement will be highlighted (white text on blue background).
23. Click the + icon in the Data Sets panel. A new data set row appears.
24. Double click the Data set name field in that row. The field turns white and is ready for you to enter the name of the data set you are going to enter or upload.
25. Enter your data set name. See examples above at point 17.
26. When you finish typing the data set name hit Enter on your keyboard. The Data set name field will return to blue with white text, indicating that it is selected and ready for you to enter or upload numerical data.
27. There are two ways to enter numerical data
    1. Manually by clicking the + icon at the bottom of the Experimental Data panel (useful for entering a few points)
    2. Automatically by clicking "Import..." at the bottom of the Experimental Data panel
28. Usually you will be importing from an Excel file
    1. Click "Import..." at the bottom of the Experimental Data panel. The Import from Excel dialog appears.
    2. Click the "Browse" button to select your Excel data file on your computer. Click OK.
    3. Click the "Select..." button. The Select Region dialog appears. You should recognize your spreadsheet, including its named tabs.
    4. In this dialog select (by dragging) the block of cells in your spreadsheet that includes the data you want to upload for this Data set. Usually time will be in the first column you select and the data you want to upload will be in the last column you select. Be sure you get all the rows (all the time points) you want in your selected region. You only need the numerical data, not the column headings.
    5. Click OK. The selected sheet name and region are automatically entered in your Import from Excel dialog.
    6. By default, ProcessDB assumes the first column you selected is the Time Point column, and the last column you selected is the experimental data Value column. If not you can edit the columns by double clicking the column identifier letters. Non-adjacent columns are selected the same way: drag over a block of cells from the first time point to the last data value. By default ProcessDB will treat the first column you select as time and the last column as data value. Only two columns will be imported; the intervening columns are ignored. Of course, you can import any of those intervening columns with another Import.
    7. Click OK. Your data will be uploaded.
29. The Data Import Results message will tell you how many rows of data were imported, and the time value pairs will be displayed in the Experimental Data panel of your Experiment.
30. Click File/Save or the Save icon on the Main ProcessDB toolbar to save your work to the ProcessDB database.
31. Click OK and you are ready to go back and add your next Measurement name by clicking + at the bottom of the "Experimental measurements made during this experiment" panel.