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). Each experiment that has been recorded in Step 3 can have as many sets of experimental data linked to it 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 readings and the second column is the output data. Once captured, these data will appear in ProcessDB as part of the Experiments screen that was introduced in Step 3 (PRDB015), on the measurements tab.

In progress: Step by step instructions for capturing 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 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.
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.