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When an experiment is performed on an instrument, two fundamental types of information become associated with that experiment. The most obvious information generated by the experiment is the raw data or set of measurements made by the instrument. The less obvious, but equally important, information associated with the experiment is how the experiment was performed (i.e., the set of parameters which specify how to do this experiment). These parameters, collectively called an experiment specification, must be configured ahead of time (by you) so that the AfterMath software (and the instrument being controlled by AfterMath) can perform the desired experiment.

Once the experiment is completed, it is very important to bind together both the raw data and parameters which describe how the data was generated. This binding of experimental data with an experimental specification is strictly enforced by the AfterMath software.

When you look into an AfterMath archive which contains the results from a previously completed experiment, this strict binding is very apparent. In the example to the left, an experiment (represented graphically as a flask) contains two other items. The first item is a data table (named “results”) containing the measurements made during the experiment. The second item is an experiment specification (named “specification”) which is a record of the parameters used to make the measurements.

Unlike most other items found in an archive, AfterMath will not permit you to delete, move, or otherwise separate the experiment data from the experiment specification. The specification is “frozen” in a read-only state so that you do not accidently change the record of how the experiment was performed. However, AfterMath will permit you to make an “editable” copy of the experiment specification and store it somewhere else in the archive. The purpose of this editable specification is to give you an easy way to repeat the experiment using the same set of parameters, or if you wish, to make some modifications to the parameters in order to perform a slightly different, but related, experiment.

An reasonably sized archive is likely to contain many different experiment specifications. Some of these experiment specifications are likely to be bound to an experiment (“frozen”) while others are not bound to any experiment (“editable”). The latter might be humorously referred to as free range specifications as they are not confined to any one location in the archive and can be moved freely to any folder you wish.

In the example archive shown below, there are three freely “editable” specifications (located in the folder called “A Few of My Favorite Expts”), and there is one specification that is “frozen” because it is bound to the record of a previously completed experiment.

Editable specifications are usually the first kind of specification that you will create in an archive. When you are ready to configure a new experiment, you will first create a new “editable” specification which describes the experiment at some location in your archive. Then, you will issue a command to the instrument to perform the experiment. When the experiment is completed, AfterMath will automatically store the experiment results in the same location in the archive. AfterMath automatically makes a “frozen” copy of the specification and binds it to the experiment results.

Editable specifications are quite useful in those situations where you perform experiments with the same parameters over and over again. You can use an editable specification to store these parameters, and then reuse the same specification repeatedly to perform a series of identical experiments.

An editable experiment specification can be created in an archive by right-clicking on the folder in which you would like to place the specification. Choose the “New»Experiment” option from the popup menu (see below), and then select the kind of experiment you wish to configure. In the example below, a new specification for a cyclic voltammetry experiment is created.

Once the new specification has been created, you may edit the parameters in the main viewing area. Parameters which are shaded in yellow are mandatory. If you provide an invalid value for a parameter, it will be shaded in pink. If you would like a set of default parameters to be provided by the software, click on the “I Feel Lucky” button.

The “Basic” tab on an experiment specification contains those parameters which are most often needed. The other tabs generally hold more advanced options which are not as frequently changed.

Within the tree-like structure of an archive, you are free to create folders in which to organize your data. Each folder is represented by the symbol shown to the left. You may also create folders within folders so that your archive has a multi-level internal structure.

A folder is created with a right-click on an existing folder or archive in the “tree control” on the left side of the screen (see figure below). When you right-click on a folder or archive, a popup menu appears. Select the “New  Folder” option from the popup menu.

A new folder is always created on the level just below the folder or archive on which you right-clicked. Once you have created a folder, you may move it to any location you wish.

As is the case with most other items in an archive, a folder may be moved, copied, or duplicated almost anywhere in the archive using standard cut, copy, and paste methods or using drag-n-drop mouse actions.

You can also copy folders from one archive to another archive. When you move or copy a folder, the folder plus its entire contents are moved or copied.

You may delete a folder by simply selecting it in the “tree control” and pressing the “Delete” key on your computer's keyboard. You will receive one warning message before the folder is deleted (see below).

Most of the individual items in an archive have a printable representation suitable for sending to a hard copy printer. When you print an individual item in this manner, you are only able to print one item per page. Sometimes, it is desirable to print more than one item per page. For example, you may wish to put a plot of some experimental results at the top of a page and also include a list of the experimental parameters at the bottom of the same page.

When you want to print more than one item per page, you need to create a page layout. Proper page layout preoccupies the mind of many a graphics designer, but most scientists have fairly simple needs when it comes to reporting results in hard copy form. AfterMath lets you configure a grid-based layout using one of several standard international page sizes.

Creating an AfterMath layout involves choosing a paper size, deciding how many grid elements are needed on the page, and then literally dragging the items from the archive on to the various grid elements. This last step is performed using drag-n-drop mouse actions.

Step 1

The first step in creating a new layout is to decide where in the archive to put the layout. In general, it is good practice to copy all of the items that will appear on a layout into the same folder and then create a new layout item in that very same folder. In the example below, several items have been copied into a folder called “Acid Analysis Testing Folder”. A new layout is created in the folder by right-clicking on the folder and choosing “New » Layout” from the popup menu.

Step 2

By default, a new (empty) layout has only one grid element which consumes the entire page. You can change the number of grid elements (and the paper size) by right-clicking on the layout and choosing the “Properties” option.

On the “Layout Properties” box, there are a variety of grid configurations available, allowing you to place anywhere from one to nine different items on the page.

Step 3

After you have selected the proper grid configuration, then simply drag-n-drop items from the archive on to the layout. You may drag any item from the “tree control” on the left side of the screen over to any of the grid locations.

Once you have created a layout, you can move it to any location within the same archive that you wish. But it is usually a good idea to keep it in the same folder as the items which you have placed on the layout (see note below).

All scientists need to write down notes as they are performing laboratory experiments. While most of these notes should eventually find their way into a traditional laboratory notebook, it is often helpful to add notes to computer-based data files as you are acquiring data from an instrument. AfterMath allows you to add one or more notes, like the one shown in the figure below, to any item in an archive. AfterMath notes support multiple fonts, styles, and colors and many text formatting options which are important to scientists, such as superscripts and subscripts.

A note may be attached to any item in the archive. Simply right-click on any existing item in the archive in the “tree control” on the left side of the screen (see figure below). When you right-click on the item, a popup menu appears. Select the “New » Note” option from the popup menu.

The action described above will attach a new note to the item you selected. Once the new note is created, you may edit it in the Main Viewing Area on the right side of the screen (see figure below).