Method Editor Prototype User Manual
Introduction
The tasks, devices and software involved in planning and executing a high-throughput version of a trypsin-based assay were analyzed at CELISCA. The analyses were used to generate design recommendations for improving the existing SAMI interfaces that are used for method programming. Based on the interface design recommendations, a prototype for a new method editor was developed.
The existing SAMI method editor is device-oriented, that is, programming a method involves dragging device icons to a central workspace and connecting them to indicate movements of microplates among the devices. However, a process-oriented approach to method programming may be more intuitive and easier to work with. A process-oriented system requires the user to first describe the testing procedure, rather than the devices used to run it.
The new method editor prototype developed by NC State University uses a process-oriented approach. To enter a new method, simply type in a sequence of instructions in your own words (e.g., “...Remove 1 family of test microplates from incubator and label using the barcoder...”) in the Assay Procedure window. As you type, keywords in the text representing objects such as devices, equipment or materials will become hyperlinks. Red hyperlinks represent objects for which the system needs further information in order to operate (for example, what kind of label should the barcoder apply?). Yellow hyperlinks represent partially defined objects for which the system needs some information, but even if this information is not provided, the method will run, as the system will use its default values. Green hyperlinks represent objects for which the system has all the necessary information – they are fully defined. Click on red and yellow hyperlinks to configure the different objects; after you do so, they will become green. As you type in text, a flow chart will be created in the Process Flow Chart window, documenting the different steps from a microplate viewpoint. The numbers of devices and amounts of materials will also be updated in the Tools and Ingredients windows of the new prototype interface.
The new method editor is presented in more detail below. To experiment with its different features, please open the prototype (with Internet Explorer) located at
http://people.engr.ncsu.edu/dbkaber/NSF_ITR/sami2/sami_method_editor.html and type “Remove 1 family of test microplates from incubator and label using the barcoder.” into the Assay Procedure window. The features described below will then be made accessible.
Features Guide
Assay Name field – Enter the assay name.
Assay Procedure window – Enter the assay procedure, sequentially, in your own language. As you type, keywords in the text representing objects such as devices, equipment or materials will become hyperlinks. Red hyperlinks represent objects for which the system needs further information in order to operate. Yellow hyperlinks represent partially defined objects for which the system needs some information. Green hyperlinks represent objects for which the system has all the necessary information. Click on red and yellow hyperlinks to configure the different objects; after you do so, they will become green.
Process Flow Chart window – As you enter a method into the Assay Procedure window, a flow chart will be created, documenting the method from the perspective of a microplate. Different box colors represent different types of microplates; boxes that have two colors represent pipetting from one type of microplate to another. Red and yellow hyperlinks will appear in this window as well as in the Assay Procedure window, and will function similarly.
Tools window – This window reflects the number of times each device, microplate type, or pipetting tip type is used in the method. Red and yellow hyperlinks will appear in this window as well as in the Assay Procedure window, and will function similarly. New devices can be added to the tools list using the Add Device... button. Select a device type, then the device manufacturer, and finally its model. Unused devices can be removed using the Delete Device... button, by simply checking the device to be removed. Microplates and pipetting tips can be added or removed in a similar manner.
Ingredients window – This window displays the “ingredients” used in the assay – stock solutions, reagents and test compounds. Similar to the Tools window, items can be added to or removed from the ingredients list.
Barcoder action/configuration dialog – Clicking on any barcoder hyperlink (in the Assay Procedure, Process Flow Chart, or Tools windows) will open this dialog. If your process requires applying a new barcode to microplates, the Print and Apply tab will be active; if scanning an existing barcode is necessary, the Read tab will be active. In the Print and Apply tab, click on the rotate icon at the bottom-right corner of the microplate image to rotate the microplate to the side to which you’d like to apply a barcode label. Click on the type of label to apply (indexed label, label from file, etc.), then click on the microplate grid in the desired label location. A dialog box will open to let you set the label content. After configuring the label, you can change other barcoder settings at the bottom of this dialog. Click Apply to save your settings and return to the main method editor screen.
Incubator action/configuration dialog – Clicking on any incubator hyperlink (in the Assay Procedure, Process Flow Chart, or Tools windows) will open this dialog. Here, you can set minimum and maximum incubation times, the temperature and CO2 level in the incubator, and whether door, gate and fan heating should be turned on or off. Click Apply to save your settings and return to the main method editor screen.
Microplate dialog – If the method you entered in the assay procedure window does not specify which type of microplate to use, the microplates hyperlink will be yellow, meaning that the default microplate will be used unless otherwise specified. Clicking on this hyperlink will allow you to select a specific type of microplate. Click OK to save your settings and return to the main method editor screen.