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Tips from the Club

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In the last issue of T³ Update, we introduced you to the Club Biomek User Forum, a web-based community of our Biomek users. In case you missed that article, check here for a brief FAQ about the site and to review some exciting tips.

In this issue, we explore three topics that are consistently of interest to the readers of the User Forum.

Click here for Beckman Coulter User Forums

Advanced Dataset Handling
Original Posting
In this thread, Doug Becker, software lead for the Biomek® 3.3 software, posted a user-contributed new Dataset Processing step. This handy step allows calculations using more than one data set (thus overcoming a limitation of the built-in Dataset Processing step). Doug also describes how to do advanced calculations inside expressions using simple-to-learn techniques. Because this step has a user interface similar to the built-in steps in the Biomek software, it is can be easily used by anyone familiar with the Biomek software.

This new step, which is really just a script step with a customized HTML front end, demonstrates the flexibility of the Biomek software. Standard users may find the Advanced Dataset Processing step useful as is; our most advanced users may wish to study the step to understand how it is put together, to serve as a template for creating their own customized steps.

Remapping Wells
Original Posting
This topic is so popular that it has been "pinned" to make it easy to find in the Software sub-forum. One of the most common questions that comes up when writing advanced Biomek applications is how to remap wells to accommodate a numbering scheme different from the standard one that the Biomek utilizes (numbering across from left to right, then down the rows). Although the Biomek software is locked into the SBS-standard numbering scheme as a purposeful design decision to ensure consistent data, data that feeds the Biomek can be converted by some simple script from other formats into the standard one.

While there are several solutions to the well remapping/transposing issue, the definitive solution was posted by Ernie Anderson earlier this year. Ernie was the software lead on the initial version of the Biomek software and remains active on the Club Biomek Forum today. The solution allows for the conversion of data from any of four different input numbering schemes into the style format the Biomek will recognize. He provides a script function that performs the conversion itself, as well as an example of how to read in a data file, apply the conversion and write the converted data out to a file in the proper format.

Prompting for Filenames at Runtime
Original Posting
Questions often arise about alternative ways to collect data from users during runtime. The Start Step provides a built-in method to prompt for variables at the start of the run, and is documented well in the Biomek software manual. However, there are times when users wish to construct advanced methods that can prompt for information during the course of the run, not necessarily at the start of the run. And frequently, the information to be collected is desired as a filename selected via traditional Windows browsing capability.

Fortunately, these scenarios have solutions within the Biomek software. In fact, there is an entire thread devoted to the "Runtime Filename Input" topic. A method is posted there that contains a user-contributed step that accomplishes the task. The step has a convenient user interface so that no scripting or other advanced knowledge is necessary to utilize the step. It allows for the entry of a default file to be used for the purpose of validating the method, and it allows the method author to specify the name of the variable that will hold the file name. The variable will then be available throughout the rest of the Biomek method, for use either in standard steps (like Transfer From File for example) or in script steps.

Prompting for Text at Runtime
Original Posting 1
Original Posting 2
For prompting for text input, there is a script command called "PromptUser" that allows the input of text. While it is a script step, it is easy to use and there are several examples of implementing it found on the Forum. Two of these are highlighted here, but you can also use the convenient search tool at the Forum and pull up other references to PromptUser.

These examples demonstrate how everyday users can make use of some of the underlying power of the Biomek software to accomplish even the most demanding applications. More importantly, it demonstrates the power of a dedicated, professional user community who help each other get the most out of their research efforts.

Not yet a member of the Club Biomek User Forum? Join today!

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For Research Use Only; not for use in diagnostic procedures.

For comments or questions about T³ Update, please contact the T³ Editor.

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