Molecular Biology Research on NetBeans

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Molecular Biology Research on NetBeans

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I am Bob Rutledge, a Canadian government research scientist working on the molecular biology of somatic embryogenesis in conifers. During my early work on gene expression analysis, I developed the ability to conduct quantitative real time polymerase chain reaction (qPCR) using sigmoidal mathematics, which led to the derivation of two novel functions that evolved into a data processing method I called "Linear regression of efficiency" (LRE). Unfortunately, LRE analysis proved to be too labour intensive when conducted manually using Excel, which was the platform upon which LRE analysis was developed. It was also apparent that without an automated capability, acceptance of LRE as an alternative to current qPCR methods would most certainly be limited, at least in the short term, but this is another story.

After several failed attempts over about 18 months to establish a partner for programming LRE analysis, it occurred to me that it might be possible to do the coding myself, based on the extensive online resources for learning Java, and of course, the availability of the NetBeans IDE. This lead to development of a small Java program, which was released as a supplement to my first publication introducing LRE.

After some failed attempts to develop a full fledged desktop program based purely on Java Swing, it became obvious that the NetBeans Platform could provide the required infrastructure, despite the intimidating prospect of learning how to use it, particularly in view of my limited expertise. Due in part to the resources that have been provided, I was sufficiently successful to produce LRE Analyzer, an open source program that we now routinely use for all of our qPCR work:

As might be expected, many aspects of the program are crudely implemented, but in view of the technical complexity involved, it is a testament to the power of the NetBeans Platform to provide capabilities that allow even a novice to be (reasonably) successful.

Anyway, all of this would not have been possible without these online resources, and I am are thus very grateful for the efforts of the NetBeans team, along with Sun's decision to provide free access to both Java and NetBeans, and of course, to Oracle's decision to continue support for these resources.


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