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Tool for Processing and Displaying Genomics Data in Spreadsheets

ChromaBlast is a computer program that facilitates and accelerates processing and display of data by use of Microsoft Excel or other spreadsheet software that affords similar capabilities. The development of ChromaBlast was prompted by a need for improved means of analyzing and reviewing massive data sets produced in genomics and microarray-based gene-expression experiments. ChromaBlast is also generally applicable to other data sets that are amenable to spreadsheet representation.

Heretofore, analysis of such data has been facilitated by costly integrated software packages. Often, those packages offer no spreadsheet functionality and little or no other functionality for reduction or manipulation of data. As a result, a researcher must use spreadsheet software, then export the data to analysis software. After each run of the analysis software, the data must be reformatted or reduced in the spreadsheet. The process as described thus far must be repeated until the final set of data is appropriately formatted for the analysis package.

ChromaBlast is one component of a suite of software tools, called "BioTools.XLA," designed to enable the use of spreadsheet software to perform data reduction or basic analysis without having to manually switch back and forth between the spreadsheet software and the analysis software. ChromaBlast can be in stalled alone or as part of the suite. ChromaBlast normalizes columnar data, sorts the data into range bins selectable by the user, develops a color heat map from the data (see figure), and puts out the heat map and the bin assortment for review. By use of intrinsic tools in the spreadsheet software, output data can be filtered and sorted to emphasize data patterns and thereby facilitate rapid review of the data.

ChromaBlast is coded in Visual Basic for Applications (VBA) — a programming language designed to connect the macroinstruction programming functions of Excel with relatively sophisticated manual coding in a development environment. Preliminary macroinstructions (defined by keystrokes and program functions recorded during use of Excel) can be used to quickly construct a template for a specific piece of work. The macroinstruction record then serves as a conceptual framework for implementation of generalizations, functional options, and input from the user. Within VBA, it is also possible to add a multitude of functions that are not accessible in the macroinstruction-recording process. Thus, the programmer can quickly construct a template by use of macroinstructions, then add functionality and usability inside the VBA environment. VBA can also be used by itself to develop code from the beginning, as can any typical programming language.

This work was done by Barry N. Ford, Yimin Shei, and Stephen Bjarnason of Defence Research and Development Canada, and Catharine Richardson of Webgenii Consulting.

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Topics:
Computer software and hardware Data management Medical, health and wellness Medical, health, and wellness Research and development Software Technical review
This Brief includes a Technical Support Package (TSP).
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Tool for Processing and Displaying Genomics Data in Spreadsheets

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    Defense Tech Briefs Magazine

    This article first appeared in the October, 2008 issue of Defense Tech Briefs Magazine (Vol. 2 No. 5).

    Read more articles from the archives here.

    Overview

    The document titled "ChromaBlast - a Data Visualization Tool" is a technical memorandum published by Defence R&D Canada - Suffield in June 2006. It addresses the challenges faced by researchers in the field of biology, particularly in managing and analyzing the vast amounts of numerical data generated by experimental systems.

    As biological research increasingly relies on large datasets, the need for effective data analysis tools has become paramount. The document highlights that while integrated software packages can handle large-scale data analysis, they often lack essential data reduction and manipulation functionalities, such as those found in basic spreadsheet applications. This limitation forces researchers to frequently switch between different software tools, complicating the data analysis process.

    To address these challenges, the authors have developed ChromaBlast, a set of analysis tools designed to work within Microsoft Excel. ChromaBlast enhances the capabilities of Excel by providing features that allow users to normalize columnar data, sort it into user-selectable bins, and create color heat maps for visual representation. This functionality enables researchers to filter and sort output data effectively, facilitating rapid data review and pattern recognition.

    The document outlines the key features of ChromaBlast, emphasizing its ability to streamline the data analysis workflow. By integrating these tools into a familiar spreadsheet environment, researchers can perform data reduction and basic analysis without the need to constantly reformat data or switch between software applications. This not only saves time but also reduces the potential for errors during data handling.

    Additionally, the document includes a section on keywords and descriptors that characterize the content, such as "microarray," "genomic fingerprint," and "data analysis," which are relevant to the tool's application in biological research. The memorandum is classified as unclassified, indicating that it is accessible for unlimited distribution, particularly to defense departments and contractors.

    In summary, the document presents ChromaBlast as a valuable tool for researchers in biology, aiming to simplify and enhance the data analysis process by leveraging the capabilities of Excel. By providing essential functionalities within a widely used software platform, ChromaBlast addresses the critical need for efficient data management in the face of growing experimental data volumes.

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