Software designed by biologists for biologists

By Stacey Ryder

SEATTLE, July 17, 2006 — VizX Labs' GeneSifter® is a GeneChip-compatible™ software package that helps bench researchers generate and interpret gene expression patterns. The software, which combines validated statistics with numerous analysis options, was developed to help scientists better understand the underlying biology of their microarray experiments. VizX CEO J. Thomas Ranken recently spoke to Affymetrix about GeneSifter and its benefits for lab researchers.

Background

As the number of large-scale genetic studies expands—along with the number of scientists analyzing vast amounts of data—software providers such as VizX have begun to develop products intended specifically for the scientists doing the research, instead of biostatistics experts.

“If you look at data analysis products that existed five years ago, they were mainly marketed towards biostatistics and bioinformatics people, not to lab bench researchers,” said Ranken. “GeneSifter is a system designed by biologists for biologists. Good analysis packages should not require the user to have a statistician's knowledge of statistics. It's the lab bench researchers that we're trying to help.”

VizX designed GeneSifter to be as easy to use as possible so scientists can find insightful answers to specific biological questions, said Ranken. That means making sure that important features are very well developed, omitting unimportant features, and by utilizing a browser-based interface that is easier to use than typical technical software, he added.

“Because of a lack of available equipment and resources, many bench researchers employ experts to run the arrays and generate static gene lists on their behalf,” said Ranken. “However, because these gene lists are often not produced by biologists, they tend to offer more statistical insights than biological guidance.” For example, a statistician may identify the top 25 genes that might be relevant to them, whereas a biologist might be more interested in understanding the gene functions or pathways.

By examining the gene list as a whole, GeneSifter users can identify broad biological themes of importance. The sophisticated data management tools, analytical algorithms, and easy-to-interpret graphical analysis options help improve the quality and productivity in the experimental and decision-making processes, Ranken added.

Key Benefits

“GeneSifter helps researchers go beyond the statistical printout. We look at the analytical methods that researchers need and then we build them into GeneSifter,” said Ranken. A few of the features include:

• Tabular and graphical representations that are hot-linked to relevant information, including individual genes or descriptions of ontologies.
• Point-and-click navigation, so users can create and manage their own gene lists.
• A combination of common analytical microarray methods and graphical representation to help researchers identify the genes that contain enriched expression levels or those that may be statistically important.
• Automatic updates, so researchers stay up to date with recent data about genes of interest.
• A Web-based, open-source system that can be accessed from any Internet browser or operating system. The Web-based interface enables scientists to input and analyze data without having to know “R” scripting or programming.

GeneSifter customers have told VizX that the system takes less than two hours to learn. “Our customers become skilled at a sophisticated scientific analysis software system in less time than it takes most people to learn how to play a video game,” said Ranken.

“There will always be a Ph.D.on the other end of the line, if a customer needs it. Researchers feel more comfortable knowing the results have been replicated by our field support team.” — Thomas Ranken, CEO, VizX Labs

VizX takes the information from native Affymetrix files—commonly known as chip files or the raw probe files—and then loads it directly into GeneSifter. The software helps users generate gene lists showing every single gene that contains enriched levels and might be statistically important.

Users also have instant access to analytical algorithms, statistics, and information from more than a dozen annotation sources and other publicly available databases to analyze the active genes and compare them to sets of thousands of healthy genes.

This information helps them prioritize individual genes based on biological function and identify targets for further study.

In addition to its software, VizX Labs also offers peer-to-peer scientific support for experimental design and analysis, as well as additional technical training and support resources. “There will always be a Ph.D. on the other end of the line, if a customer needs it,” said Ranken. “Researchers feel more comfortable knowing the results have been replicated by our field support team. We do not normally deal with many software support issues, though, because the system doesn't require it.”

Pricing

VizX Labs' GeneSifter licenses are available in several competitively priced packages: the Lab Edition license with two simultaneous users, a full commercial license for a single seat, as well as multi-seat licenses that are priced depending on the number of seats and training. “When you're trying to target an actual bench researcher, you have to build a product that can be used effectively—and that can be afforded,” said Ranken.

More Information

GeneSifter is currently being used by researchers at about 175 different institutions in more than 12 countries. The product was recently honored with the Frost & Sullivan “Best Practices Award for Product Innovation” in the Bioinformatics in Drug Discovery category.

To test VizX Labs' GeneSifter with your own data, click here.

Learn more about these products or request to have an Affymetrix representative contact you.

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