Skip to main content
Premium Trial:

Request an Annual Quote

In PathwayPrism s Latest Iteration, BioAnalytics Group Takes Over Development from BioSoftware


PathwayPrism, one of the first pathway-analysis software products to hit the market, has had a tangled history over the last few years, but now it's back in the hands of one of its original developers, who believes that there is still plenty of opportunity for the technology.

Scott Lett, CEO of the BioAnalytics Group, told BioInform this week that his firm is now developing a new version of PathwayPrism, which he helped develop at Physiome Sciences before the company was acquired by Predix Pharmaceuticals in 2003 [BioInform 09-01-03].

The new version of the pathway-modeling software, called BioPathwise, is just entering beta testing and is scheduled to be launched later this year. Joanne Gere, launch consultant at the BioAnalytics Group, said that the company is seeking partners in the beta program who can use the software in different parts of the pharmaceutical "food chain" — from target discovery through to product development and even post-market surveillance.

PathwayPrism was originally launched in 2001 — well before the pathway informatics market took off and competing products from Ingenuity Systems, Ariadne, GeneGo, and others arrived on the scene to meet growing demand.

"Our strategy before was not to develop our own software in this space … So there was a lot of soul searching in the decision that it wasn't going to happen unless we did it."

Soon after Physiome was acquired, two firms founded by former Physiome employees — the BioAnalytics Group and BioSoftware Systems — licensed the rights to PathwayPrism and other technology for further development. The BioAnalytics Group incorporated components of several Physiome software products into its services offering, called Model-Based Assays, which simulates biological systems within the context of experimental protocols [BioInform 11-17-03]. BioSoftware Systems, meanwhile, set out to resell PathwayPrism as a standalone software product under the name of BioPathway Explorer [BioInform 07-05-04].

The two firms maintained a close relationship and signed an agreement in 2004 under which BioPathway Explorer would serve as the front end to the BioAnalytics Group's Model-Based Assays offering.

But BioSoftware Systems was forced to cease operations last year, which left the BioAnalytics Group high and dry. "That left us needing to figure out what we were going to do in the future for pathway modeling solutions," Lett said. "So we did a big review of the state of the art and all the commercial and academic products that were out there, and we decided that there wasn't anything out there that had become competitive with PathwayPrism."

As a result, Lett said, even though the BioAnalytics Group was originally founded with the intention of avoiding the shrink-wrapped software market, "We decided that we were going to develop and release a product in that area based on the PathwayPrism technology," Lett said.

"Our strategy before was not to develop our own software in this space, and I was really hoping to find that somebody had solved that problem," he said. "So there was a lot of soul searching in the decision that it wasn't going to happen unless we did it."

Last week, the company announced that it had hired Ned Haubein as senior scientist to lead development of BioPathwise. Haubein was a developer at Physiome and chief scientist at BioSoftware Systems, and had been working as a contractor at the BioAnalytics Group after BioSoftware Systems closed.

Lett said that the beta program for BioPathwise is just getting underway, but the software is already being used by researchers in the PRIME (Program for Research on Immune Modeling and Experimentation) initiative, a $17 million project funded by the National Institute of Allergy and Infectious Disease and led by the Mt. Sinai School of Medicine.

The goal of the project, which also involves researchers from Princeton University and Ohio State University, is to develop models of human dendritic cell-signaling response to pathogenic viruses.

Lett said that some former PathwayPrism customers have been volunteering to be part of the beta program for BioPathwise. "A lot of the people who have been customers of some of the other commercial products out there have contacted us saying that they've never seen anything that really competed with what PathwayPrism was before," he said.

PathwayPrism's history in the marketplace was a big factor in the BioAnalytics Group's decision to enter the increasingly crowded pathway software sector, Lett said. "If we were completely new in trying to figure out new technology in this space, there would be a 100-percent chance that I wouldn't want to enter into it, but in some ways we have a head start in terms of the marketing," he said. "People already know a lot about what PathwayPrism was. And even though they've been using other products over the last couple of years, they've been comparing it to what that was before."

In addition, because BioPathwise, like PathwayPrism, combines pathway analysis with simulation, Lett said that it is complementary to many other tools in the market, which are limited to "static" pathway representations.

One drawback of most pathway-analysis tools, he said, "is that your data doesn't change how it's connected — it doesn't tell you whether a pathway in diabetes is connected to a pathway in cancer." In addition, he said, "tools like Ingenuity are beautiful and can give you a head start, but if you're an expert on what's known about those pathways already, and you're trying to change them, then the tools that are static and have a static representation of pathways really aren't going to help you at all."

The Road to Diagnostics

The BioAnalytics Group isn't putting all of its eggs in the BioPathwise basket, however. Last year, the company entered into a collaboration with Ventana Medical Systems in which it is developing image-extraction and image-analysis software for use with Ventana's next-generation tissue-analysis platform.

Ventana is developing an assay platform that uses nanocrystals to study multiple analytes in single cells. "What that has raised is additional complexity of extracting data, of compiling data, and of reporting the data," said Gary Pestano, director of discovery at Ventana.

The BioAnalytics Group's software has "really allowed Ventana to access the world of bioinformatics," Pestano told BioInform. "It's moving us from single analytes and analysis on single slides into [higher]-throughput, more complex data analysis, and we see this relationship as a key one."

In the short term, Pestano said, Ventana will target this new analysis system to the research market, but the long-term goal is to move it into the clinical market. He stressed, however, that the system, which combines the software with the instrument platform, is "is not near a product yet."

Eventually, though, "the two will be tied together so that the software for data analysis ties to a certain multiplex panel of diagnostic utility," he said.

In December, Ventana presented some early results from the collaboration at the San Antonio Breast Cancer Symposium. Company scientists discussed how they had combined computer modeling with immunohistochemistry data from 147 patients to predict likely patient outcomes after treatment with Herceptin.

Lett said that in both the PRIME and the Ventana collaborations, the BioAnalytics Group is working closely with laboratory scientists — a strategy that he described as key to overcoming the "rate-limiting" factor in the widespread adoption of simulation software.

The target market for most modeling packages "has always been these quantitative engineers who want to do modeling, and the target has rarely been the people who are spending many millions of dollars collecting data and are having trouble interpreting it," he said.

"When we were with Physiome Sciences, we were pretty much pushing this combination of pathway diagrams and computational modeling as a way to reach across that gap between the physical scientists who do more of the mathematical stuff and the biological scientists," Lett said. "Now, in the intervening years since Physiome stopped doing that, a number of products have come out that have tried to fill that same gap that was left by Physiome."

While acknowledging the highly competitive nature of the pathway informatics market, Lett said that the large number of players in the space today only serves as validation of Physiome's technology. "One of the areas of growth [in the bioinformatics market] has been in this pathway and modeling area, and a lot of nice products are coming out, a lot of good ideas," he said. "So what that says is that we were on the right track back then, and just ahead of where the market was."

— Bernadette Toner ([email protected])

Filed under

The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.