Promoting interoperability and open standards for the life science market, Microsoft officials this week updated developers on the company’s guidelines for building service-oriented architectures and demonstrated some solutions that its software partners have developed in line with those recommendations.
At Microsoft’s annual Health & Life Sciences Developer Conference, held in Atlantic City, NJ, this week, Microsoft representatives explained that one such recommendation, the Connected Life Sciences Framework, or CLSF, introduced in June 2007, has only recently begun to attract developers and shared examples of several projects that have successfully used the approach.
Perhaps the most comprehensive such project to date is the Scientist Workbench, a knowledge-management platform for chemical and biological information developed jointly by Infosys and Microsoft that is currently in use at Pfizer. Microsoft is also working with other partners on projects based on the CLSF, including Thermo Fisher Scientific and Accelrys.
CLSF is a way of building and organizing life-science applications and software components to ensure interoperability between them, said Les Jordan, industry technology strategist in Microsoft’s Life Sciences Industry Unit.
As Jordan explained, unlike the clinical arena, in which standards are well-established for many types of data, such as the CDISC clinical data-interchange standard, there is no equivalent for the life sciences. “Right now the standard that companies are working toward and [the one] we are working on with them is Open XML,” which is an important part of CLSF, he said.
Jordan admits that the term “open standards” has not been widely associated with Microsoft. “Here is what I say, and in every presentation I get gasps when I say it: ‘Microsoft wants to play nice in the sandbox.”
In February Microsoft backed up that declaration by announcing “strategic changes in technology and business practices” that include promoting data portability and enhancing support for industry standards.
While Open XML does not reach data-level semantic interoperability, it does allow transport interoperability — a standardized mechanism for transporting data in a platform-independent fashion such that data can be pulled from different applications, he said. “We want to have the data from your laboratory equipment move over to Excel very seamlessly, without going through all sorts of transformations,” Jordan said.
“Companies can build to that framework,” said Rudy Potenzone, pharmaceutical industry technology strategist in Microsoft’s Enterprise and Partners Group. He said that the service-oriented architecture involves no licensing of software or other formalities, just adherence to the CLSF recommendations.
“When I say application interoperability, I don’t mean just Microsoft,” said Jordan, adding that the company defines interoperability in the context of CLSF as enabling communication between many pieces of equipment populating academic or industry laboratories from varying vendors and with different file output types. Through the CLSF, Microsoft is encouraging partners to build to a framework that allows application interoperability in this diverse lab landscape.
Redmond Spots Life Sciences
Microsoft has ramped up its involvement in the life sciences considerably in recent years through efforts such as the CLSF recommendations, as well as initiatives like its Bio-IT Alliance and internal-development projects within Microsoft Research geared toward basic research that will not have an immediate impact on the company’s business but are focused on a longer-term application horizon.
“In order to make Microsoft relevant in the life-sciences space, we have to talk the life sciences-language,” said Jordan.
“By and large the focus at Microsoft has been the base platform itself, making sure that Office works and the systems work,” said Potenzone. More recently, the company has recognized that it must also pay attention to how particular user groups work with its technology. “I can’t imagine a piece of scientific data that doesn’t spend some of its life inside a Microsoft project, especially Excel, Word, PowerPoint,” he said.
In that sense, explained Michael Naimoli, molecular biologist and director of Microsoft’s Life Sciences Industry Solutions group, the company’s life sciences unit members must “build a bridge between the product teams and our industry.”
When it was created eight years ago, the entire health and life-sciences group at Microsoft employed five people. Today it employs more than 600, Jordan said.
The conference’s goal was to speak to the company’s developer community in various organizations and, that way, to “get that community to embrace the ideas and the framework,” explained Naimoli.
“Here is what I say, and in every presentation I get gasps when I say it: ‘Microsoft wants to play nice in the sandbox.’”
To date, Microsoft has formed CLSF partnerships with several companies, including Thermo Fisher, Infosys, and Accelrys, with more solutions slated to emerge shortly, said Jordan.
Thermo Fisher is choosing service-oriented architecture and shifting away from proprietary programming languages to provide solutions for its instruments on the Microsoft .NET platform with software supporting Open XML.
Séamus Mac Conaonaigh, director of technology informatics at Thermo Fisher, said in a presentation at the conference that Microsoft is a “good bet,” particularly in light of Thermo’s size and broad product portfolio.
In the wake of the late 2006 merger between Thermo Electron and Fisher Scientific, many of the company’s products must be managed as legacy instruments, Mac Conaonaigh said. “It makes a lot of sense to consolidate on one platform and that platform is Microsoft .NET and the services associated with that.”
This concept, he said, stems from customers recounting their challenges: data located in unconnected and frequently incompatible systems across the organization, with a lack of integration among the devices in the lab and a variety of systems required for data integration, search, and analysis.
Mac Conaonaigh said that Thermo Fisher has found that some of Microsoft’s products help manage this situation. For example, the company’s SharePoint enterprise information portal “is extensible, with Thermo and others building on it, adding value,” he said.
Microsoft’s Jordan explained that scientists can let data flow directly from a Thermo Fisher instrument into SharePoint so that it can be shared across the organization. “Now the information is going through a web service, directly from the equipment, into a document library in SharePoint and you have access to that information,” he said.
In other partnerships, Irvine Calif.-based Neudesic released an electronic lab notebook in November 2007 built on the CLSF guidelines, while Accelrys this week announced a collaborative effort with Microsoft to support SharePoint Server as a publication platform for its applications (see briefs, this issue).
Giving Scientists a View
Perhaps the most comprehensive solution package created within the CLSF framework is Scientist Workbench, developed jointly by Infosys and Microsoft.
The system began as an Infosys software package in 2005 called Chemistry Workbench. The following year Infosys and Microsoft teamed up to build a solution for Pfizer that resulted in Biologist Workbench, a system tailored for the pharmaceutical firm.
Biologist Workbench is a toolbox built on Microsoft’s .NET 3.0 framework, Windows Presentation Foundation, Office SharePoint Portal Server, and SQL Server that allows researchers to query data in “new ways,” explained Anirban Ghosh, principal consultant at Infosys and a specialist for research informatics.
The tool allows biologists “to ask questions of chemical data and pharmacological data” in a way that covers “a larger use case perspective than what [existing] individuals tools could do,” he said.
“The biologists are trying to ask questions around data that the chemists typically have generated,” said Ghosh, noting that scientists studying target-based analysis, cell-signaling pathways, RNA-based silencing, or other emerging research areas often need to integrate, analyze, query, and visualize data from both the biological and chemical domains, sometimes from areas that are further away from their original experiments.
“The way to ask questions, slice and dice the questions, [and] make the query more intuitive” is what motivated the team working on Biologist Workbench, he said.
In a case study on the Pfizer project published by Microsoft, Rick Somes, Pfizer’s director of global screening and molecular informatics, said that the Biologist Workbench has helped the company’s researchers “collaboratively share research,” which is expected to help “shorten time-to-decision, streamline and enhance drug discovery, and lower cost.”
The Workbench draws on SharePoint, which provides enterprise-wide access to geographically distributed data repositories. “So people in two different geographies can see the data, they get alerts, and project feeds,” said Ghosh.
The system also relies on an “inference engine” that is applied across the information, said Ghosh. “It helps the community of scientists at the middle level of a pharma to orchestrate their thoughts in a more structured flow of events such that … any data available can be tracked better.”
After completing the Biologist Workbench project for Pfizer, Infosys further developed the system into the Scientist Workbench, which includes additional ways to help find information. For example, a compound name can be labeled with a SmartTags in a Word document so that a user can search public and internal sources contextually on that compound. Other facets of Scientist Workbench include the ability to integrate information from laboratory equipment or to visualize and analyze data using Microsoft products such as SilverLight and PerformancePoint.
Infosys is currently marketing Scientist Workbench as a customized service offering for a range of industries, though the current focus is in the life sciences, said Chuck McNamara, Microsoft regional alliance manager at Infosys.
Right now, Infosys is assisting epidemiologists at an undisclosed research institute who are seeking to share ideas and information for research and grant-writing. Scientist Workbench can help them to “ask questions in a collaborative fashion, re-use what others have done, re-visit what others have done in their perspective,” Ghosh said.
Microsoft on the Phone
Microsoft’s Naimoli said that the company sees an opportunity for its approach in the life science market, where organizations “are trying to collaborate outside the firewall as well as inside.” But he and other Microsoft officials acknowledged that it has taken some time for the company to establish bonds with life science customers.
For example, during the collaboration with Pfizer, there was a typical reaction at first: “‘Oh, Microsoft is calling. You don’t want to talk to the scientist, you want to talk to the IT guy,’ and they’d hand off the phone,” said Jordan. That has changed as Pfizer and other customers have realized that Microsoft is seeking to understand use cases, he said.
Potenzone said that a combination of factors is propelling this change in Microsoft. “It’s the collaboration side coupled with the explosion of data. It screams that IT is at least part of the solution.”
The CLSF-based solutions are “trying to take a step above and look across all of the types of information you know and give you that overview,” he said. A scientist can then look across the scope of an entire project and drill down into individual pieces of information, when needed.
Furthermore, as new data emerges, these solutions allow companies and scientists to return to older data and re-analyze it in light of new evidence.
It has taken a while for the developer community to warm up to the concept of the framework, but Microsoft officials cited existing partnerships based on CLSF as examples of ways that companies can manage their innovative process, an approach that they hope will spread throughout the life sciences.
Further information about CLSF is available here.