Microsoft Server Product PortfolioCustomer Solution Case Study

Epilepsy Study Chooses Microsoft for EDC, Global Collaboration, and Data Management

OverviewCountry or Region: United StatesIndustry: Public sector—Life sciences

Customer ProfileThe University of California at San Francisco is dedicated to advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care. It has 10,000 employees.

Business SituationThe university needed an unusually large and sophisticated technology platform to support hundreds of researchers at more than 26 centers around the world, while minimizing the burden on the informatics staff.

SolutionProject directors chose to base their public website, intranet portal, applications, and databases on Microsoft technologies from end to end.

Benefits Speeds development by 50

percent Provides exceptional ease of use

“This is such an advance for the field of clinical research informatics that we’re looking at making components of the architecture available to others in the research community.”

Gerry Nesbitt, Director of Bioinformatics, the Epilepsy Phenome/Genome Project,

University of California at San FranciscoUnlocking the genetic secrets to epilepsy might provide the key to better treatment and prevention. To pursue that possibility, hundreds of researchers at more than 26 academic medical centers throughout the United States and Australia are working on the global Epilepsy Phenome/Genome Project (EPGP)—a large-scale effort to collect detailed clinical and genomic information on thousands of patients. They face major challenges in collecting, processing, storing, accessing, and analyzing huge amounts of data, and in collaborating with colleagues. To solve those challenges, the researchers chose Microsoft technologies for patient tracking, electronic data capture, global collaboration, and data management. The resulting solution provides reliable and efficient data collection, low-cost support and training, faster application enhancement, faster knowledge discovery, and improved productivity.

SituationAccording to the World Health Organi-zation (WHO), epilepsy afflicts more than 50 million people worldwide. Epilepsy can strike the young as well as the old. Symp-toms can range from brief staring spells to full-blown seizures. There are treatments but no known cure. Although some pa-tients respond well to the first anti-epilepsy drug they take, others experience intract-able forms of epilepsy that do not respond well to medications. They may require massively invasive surgery, such as the removal of part of the brain, to achieve a level of relief.

In 2007, the National Institutes of Health provided a grant of U.S.$15 million to establish the Epilepsy Phenome/Genome Project (EPGP) consortium to study one of the least understood aspects of epilepsy: its genetic basis. EPGP has become a center-piece for what is an international, multi-institutional, multiyear, collaborative research effort at more than 26 academic medical centers throughout the United States and Australia, making it one of the largest such studies of epilepsy ever conducted. The broad scope of the project—which encompassed thousands of data points for each of thousands of research subjects—was necessary to give researchers a study population large enough that they could identify and link genetic information to phenotypic data.

It wasn’t only the research population that needed to be large. The researchers quickly realized that they needed an informatics infrastructure and application architecture that were

as large and sophisticated as the questions they were studying. One reason was the large volumes of data that re-searchers would need to store and access. Another was that the researchers—who, after all, were experts in biology, not com-puter science—needed the ability to easily work with and analyze that computerized data.

In addition, the large numbers of geo-graphically dispersed researchers meant that the project’s five-person informatics staff, based at the University of California at San Francisco, couldn’t possibly provide in-depth technical support; the project there-fore needed applications that were as easy for the researchers to learn and use on their own as they were easy for the informatics staff to deploy, administer, and support.

That the group of researchers was large and dispersed also indicated the need for collaboration and workflow tools, so that researchers halfway around the world could work together as though they were down the hall from one another. Reliability was another requirement because project leaders knew that they couldn’t afford to lose or compromise any of the research data.

The project’s informatics staff had a com-plex, multifaceted set of requirements to meet—and not much time in which to meet them. The staff had just eight months before the project was slated to enroll its first research subjects, and informatics systems had to be live by then to accept incoming data.

“We chose Microsoft technology and servers running Windows over LAMP because we needed 100 percent reliability and scalability, and we had very little time to get the solution into production.”

Gerry Nesbitt, Director of Bioinformatics, the Epilepsy

SolutionThe first step in developing the informatics infrastructure was to identify the services and functions that the solution would have to support. Working closely with the researchers, the informatics staff developed a list of requirements that included everything from collecting and managing detailed phenotypic data, electroencepha-lographs (EEGs) and magnetic resonance images (MRIs), to tracking the status of participants and their blood specimens throughout the term of the study.Off-the-Shelf or Custom Development?The next step was to decide how to implement this functionality—that is, whether to purchase and modify an off-the-shelf solution or to develop a custom solution. The responsibility for that decision fell to Gerry Nesbitt, the project’s Director of Bioinformatics. He and his team consid-ered commercially available software for clinical trial management, such as Oracle Clinical and PhaseForward InForm, and found them wanting—some were too expensive, others were unable to accom-modate the electronic collection of large phenotypic data sets, and most were not scalable enough.

That left custom development. The most common technology platform in academia is the so-called LAMP stack—the Linux operating system, Apache web server, MySQL database, and PHP programming language—with Apple Macintosh comput-ers on the front end. But Nesbitt and his colleagues made a different choice.

Choosing the Right Platform

“We chose Microsoft technology and servers running Windows over LAMP because we needed 100 percent reliability and scalability, and we had very little time to get the solution into production,” says Nesbitt. “Enterprise-class data management was essential, and SQL Server provided that. SQL Server also gave us fully sup-ported, out-of-the-box, and third-party options for reporting and analysis. MySQL didn’t. Similarly, SharePoint Server 2007 gave us the features, again built-in, that we needed for both a public website and an internal collaboration site.”

In addition to Microsoft SQL Server 2008 data management software and Microsoft Office SharePoint Server 2007, the project’s informatics solution was based on Micro-soft technologies including the Windows Server 2008 operating system, Microsoft ASP.NET, the Microsoft Visual Studio 2005 development system, and, later, Visual Studio Team System 2008 Team Suite.

Six Applications and a PortalThe informatics team worked for eight months, and its solution went live in Jan-uary 2008. That solution consisted of six applications accessed through a secure intranet portal. All components of the solu-tion were web based, which addressed the requirement that the solution be easily accessible both to global users and to informatics maintenance and support personnel.

Those components included the following: A public website to provide

information about the project and to solicit volunteer participation as research subjects

“Enterprise-class data management was essential, and SQL Server provided that.”

Gerry Nesbitt, Director of Bioinformatics, the Epilepsy Phenome/Genome Project,

University of California at San Francisco

A private intranet portal for researchers, which provided access to the appli-cations, to the study’s documents, and to collaboration tools

Participant activity tracker applications that made it possible for each clinical site to track its participants’ visits, manage events and issues, and complete pheno-typic data collection

A specimen-tracking system to manage the life cycle of blood specimens from the moment a blood sample was drawn to its arrival at the specimen repository

A case-report form designer and data-collection tools

Applications for EEG data collection and reviews by neurophysiology experts

Applications for MRI data collection and reviews by imaging experts

Secure file transfer for EEG and MRI files

A central database repository providing data storage, validation and integration, and robust security

A data warehouse through which researchers query the data using Microsoft or third-party tools including Microsoft Office Excel spreadsheet software, Office Access database soft-ware, SQL Server Reporting Services, Office PerformancePoint Server 2007 (a part of Office SharePoint Server 2007), and Visokio Omniscope™

These applications are hosted in a West Coast data center and mirrored for backup and disaster recovery in an East Coast data center. Each data center hosts a pair of databases. One is a transactional database, with which researchers interact through the various applications for data

collection, tracking, and transmittal. The other is a reporting database that provides the basis for analysis, data visualization, and reports in response to queries from the research-ers’ business intelligence tools.

BenefitsThe massive research project was up and running in just eight months and now gives researchers easy and dependable access to applications and data. In addition, it mini-mizes the support burden on the lean informatics staff.

“By using Microsoft technologies, we’ve been able to give our researchers and coordinators a level of informatics sophis-tication rarely seen on projects funded by the National Institutes of Health,” says Nesbitt. “We’re seeing more reliable and efficient data collection, fewer resources needed for support and training, faster completion of application enhancements, faster knowledge discovery, and higher productivity overall.”

Speeds Development by 50 PercentTo build the large and sophisticated informatics solution on an aggressive project schedule, the EPGP developers turned to an Agile development strategy, which they implemented through the use of Visual Studio 2005 and, later, Visual Studio Team System 2008 Team Suite. Nesbitt estimates that because the team used the Visual Studio tools, development time was about 50 percent less than it would have been using the alternatives Nesbitt might have chosen.

“By using Microsoft technologies, we've been able to give our re-searchers and coordina-tors a level of informatics sophistication rarely seen on projects funded by the National Institutes of Health.”

“The Visual Studio tools allowed our team to get a real jump-start on development,” Nesbitt says. “We took advantage of the tools’ strong interoperability with our foundation applications, such as SQL Server, and of their features for collaboration among developers, such as check-in and check-out of code and strict version control. That helped us to achieve smooth collaboration between our domestic team and our outsourced developers in Chennai, India.”

For example, the Microsoft tools supported a 24-hour development and quality assur-ance (QA) cycle in which local developers created code and performed QA before the end of day, and then passed their work on to the developers in Chennai to address bugs and other issues. The outsourced developers finished their work just in time for Nesbitt’s local developers to pick up again with the new code. That shortened development considerably.

The Microsoft technologies also helped to speed development by providing compo-nents—such as business intelligence in SQL Server and collaboration tools in SharePoint Server—that eliminated the need to build or buy this functionality and then integrate it with the rest of the system. Master pages in Office SharePoint Server made it easy for the developers to add logos, colors, and typefaces into the public website, and then to make the use of those visual elements consistent throughout that site. Nesbitt proudly notes that his team got the public website and intranet portal up and running in less than one week.

Further, the same capabilities that supported the fast development of the solution are now used by the project developers to speed application enhancements and extensions.

Provides Exceptional Ease of UseThe EPGP informatics applications had to be as easy for researchers to use as they were easy for the informatics team to develop. The Microsoft technologies also helped the informatics team to meet that requirement, according to Nesbitt.

The informatics team used Microsoft Office SharePoint Server 2007 to create a public website that doesn’t look like a “typical SharePoint site.”

Researchers benefit from the use of Office SharePoint Server for the intranet portal, which provides a convenient, central place to find all of the EPGP applications, all of the research data and tools, and all of the reports and other study documentation.

The intranet portal also gives researchers a broad choice of analysis tools. Researchers can work through familiar tools such as Microsoft Office Excel; visual dashboards based on Office PerformancePoint Server; and research-specific, third-party tools such as Omniscope. Because the informatics solution uses web-based tools for tracking participants and phenotypic data collection, researchers and study coordinators

gain real-time access to subject enrollment statistics, study metrics, and research data.

Researchers also find that their work is expedited—and that the impact of having colleagues spread among various research centers is mitigated—by collaboration tools, especially those available in Office SharePoint Server. For example, they use discussion boards for ongoing virtual conversations, while wikis provide a way to share best practices—such as how to boost subject recruitment—among study coordinators.

Even non-research functions are made easier for project researchers through the use of Microsoft technologies. The public website, for

example, is maintained not by dedicated informatics staff but by two researchers whose work on the site is one of their many duties. That work is made easier both by the publishing tools in Office SharePoint Server and by the software’s workflow tools, from which Nesbitt and his colleagues created an automated workflow that routes proposed content to authors, editors, and reviewers for approval prior to posting.

And researchers aren’t the only ones who can work effectively because of the Microsoft technology underlying the solu-tion. The easy-to-use applications and tools make it possible for study coordinators to complete their tasks quickly, contributing to the widespread acceptance of those applications, higher productivity among coordinators, and reduced turnover in staff.

“The applications had to be especially easy to use for two reasons,” says Nesbitt. “First, anything that distracts our researchers from doing their real work is a problem. Second, research projects generally have a high turnover of study coordinators—which requires us to continually train new coor-dinators. Because the applications are based on Microsoft technologies, we can train new coordinators in one hour, fully equipped with the skills and confidence to use the applications immediately.”

Delivers Near 100 Percent Uptime, Minimizing Support NeedsIn choosing a technology set for their applications, Nesbitt and his

colleagues were also looking for platform that would minimize ongoing support demands. The Microsoft technologies meet that require-ment, too, and do so in a variety of ways.

First, the project solution is fully scalable, able to support the hundreds of broadly dispersed, simultaneous users who contrib-ute to the project. Should the population of researchers ever grow beyond the limits of the current architecture, the informatics team can add web and database comput-ers cost-effectively, using commodity hard-ware. In addition, because all the informat-ics applications are web based, the Epi-lepsy Phenome/Genome Project spends less on deployment than it would to deploy traditional client-server applications, and it also saves on the maintenance costs of keeping servers and workstations updated and trouble-free.

The system is also highly reliable. Built-in validation rules and checks in the applica-tions and databases help to ensure that the collected data is correct and verifiable, and that it follows the study’s protocols. Should problems occur with the databases, SQL Server data mirroring between the East and West Coast data centers helps ensure that data is available for backup or recovery.

Not that Nesbitt is anticipating such prob-lems—to date, the system has experienced negligible unscheduled downtime, provid-ing the equivalent of near 100 percent up-time. Even scheduled downtime for mainte-nance is just 2 to 3 hours per month, 50 percent of the downtime that Nesbitt

“Because the applica-tions are based on Microsoft technologies, we can train new coordi-nators in one hour, fully equipped with the skills and confidence to use the applications immediately.”

says he would have seen with other platforms.

All this means that researchers can use the applications and data as they need to, without having to consider limits to system availability. Nor does the IT staff need to devote significant resources to system support. Help-desk calls are running at the rate of one or two per day—a very small number for an endeavor the size of the Epilepsy Phenome/Genome Project, according to Nesbitt.

“Using Microsoft technologies, we’ve built a major platform that delivers enterprise-level scalability and reliability, along with the functionality and ease of use that our researchers need, all of which is supported by an informatics administrative and development staff of five,” says Nesbitt. “This is such an advance for the field of clinical research informatics that we’re looking at making components of the architecture available to others in the research community.”

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For more information about the University of California at San Francisco, call (415) 476-9000 or visit the website at: www.ucsf.edu

This case study is for informational purposes only. MICROSOFT MAKES NO WARRANTIES, EXPRESS OR IMPLIED, IN THIS SUMMARY.Document published June 2010

Software and Services Microsoft Server Product Portfolio

− Microsoft SQL Server 2008 Enterprise

− Windows Server 2008 Enterprise Microsoft Visual Studio

− Microsoft Visual Studio Team System 2008 Team Suite

Microsoft Office− Microsoft Office Access 2007− Microsoft Office Excel 2007− Microsoft Office SharePoint

Server 2007

Hardware HP/Compaq servers Network Appliances storage area

devices