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Bio·IT World Best Practices Awards 2004
Bio•IT World’s Best Practices Awards program hopes to capture the imagination and effectiveness of advancing technology being used to drive biomedical advances.
· A Best Practices Odyssey 
By John Russell
· Francis Collins Receives President’s Award
By Kevin Davies
· Keynote Speakers Chide Industry Leaders
By Anthony Strattner
· The Technology Providers That Enable Best Practices
Grand Winners
· Curbing a Killer
Drug Discovery and Development — Iconix Pharmaceuticals
· Tracking Better Lab Operations
IT Infrastructure and Informatics — Baylor College of Medicine
· Interactive Decision Making
Knowledge Management and Collaboration — SurroMed
· The Pursuit of Process
Regulatory Compliance — Endo Pharmaceuticals
 
· I, Virtual Patient
Clinical Research and Trials — Roche Diagnostics
· Project Summaries of All Entries
Agilent Technologies Life Sciences and Chemical Analysis
www.agilent.com/chem
Scripps Research Institute scientists were trying to identify blood-based biomarkers for sepsis, but their efforts at studying plasma were stymied by two common problems: the presence of six highly abundant proteins in plasma that masked the rare proteins they sought; and the tremendous amount of time required for mass spectrometric data analysis and review. Their breakthrough came when they combined a three dimensional LC/MS/MS approach with two new proteomics products from Agilent Technologies. The first product was Agilent's Multiple Affinity Removal System, an LC column that removes plasma's six most abundant proteins. By using this depletion strategy, the researchers unveiled lower-abundance proteins that could not previously be seen. They then separated the resulting protein digests using an automated separation process. At the back end, they accelerated their data analysis using the Agilent Spectrum Mill MS proteomics workbench software, which enabled them to perform 30 days of analysis in two days.

ClinPhone 
www.clinphone.com
Wanting to erase the inefficiencies caused by lack of integration among clinical trial technologies, Procter and Gamble Pharmaceuticals realized an opportunity to optimize the capabilities of ClinPhone's Interactive Voice Response (IVR) platform and Phase Forward's InForm Electronic Data Capture (EDC) platform with an integrated system. With this solution, P&GP has been able to maximize features of each system to shorten IVR calls, simplify EDC entry, and pass IVR patient diary data into EDC case report forms. P&GP staff had extensive experience using Phase Forward's InForm software for EDC and were already taking advantage of the accelerated data entry and query cycles the tool offers. They also had experience working with ClinPhone's IVR systems to perform patient screening and randomization, emergency unblinding, and to manage the medication supply chain. The two technology companies also had support teams available 24x7 and could integrate their help desk procedures for the integrated studies.

Entelos 
www.entelos.com
Entelos, in collaboration with Organon, conducted in silico research using Entelos' Rheumatoid Arthritis PhysioLab platform to identify novel targets for the treatment of RA and prioritize those targets, along with 25 other targets provided by Organon researchers, as to their therapeutic efficacy in RA. The novel targets were identified using a systematic sensitivity analysis of the PhysioLab platform to identify key pathways having a significant impact on the clinical outcome in RA. Entelos PhysioLab platforms integrate the dynamics of biology into a mechanistic model of human physiology. Using this research platform, scientists have access to and can visualize all model variables over the time-course of the simulation, allowing the dissection and quantification of the impact of therapies and their underlying mechanisms and the assessment of competing hypotheses. Entelos' Rheumatoid Arthritis PhysioLab platform provided an environment for the identification, evaluation, and prioritization of multiple, complex targets.

Entelos collaborated with Roche Diagnostics to assess the use of multiple metabolites and hormones from a single blood sample as a biomarker of insulin sensitivity. Sixty-two virtual patients were developed in Entelos' Metabolism PhysioLab platform, a large-scale mathematical model of human metabolism. The platform can simulate human in vivo plasma levels for over 20 metabolites and hormones (e.g., glucose, insulin) all of which, singularly or in combination, might provide a biomarker for insulin sensitivity. The diabetic virtual patients exhibited a diversity of both phenotype and pathophysiology, and had behaviors comparable to those observed in clinical diabetic populations.

IBM Life Sciences 
www.ibm.com
IBM worked with the Fred Hutchinson Cancer Research Center (FHCRC) to develop a distributed database query system, in order to ease data-sharing, improve potential for collaborations, and enhance research opportunities for immune-system geneticists. Using IBM's DiscoveryLink product, FHCRC informaticians and IBM completed the first major phase of a project designed to address these concerns. In the first phase, four laboratory research databases and one clinical research database were all linked and made accessible to researchers via a single, easy-to-use application interface. This has allowed researchers direct access to run their own queries and perform analyses on the resulting data sets. One of the most important advantages of this new system is that the query process now involves a single step and no manual manipulations. According to Fred Hutchinson staff involved in the project, advantages gained by using DiscoveryLink included: ability to integrate diverse (relational and non-relational) data sources; ability to query heterogeneous data sources with a single SQL query; excellent performance; and no disturbance to existing IT infrastructure or data sources.

IBM Deep Computing 
researchweb.watson.ibm.com/dci/
Locus Pharmaceuticals developed a proprietary fragment-based method for de novo design of protein ligands. Computations are performed on the 1,000-node Locus computing cluster, which delivers 2.3 teraflops of operational speed, with additional peak capacity accessed via the IBM Deep Computing On Demand center. As a first step in molecular design, the method is applied to the identification of all possible binding sites on a protein surface by mapping fragment-protein interactions across the surface. This provides a quantitative measure of the suitability of binding sites for drug design.

Insightful 
www.insightful.com
Biomarket-focused drug developer SurroMed integrates data from sources including MLS cytometry, mass spectrometry, proteomics, metabolomics, and gene expression. These data are managed in an Oracle data warehouse. Data management and analysis is achieved through an inhouse integrated software system, SurroStat. Two key components of SurroStat are Insightful's S-PLUS Server and Spotfire's Decision Site. Insightful's S-PLUS Server provides advanced statistical analysis and interactive tabular and graphical reports using S+Graphlets and the S-PLUS XML reporting gateway. Spotfire's Decision Site provides advanced interactive visualization as well as user-defined Guides and Decision Site Posters for analysis sharing. DecisionSite Posters allows SurroMed to securely distribute and manage their analysis data and findings using the Poster library. The S-PLUS Server and Decision Site are integrated within the SurroStat user experience. Surrostat users can prepare data sets using Decision Site, then send the data set to S-PLUS Server for statistical analysis and reporting. Results from the S-PLUS Server are returned as either reports (HTML, PDF, etc.) or data sets for continued interactive analysis in Decision Site.

NeoScale Systems 
www.neoscale.com
To alleviate HIPAA regulatory requirements, the University of Texas Health Science Center implemented storage security appliances - NeoScale's CryptoStor -- to protect sensitive data within its storage area network (SAN). Public health information (PHI) data from a variety of medical applications can be stored centrally. As information is sent to the storage environment, CryptoStor encrypts the data - essentially concealing the PHI data. The PHI data stored in the SAN is protected according to regulations without affecting storage processing, without disrupting business services, but while reducing additional HIPAA data classification, management, and infrastructure costs, the Health Science Center reports. Since CryptoStor is application- and platform-agnostic, HSC says, it can realize security benefits as its applications and SAN evolve.

Octagon Research Solutions 
www.octagonresearch.com
Octagon Research Solutions collaborated with Endo Pharmaceuticals to develop Endo's electronic submission capabilities. In the Submission Management Pilot, ViewPoint, Octagon's submission process management solution, was applied to Endo's current processes to improve process visibility, manage issues, and develop process metrics. Octagon collaborated with Endo on the design and execution of the pilot project. It was designed to mirror typical document processing tasks and procedures. Endo selected ViewPoint to manage the entire process including resources, tasks and issues. ViewPoint was used throughout the course of the pilot project to track and manage the process.

OpenText 
www.opentext.com
When it came time to build a globally integrated electronic document management system, DSM Nutritional Products selected Livelink from Opentext as an "efficient and cost-effective technology platform." The deciding factor for choosing Livelink was its ability to build upon business processes as they existed rather than having to change processes to fit the system, DSM says. Paper forms were converted to electronic. Checkboxes and drop-downs were added for routing. Loop-backs were built into the process to handle any rejections. With all forms now stored electronically, they are easily retrievable. DSM has set up stations to scan all paper forms, eliminating the need for paper copies. During routine audits, documentation of a change in procedure, operating records, or equipment can be provided quickly from the Livelink-based system.

Phase Forward 
www.phaseforward.com
Wanting to erase the inefficiencies caused by lack of integration among clinical trial technologies, Procter and Gamble Pharmaceuticals realized an opportunity to optimize the capabilities of ClinPhone's Interactive Voice Response (IVR) platform and Phase Forward's InForm Electronic Data Capture (EDC) platform with an integrated system. With this solution, P&GP has been able to maximize features of each system to shorten IVR calls, simplify EDC entry, and pass IVR patient diary data into EDC case report forms. P&GP staff had extensive experience using Phase Forward's InForm software for EDC and were already taking advantage of the accelerated data entry and query cycles the tool offers. They also had experience working with ClinPhone's IVR systems to perform patient screening and randomization, emergency unblinding, and to manage the medication supply chain. The two technology companies also had support teams available 24x7 and could integrate their help desk procedures for the integrated studies.

Proteome Systems 
www.proteomesystems.com
To provide fee-for-service proteomic research to the life science industry, Charles River Proteomic Services formed a joint venture with Proteome Systems. CRPS adopted Proteome Systems' ProteomIQ - a fully integrated, scalable, secure, high-throughput proteomic platform coupled to infrastructure technologies of IBM. Incorporating an informatics backbone (BioinformatIQ), the ProteomIQ platform enables CRPS to offer its customers a comprehensive range of proteomics testing services-from sample collection through protein identification and annotations with the unrivaled degree of outsourcing transparency afforded by secure, Web-enabled real-time and unfiltered data access.

Quantum Dot 
www.qdots.com
French researchers at the Laboratoire Kastler Brossel at the Ecole Normale Superieure, Paris, used quantum dots developed by Quantum Dot Corp. (QDC) to track glycine receptor dynamics for extended periods in living cells for the first time ever. The insights their work revealed may prove critical to understanding the fundamentals of cell biology and furthering the development of drugs that more effectively interact with human cellular targets. QDC's quantum dot nanocrystal products are essentially molecular-scale "light tags" that help researchers reveal the secrets of biology in more detail than ever before, offering new ways to visualize the actual mechanisms of life. Researchers using QD bioconjugates with a variety of imaging instruments can see what's happening inside cells by tracking the attached nanocrystals; they can also use the QDs to color-code different aspects of a cell or of an experiment.

SAS 
www.sas.com
At biopharma XOMA, access to clinical study data is automatic. Using SAS software for Web-enabled reporting and analysis, XOMA programmers developed a clinical decision support system (CDSS) to integrate clinical study workflow for more efficient CSR preparation. Researchers can view clinical trial data from their desktops even while a trial is ongoing. The CDSS, built with SAS/IntrNet software, provides important safety and efficacy data about each of the company's ongoing clinical studies; it also generates most of the content for the Phase I CSR and most of the safety-related content for the Phase II-III CSR. The SAS application server and Oracle Clinical server are connected to an LSI Metastor 4400 SAN where all clinical data are stored.

Scientific Software Tools 
www.sstnet.com
In 2003 Radiant Research wanted to conduct a s tudy involving hundreds of physicians and thousands of patients, and the study sponsor wanted to deliver published results one year after enrollment. Radiant collaborated with Scientific Software Tools to develop a digital solution using a custom EDC application for a Palm Tungsten PDA. For recruitment, SST developed a remote site assessment tool accessible through the study Web portal to quickly screen hardware and software capabilities at potential study sites. For data collection, SST used a secure Web portal to upload PDA data from the remote computers to the master study database. SST developed the portal using Microsoft ASP.NET. To encourage sites to report new data quickly, SST used Web services to monitor site activity and to automate faxing and e-mailing sites weekly status reports on their progress. Radiant achieved its accelerated timeline and submitted the study results for publication less than one year after enrolling the first patients.

SciQuest 
www.sciquest.com
Enanta Pharmaceuticals chose SciQuest to create one system that integrated both materials management and procurement. SciQuest's Web-based SelectSite system required minimal effort from Enanta's IT department and minimal training for purchasing managers, researchers, and others using the system, the drug developer says. It also allowed Enanta to implement custom controls within the purchasing group, allowing managers to consolidate multiple requisitions from each day into one purchase order. SciQuest's project and technical management methodologies provided Enanta with e-procurement software with a disciplined solution management approach. SciQuest says it can optimize project scheduling and delivery through a team approach with the customer and its partners, minimizing ongoing support and maintenance costs.

Spotfire 
www.spotfire.com
Biomarket-focused drug developer SurroMed integrates data from sources including MLS cytometry, mass spectrometry, proteomics, metabolomics, and gene expression. These data are managed in an Oracle data warehouse. Data management and analysis is achieved through an inhouse integrated software system, SurroStat. Two key components of SurroStat are Insightful's S-PLUS Server and Spotfire's Decision Site. Insightful's S-PLUS Server provides advanced statistical analysis and interactive tabular and graphical reports using S+Graphlets and the S-PLUS XML reporting gateway. Spotfire's Decision Site provides advanced interactive visualization as well as user-defined Guides and Decision Site Posters for analysis sharing. DecisionSite Posters allows SurroMed to securely distribute and manage their analysis data and findings using the Poster library. The S-PLUS Server and Decision Site are integrated within the SurroStat user experience. Surrostat users can prepare data sets using Decision Site, then send the data set to S-PLUS Server for statistical analysis and reporting. Results from the S-PLUS Server are returned as either reports (HTML, PDF, etc.) or data sets for continued interactive analysis in Decision Site.

SPSS 
www.spss.com
At Children's Memorial Hospital in Chicago, Dr. Eric Bremer is building a gene-expression database for pediatric brain tumors. His challenge is to continually make sense of the 7,000 to 30,000 data points for each brain tumor sample. To accomplish this, Bremer uses Clementine from SPSS, which enables him to quickly analyze the voluminous amounts of data in different ways, while identifying patterns and relationships in the data. Clementine enables access to multiple data stores and types, and provides a variety of data preprocessing tools, predictive modeling techniques, interactive visualization capabilities and methods for interpreting results, as well as an external module interface for adding external tools.

Bremer then uses LexiQuest Mine from SPSS to sift through mountains of scientific literature to extract patterns that, for example, when combined with genetic patterns identified from his tumor database with Clementine, help him evaluate prime drug targets that would form the basis for a cancer cure. LexiQuest Knowledge Management Suite is used for the discovery of knowledge in unstructured text.

Stone Bond Technologies 
www.stonebond.com
Stone Bond Technologies implemented its Enterprise Enabler Laboratory Information Management System (LIMS) at Baylor College of Medicine's Department of Molecular and Cellular Biology Core Lab, The Stone Bond system replaced the lab's paper-based system and automated the entire core processes with an "out-of-the-box" solution. Baylor reports that the Enterprise Enabler LIMS streamlined the flow of data information, allowing researchers and administrators to use a single integrated system throughout the full research cycle of submitting and monitoring research requests, updating status reports, safeguarding proprietary information, mining resources, and expediting billing. The flexibility of the automated Web-based system offered broader usability and accessibility with handheld PDAs and PCs while improving users' experience and a faster workflow.

Sun Microsystems 
www.sun.com
With plans to expand from 100 servers to between 700 and 1,000, the Southwest Foundation for Biomedical Research was interested in implementing the best OS for its needs. Sun's Solaris was the SFBR's incumbent OS. To determine if it should continue with Solaris, the Foundation tested Linux and Net BSD to see if they could outperform Solaris? The SFBR retained Solaris based on performance and support reliability and technical stability. "Linux clustering solutions were not networked ideally, and its network stack and multithreading model were not as mature as Solaris'," the Foundation says. Net BSD was not an ideal solution either because Sun Gridware had not been ported to Net BSD, which would have required a customized port. OS testing also found that Sun's technical support could handle "the most obscure issue," while Linux support was offered through newsgroups and freeware developers. When it came to the SFBR's choice of servers and processors, Sun's collaboration with AMD was very important: the SFBR has invested in 650 dual-processor servers based on AMD technology.

TurboWorx 
www.turboworx.com
Ace BioSciences integrated TurboWorx Enterprise into its production High Performance Computing (HPC) environment to achieve results faster and with fewer resources in analyzing peptide sequence data generated by mass spectrometry and other methods. The company uses TurboWorx's Builder product to create a functional production analysis pipeline consisting of bioinformatics applications and data sets. These applications are distributed and executed across Ace's computing infrastructure using the TurboWorx Enterprise engine. TurboWorx also provided ACE BioSciences with consulting services to configure the software, wrap bioinformatics applications to create application components, and design workflows.

Karo Bio, a drug discovery company for the development of precision drugs to treat diseases in the field of nuclear receptors, uses TurboWorx's Suite of workflow automation products. (TurboWorx recently unveiled the suite as part of its Research and Development Workflow Collaboration Initiative.) The Swedish drug company has deployed the TurboWorx products in its Linux computing environment, which includes Linux workstations and a Linux cluster, to enable its computational chemistry and biology groups to develop, automate, execute, and share scientific computational workflows. "TurboWorx is providing us with an excellent way to deliver advanced bio- and chemo-informatics tools to our research scientists in a secure environment," says Konrad Koehler, principal scientist, at Karo Bio. Karo Bio's computational scientists are utilizing TurboWorx software to integrate disparate applications into a number of workflows.

MDS Proteomics deployed TurboWorx software to achieve improvements in the automation and acceleration of analytical processing workflows and processes integrating disparate data and applications.



For reprints and/or copyright permission, please contact  Terry Manning, 781.972.1349 , tmanning@healthtech.com.