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By BIO-IT World
 Drug Discovery and Development | Entrant | The Project | Ace BioScienceswww.acebiosciences.com
Project Leaders: Angus King, CSO; Morton Christensen, IT manager
Key Tech Partner: TurboWorx
| Integrating and Accelerating EMBOSS Workflows Ace incorporated TurboWorx Enterprise into its production environment to achieve faster results analyzing peptide sequence data, with fewer resources. ROI: With EMBOSS applications linked into automated pipeline workflows, scientists have more time to do science, and IT doesn't have to write custom scripts. | Compugen (www.cgen.com)
Project Leader: Galit Rotman, director, biological research | Naturally Occurring Antisense Transcription Compugen scientists developed a novel algorithm that identifies NATs through analysis of millions of expressed sequences and corresponding genomic loci. ROI: Better understanding of gene regulation, advantageous to target discovery, pathway analysis, and antisense drug design. | Entelos/Organonwww.entelos.com
Project Leaders: Didier Scherrer, director of immunology research, Entelos; Andrea Van Elsas, senior scientist, Organon | Translating Molecular Targets to Human Clinical Outcomes The collaborators conducted in silico research using the Rheumatoid Arthritis PhysioLab platform to identify novel targets for treating RA. ROI:Prioritization of 30 putative drug targets; identification of 5 novel molecular targets with significant predicted clinical efficacy | • Iconix Pharmaceuticalswww.iconixpharm.com
Project Leaders: Leslie Brown, COO; Kurt Jarnagin, VP, chemogenomics | Identifying Toxicological, Mechanistic BiomarkersIconix scientists developed mining and classification techniques to analyze data from more than 13,000 microarray experiments. Iconix validated its biomarker approach by conducting blinded studies on marketed drugs or novel compounds. ROI: Scientists demonstrated that genomic biomarkers can predict toxicity before conventional methods. | Johnson & Johnson Pharmaceutical Research & Development www.jnj.com
Project Leaders: Xiang Yao, Albert Yeung | DNA Chip III J&J developed software that enables scientists at any remote site to set up a microarray experiment, track samples, and access chip data results. ROI: Improved microarray lab efficiency and significantly reduced daily operational costs. | • Laboratoire Kastler Brossel (www.lkb.ens.fr/recherche/optetbio)
Project Leader: Maxime Ben Dahan, head of optics & biology research group
Key Tech Partner: Quantum Dot
| Dynamics of Human Cells Revealed by Quantum Dots Using molecular-scale "light tags," researchers tracked glycine receptor dynamics in living cells for extended periods. ROI: The insights they gained might be critical to understanding fundamentals of cell biology and develop more effective drugs. | • Locus Pharmaceuticalswww.locuspharma.com
Project Leader: Frank Guarnieri, principal founding scientist | Simulated Annealing of Chemical Potential Locus built a system to predict binding energies, using a conceptually simple inversion of previous computational methods that can identify all binding sites on a protein surface. ROI: Yielded 14 new chemical series with only 1.5 person years of effort. | Sankyo Companywww.sankyopharma.com
Project Leader: John Alexander, global head, R&D
Key Partner: Accenture
| Research & Development Redesign Sankyo revamped its decision-making process and instituted a global team-based approach that incorporates the best practices of its "cultures" in the U.S., Europe, and Japan.
ROI: Early indicators estimate a potential savings of $167M per compound development. | Scripps Research Institutemasspec.scripps.edu
Project Leader: Gary Siuzdak, sr. director, Center for Mass Spectrometry
Key Tech Partner: Agilent Technologies
| Sepsis Biomarker Discovery Using an LC/MS/MS approach and new proteomics products from Agilent, the researchers were able to do 30 days of analysis in 2 days, finding biomarkers in plasma that could serve as early indicators of sepsis. ROI: Identified apolipoprotein A-I as a potential biomarker. | SurroMedwww.surromed.com
Project Leader: Keith Joho, VP, informatics and bioanalytical systems
Key Tech Partner: Insightful | SurroStat Biomarker Analysis System SurroMed combined multiple data sources, Insightful advanced statistical analysis, and Spotfire interactive visualization tools to create a system for rapid discovery of biomarkers. ROI: SurroStat is an analytic and visualization platform for "deep biomarker discovery." | • Grand Prize Winner
Honorable Recognition
• Best Platform •Best Informatics Application •Best Application of New Techology | Regulatory Compliance | Entrant | The Project | Baylor College of Medicine, Office of Research (www.bcm.tmc.edu)
Project Leader: Janet Allen, director, research compliance services | eCOI: Electronic Conflict of Interest Management BCM advanced its online submission and review system with a new module to document, review, and remediate potential conflicts of interest. ROI: The data-driven system reduces the chance for human error; fully documents potential conflicts, disclosures, and management plans; and provides a Web-based vehicle for committee review and approval. | • Endo Pharmaceuticals (www.endo.com)
Project Leader: Rebecca Platt, supervisor, e-publishing
Key Tech Partner: Octagon Research Solutions | Submission Management Capabilities Pilot Endo and Octagon developed a submissions process that provides real-time visibility so managers can redirect resources or address issues that might affect a deadline. Octagon's ViewPoint was integrated into current practices to provide this visibility. ROI: Access to process data enables managers to spot trends that result in delays or consume excessive resources | DSM Nutritional Products (www.dsm.com)
Project Leader: Gail Gibson, compliance coordinator
Key Tech Partner: Open Text | Electronic System Integration Implementation DSM adopted Open Text's Livelink as the basis of an electronic document system that would allow the company to automate business processes, facilitate collaboration, and track action items. ROI: Electronic forms have resulted in faster workflow, increased accuracy, more participation by offsite teams, and better understanding of process roadblocks. | University of Texas Health Science Center at Houston (www.uth.tmc.edu)
Project Leader: Kevin Granhold, manager of network services
Key Tech Partner: NeoScale Systems | Storage Security for HIPAA Compliance To alleviate HIPAA requirements, UTHS implemented NeoScale storage security appliances to protect sensitive patient data within the storage area network, without affecting storage processing. ROI: Reduced back-end data classification and management costs, streamlined storage security function, demonstrated due diligence for HIPAA compliance. | • Grand Prize Winner
Honorable Recognition
• Best Platform •Best Informatics Application •Best Application of New Techology | Knowledge Managment and Collaboration | Entrant | The Project | ALZA (www.alza.com)
Project Leader: Ellen Rose, director, corporate communications | ALZANET Portal Design and deploy an enterprise portal that provides a user-friendly workspace, applications, and centralized information sources for all employees, in order to enhance collaboration and make timely decisions. ROI: Increase in productivity through "self service," lower intranet publishing costs, "overwhelming" acceptance by users. | Bioexpertise (www.bioexpertise.com)
Project Leader: Desmond Mascarenhas, CEO
| BioCritique Using its proprietary software platform, Bioexpertise developed a Web-based environment offering publications, forums, and other educational resources in biomedical specialties. ROI: BioCritique was given higher marks than Medscape in a user survey. | Cardinal Health, Pharmaceutical Technologies & Services (www.cardinal.com/pts)
Project Leader: Gary Dowdy, VP, e-Business & Knowledge Management
| Cardinal Health Portal Build a single site that enables dispersed teams to work together, access market intelligence (auto-categorized by the portal), and publish content. ROI: 75 collaboration sites involving 700+ people; 50,000 intelligence documents; ability to form teams quickly. | Enanta (www.enanta.com)
Project Leader: Michelle Wang, project manager
Key Tech Partner: SciQuest | Integrating e-Procurement with Materials Management Building on SciQuest's SelectSite Web-based system, Enanta replaced its paper-based materials sourcing process with a cost-effective procurement system. ROI: Time saved by eliminating searching of paper catalogs; reduction in spending due to accurate inventory reports. | Karo Bio (www.karobio.se)
Project Leader: Konrad Koehler, principal scientist, Karo; Srini Chari, general mgr., solutions, TurboWorx
Key Tech Partner: TurboWorx | Automating Workflows on Heterogeneous Networks Karo deployed TurboWorx collaboration software in its Linux environment to automate complex workflows. ROI: Scientists can tap into a wide variety of inhouse, third-party, and open-source applications within a common framework. | Microbia (www.microbia.com)
Project Leader: Kevin Durfee, IT director | Microbia Knowledge Management System The company implemented an online system for managing, searching, sharing, and annotating scientific literature, internal documents, etc. ROI: System helped prepare to new discovery projects, and saved the cost (about $250,000) of commercial document management software. | •SurroMed (www.surromed.com)
Project Leader: Keith Joho, VP, informatics and bioanalytical operations
Key Tech Partner: Spotfire | SurroStat Analysis Workflow Tool for Biomarker Discovery SurroMed needed to build a secure environment for sharing sample analyses with its partners. Spotfire's DecisionSite Posters provides the technical foundation for distributing and managing that data. ROI: SurroMed launched a new data-sharing service that goes beyond static reports. | Therastrat (www.therastrat.com)
Project Leaders: Joseph Gut, CSO; Dario Bagatto, CIO
| SafeBase Therastrat engineered an enterprise-strength system for storing, processing, mining, and visualizing theragenomic concepts related to personalized drug safety. ROI: Researchers have a system that supports prediction of ADRs and helps identify patients with potentially elevated risk. | XOMA (www.xoma.com)
Project Leader: Dan Cafaro, VP, clinical and regulatory affairs
Key Tech Partner: SAS | Clinical Decision Support System Using SAS software for Web-based reporting and analysis, Xoma developed a clinical decision support system to provide researchers with ready access to trial data. ROI: Researchers can now view trial data from their desktops even while a trial is ongoing rather than waiting months. | • Grand Prize Winner
Honorable Recognition • Best Platform •Best Informatics Application •Best Application of New Techology | Clinical Research and Trials | Entrant | The Project | • Children's Memorial Hospital (www.childrensmemorial.org)
Project Leader: Eric Bremer, director, brain tumor research
Key Tech Partner: SPSS | Data Mining to Diagnose Brain Tumors To build a database for pediatric brain tumors, Bremer and team use tools from SPSS to analyze data from samples. They use multiple neural networks to predict tumor class based on gene expression. ROI: Besides new analysis tools, the team has identified a therapeutic target for high-grade gliomas and ependymomas. | P&G Pharmaceuticals (www.pg.com)
Project Leader: Rennie Castelino, clinical data manager
Key Tech Partner: Phase Forward | Progressive eClinical Integration To reduce time and errors in trials, and simplify data entry, P&G designed a solution that integrates Phase Forward's InForm EDC software and ClinPhone's voice-recognition system. ROI: Near-real-time, accurate data acquisition, two-way data exchanges, elimination of data reconciliation tasks. | Radiant Research (www.radiantresearch.com)
Project Leader: Michael Davidson, executive medical director
Key Tech Partner: Scientific Software Tools | Custom PDA Solution Delivers the Data Radiant worked with STS to develop a custom EDC application for Palm PDAs. The system uses Web-based tools for remote site assessment, uploading PDA data to the encrypted master database, monitoring site activity, and automating progress reports. ROI: Streamlined study process, higher-quality data, high user acceptance resulting in more compliance. | • Roche Diagnostics (www.roche-diagnostics.com)
Project Leader: Terry Fetterhoff, director, technology management
Key Tech Partner: Entelos | Predictive Biosimulation in the Discovery of a Biomarker for Insulin Sensitivity Roche studied 62 diabetic virtual patients created with Entelos' Metabolism PhysioLab to identify a biomarker for insulin sensitivity. ROI: After a series of in silico biosimulations, Roche identified a candidate biomarker. | Wellspring Pharmaceutical (www.wellspringpharm.com)
Project Leader: Benjamin Levinson, VP, drug development
Key Tech Partner: Target Health | Internet-Based Clinical Trial Technology Wellspring worked with Target Health to develop an online electronic case report form without having to supply software to each study site. An auto-alert system monitors dosing. ROI: Immediate cost savings of $30,000; reduced time from data entry to data analysis; anticipated revenue increase of $500,000. | • Grand Prize Winner
Honorable Recognition
• Best Platform •Best Informatics Application •Best Application of New Techology | IT Infrastructure and Informatics | Entrant | The Project | Aventis Pasteur (www.us.aventispasteur.com)
Project Leader: Grace D'Amico, executive director, customer services | VaccineShoppe.com The company developed an e-commerce site for customers to purchase vaccines and medical supplies as well as check account information, track orders, and access educational resources. The development team has also added cross-sell and upsell functions. ROI: VaccineShop.com is now a major selling channel for the company; by the end of 2003, average order size had increased in dollars by more than 50% over 2002. | • Baylor College of Medicine, Dept. of Molecular & Cellular Biology Core Lab (www.public.bcm.tmc.edu)
Project Leader: Lisa White, director
Key Tech Partner: Stone Bond Technologies | Automating the Lab at the Microarray Core Facility Baylor sought to eliminate error-fraught paper processes and automate its core lab services, without disrupting operations. The team implemented Stone Bond's Enterprise Enabler LIMS. ROI: Streamlined processes, faster workflow, immediate availability of data, elevated accuracy. | Charles River Proteomic Services (www.criver.com)
Project Leader: Heming Xing, manager of bioinformatics | Integrated Proteomic Platform CPRS sought a platform to enable fee-for-service proteomic research services, e.g., sample processing, biomarker identification, molecular phenotyping. The company built upon ProteomIQ from Proteome Systems and infrastructure from IBM. ROI: CPRS can offer a full spectrum of proteomic services, and customers and access, participate in, and control the science as data is generated. | Fred Hutchinson Cancer Research Center (www.fhcrc.org)
Project Leader: Derek Walker, technical project manager
Key Tech Partner: IBM Life Sciences | Clinical Immunogenetic Data Integration Project FHCRC worked with IBM to develop a distributed database query system. Phase 1 linked 4 lab research databases and a clinical research database, accessible through one interface. ROI: Analyses can now be done in hours instead of weeks, and queries involve a single step with no manual manipulations. | MDS Proteomics (www.mdsintl.com)
Project Leader: John Sulja, senior director, information systems, MDS; Srini Chari, general manager of solutions, TurboWorx
Key Tech Partner: TurboWorx | Liberating Scientists from Drudgery of Data Manipulation MDS deployed TurboWorx software to improve automation and acceleration of analytical processing workflows and to integrate disparate data and applications. ROI: With a system that automates development and execution of complex workflows in a mixed computing environment, the company can focus on core scientific or business activities. | Southwest Foundation for Biomedical Research (www.sfbr.org)
Project Leader: Gerry Vest, systems administrator
Key Tech Partner: Sun Microsystems | Low-Cost, High-Performance IT Environment for Genetics Research To rebuild its infrastructure, SFBR tested OSes, servers, and storage to find the best and most cost-effective for speeding up data processing and access. ROI: The new Sun-based IT cluster can process jobs in 5 minutes that used to take an hour, while keeping costs down. | • Grand Prize Winner
Honorable Recognition
• Best Platform •Best Informatics Application •Best Application of New Techology | Back to Special Report: 2004: A Best Practices Odyssey.
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This paper discusses the MetaMiner™ (CF) data analysis platform for a broad range of CF researchers designed to: 1. Easily assemble important biological and chemical experimental data available today in cystic fibrosis research. 2. Visualize key mechanisms leading to the disease through pathway maps and network models 3. Provide the CF community a “one stop shop” tool for uploading and analyzing experimental data in a disease-centered interface. Download now
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Storage for Science
Methods for Managing Large and Rapidly Growing Data Stores in Life Science Research Environments
Sponsored by Isilon
Large and rapidly growing stores of file-based and other data are a hallmark of life science research and bioinformatics environments. Determining how best to manage those data stores has become a significant challenge for the Researchers and IT Professionals that support them.
This webcast is intended to:
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Isilon Systems ~ Senior Marketing Communications Manager
Isilon Systems is the worldwide leader in clustered storage systems and software for digital content and unstructured data. We seek an experienced marketing communications professional/writer expert in creating and delivering effective and persuasive business communications. The ideal candidate can think at the strategic and conceptual level and act, simultaneously, as a highly-effective and productive individual contributor. The position is based in Seattle, WA. For additional information click here: Lilly Singapore Center for Drug Discovery (LSCDD) - Associate Director of Informatics
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