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Microsoft’s BioIT Alliance

n 2006, Microsoft launched the BioIT Alliance. The project was largely the work of Microsoft executive Don Rule, and is now directed by Rudolph Poten- zone, Microsoft’s worldwide industry technology strategist for pharmaceuti- cals (and the former CEO of LION). Since its launch, the BioIT Alliance has grown to more than 70 members, with a stated goal of increasing membership to over 100 by year-end. While the major- ity are well known vendors in the industry—such as Thermo Fisher Scientific, Waters, IInforSense, Sun, AcitveMotif, Agilent, Ocimum Biosolutions, and ChemAxon—others are relatively unknown players, including many from Europe. A variety of other organi- zations, including IUPAC, a chemical standards body, and university groups (Hebrew University of Jerusalem) have also joined. There is a possibility that some pharma- ceutical companies might join as well. Priorities for the alliance, as Potenzone sees it, include communication— helping companies connect that hadn’t contemplated working together. To be sure, the BioIT Alliance encourages companies to use and adapt relevant Micro- soft technologies, but it also forms a nucleus of companies that, to a degree, can share pre-competitive tools, technologies and strategies. How can companies integrate research information and business intelligence for themselves and their clients? “We’re really branching out beyond just bio-IT,” Potenzone told Bio•IT World last year. “I think people tend to think of bio-IT as more focused on . We’re definitely seeing a branching out further downstream into the clinical world and into medical devices, which formally is all part of bio-IT.” The BioIT Alliance website includes regular updates on news and activities of the member organizations (www.bio- italliance.org.) A recent case study, for example, showcases Microsoft’s collaboration with Pfizer and Infosys Technolo- gies to develop The Biologist Workbench to allow research- ers to better visualize data. The Alliance’s focus is building with the partner com- munity real practical solutions that can positively impact the drug development pipeline. With Microsoft dedicating growing resources in the life sciences space, the future is looking very good indeed. Bio•IT World is pleased to publish this special sup- plement, with support from Microsoft and the participating Alliance members, to pro- vide further insight into the activities of the Alliance and some of its part- ners, and to encourage other groups to take a fresh look at the BioIT Alliance. 

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thermo fisher scientific Thermo Fisher Scientific Offers Enterprise Document Management Solution

The centralization and harmonization of unanswered until now, for a secure, cost and functionality, further cements the laboratory data is a critical and strategic effective, validated content management relationship between Thermo Fisher part of the global growth of any pharmaceu- solution that incorporates structured data Scientific and Microsoft to deliver next- tical company. Large-scale deployments from LIMS, chromatography data system generation and best of breed open solu- of integrated and web-based systems can (CDS) and other enterprise systems along tions. “We’re thrilled with the extent of now be relied upon to be more consistent with unstructured information that support our ongoing relationship with Thermo and more rapid because purpose-built laboratory processes, all in a completely Fisher Scientific,” said Mike Naimoli, U.S. laboratory information management sys- validated solution. In the past solutions life sciences industry solutions director, tems (LIMS), like Thermo Scientific Watson have been incomplete, cumbersome and Microsoft Corporation. “Organizations LIMS™, can not only facilitate superior expensive. To satisfy this need, Thermo store documents in a wide range of data exchange across the organizations, Fisher Scientific recently announced a isolated systems on multiple software but also offer a bio-directional flow of data collaborative agreement with NextDocs platforms – making the retrieval and syn- between a phar- Corporation to bundle and sell its enter- thesis of information daunting tasks. This Thermo Fisher Scientific maceutical com- prise document, quality and compliance new alliance between Thermo Fisher and  Founded: 1957 pany and with its management solution NextDocs goes a long  # of employees: 30,000+ contract research suite. The offering is way toward addressing  Location: Waltham, MA organization (CRO). a natural extension of the need for regulated  Microsoft solution This freer exchange Thermo Fisher’s port- content management, provider: 8 years of data can mean folio of LIMS and CDS integrated workflow  Top Executive: improved business products, allowing the administration and Marijn E. Dekkers, President and CEO decisions that company to offer a com- compliant collabora- www.thermofisher.com enable a life sci- prehensive, informatics tion in the enterprise ences company to and content manage- setting. We believe this deliver the right compounds faster, and ment solution to the joint solution will bring saves the time and expense of working industry. It provides enormous value to the on a compound that ultimately will prove organizations with a industry as a whole.” ineffective. It also allows for faster and complete document “By offering an enter- more automated review and submission management and col- prise content manage- of reports. For bioanalytical laboratories laboration system for ment solution that is and CROs around the world, Thermo managing documents, tightly integrated with David Champagne Scientific Watson LIMS™ provides the records (e.g. training our LIMS and CDS work- detailed protocols necessary for DMPK records), SOP’s (standard operating pro- flow for regulated laboratory environ- and bioanalytical studies in drug discovery cedures), activities and other information ­ments, Thermo Fisher is better positioned along with maximum flexibility and con- critical to the enterprise. to offer our customers the most compre- figurability so that each lab can integrate Thermo Fisher Scientific, the leader hensive informatics solution in the indus- workflows or instrumentation across study in providing purpose-built informat- try,” concludes Dave Champagne. protocols as required. ics software solutions, has partnered For a free webinar on NextDocs docu- It’s also critical for organizations to with Microsoft, the technology leader, ment management solutions or for more implement enterprise-wide document as a fellow member of the Microsoft information about Thermo Scientific management and collaboration tools to BioIT Alliance. The company’s recent Watson LIMS please call on +1 866-463- stay competitive, increase productivity and partnership with NextDocs to deliver 6522 or e-mail marketing.informatics@ comply with standards. There has been a a document and compliance suite thermofisher.com or visit www.thermo. need in the industry that has gone largely that delivers unmatched ease of use com/informatics. 

Bio•IT World september 2008 www.bio-itworld.com Thermo_Bio-IT_HR.indd 1

© 2008 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries. It’s abouteffi Now withThermoScientifi Thermo Scientifi and improveyourmargins.Nowondermorelaboratoriescounton better informedbusinessdecisions,decreaseyourtimetomarket core ofeveryThermoScientifi to thehighestlevelofeffi Thermo Scientifi Which is why it’s about time you invested in a Thermo Scientifi +1 8664636522•marketing.informatics@thermofi effi deployment ofanyThermoScientifi Thermo Scientifi a webbrowserforfull,secure,highperformanceaccess toany Moving science forwardscience Moving ciency. Isn’titabouttime?Yourtime. c LIMSthananyother. c LIMSarepurpose-builttohelpdriveyourbusiness c informaticssolution–fromanywhere.Web ciency. ciency. Webuildtheeffi c WebAccessSuite, c LIMSsoyoucanmakefasterand c LIMS.That’sallabout ™ allyouneedis ciencies into the sher.com c LIMS. and for your business.yourfor and sourcelabintegration yourforof WebAccessSuite DEMO.FREE visit www. visit DEMO,FREE a and informationmoreFor enterprise. your across compliance and efficiencies reliable and secure you giving data, and instruments people, of integration transparent thermo.com/webaccess Thermo ScientificThermo ™ - the ultimatethe -

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active motif Accelerating Downstream Understanding of Next-Gen Sequence Data

What distinguishes your company from databases in about two weeks its competitors and makes it unique? using TimeLogic hardware. They TimeLogic, a brand of Active Motif, has calculated that this task would been in the business of supplying bioinfor- have taken one century on a matics tools to the life science community standard server. for over 10 years. We offer a variety of hard- ware products ranging from CodeQuest™ What prompted you to join workstations to multi-server DeCypher® the Microsoft Bio-IT Alliance enterprise solutions. Moreover, our com- and what do you hope to get pany specializes in designing algorithm out of it? implementations using low-level languages “Microsoft’s Windows operating for custom-designed system is a ubiquitous platform Active Motif Field Programmable for the life science industry, and we want to TimeLogic’s FPGA accelerator card draws only 15 watts.  Founded: 1999 Gate Arrays (FPGA). ensure we are able to support our custom-  # of employees: This enables us to ers’ bioinformatics infrastructure,” states sequencing data analysis in conjunction <100 worldwide deliver the equiva- Darryl León, Ph.D., Informatics Product with Invitrogen, to identify ways in which  Location: Carlsbad, CA lent of nearly 500 Manager for TimeLogic. “We see the impor- our FPGA technology can deliver improved with offices in Japan CPU cores (3 GHz) tance of being part of an organization that performance and analysis quality,” states and Belgium of performance with contributes to the BIO-IT community, and we Chris Hoover, Business Development  Microsoft solution a single PCIe card. are interested in collaborating with other Manager for TimeLogic. provider: >10 years  Top Executive: We support Micro- informatics companies to advance the pace Joseph Fernandez, CEO soft Windows Serv- of discovery in the life sciences.” What’s the biggest misconception cus- www.activemotif.com ers, Linux and Sun tomers have about your technology? www.timelogic.com Solaris platforms, List the Microsoft products you support. Many people are under the misconcep- and provide three The DeCypher and CodeQuest systems, tion that TimeLogic products are all over types of user interfaces. employing our new PCIe-format SeqCrunch- $100K. However, we have products in er acceleration card, run on Windows 2003 the $30K range that give independent Name of customer(s) you’ve positively servers. To simplify genome analysis work- investigators the acceleration hardware impacted and briefly tell how? flows, we also provide the PipeWorks™ needed to pursue ultra high-throughput TimeLogic technology has enabled cus- visual workflow environment, which genome annotation and tomers to engage in large-scale, genomic includes both client and server applica- projects. comparisons projects without requiring tions for Windows Server and Windows deployment or use of a large cluster XP platforms. Briefly describe the steps and process- system. For example, one academic cus- es implemented in a typical customer tomer routinely uses the Tera-BLAST How might your company and capabili- engagement. implementation to compare two million ties be different a year from now? TimeLogic’s bioinformaticists provide GST-length sequences against a large Active Motif expects that higher next- custom benchmarks for each customer plant genome using a DeCypher system generation sequencing throughput will to ensure a level of performance and data that only requires 6U of rack space. The lead to a stronger demand for our current quality our customers demand. Work- Salk Institute in La Jolla, CA, compared acceleration products as the volume of ing closely with our customers, we also Dr. ’s Global Ocean Sampling new sequences and well-characterized determine their level of throughput and IT (GOS) data set against Pfam (about 350 data rises. In addition, “TimeLogic is requirements before proposing an optimal million comparisons) and other HMM currently investigating next-generation biocomputing solution. 

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Ocimum biosolutions BiotrackerTM LIMS — The Life Sciences Research LIMS

Ocimum Biosolutions offers one of the configurable structure. Biotracker™ LIMS utilizing a number of largest portfolios of integrated genomic Full Featured LIMS methodologies including; Waterfall, Proto- solutions. Our vision is to become the Make sure your LIMS provides out-of-the- typical, Time-Boxing, and Chunking. No. 1 outsourcing company by box the core features that are needed to The Standard Ocimum Biotracker™ providing quality solutions spanning across run your laboratories. Biotracker™ Core Implementation Process steps include: the genomics space. Pharmaceutical, features include: • Kick-off meeting Biotechnology, Diagnostic, Government • Laboratory Administration • Requirements Gathering – and Academic institutions worldwide • Project Design and Scheduling FRD Delivered utilize our comprehensive LIMS, bioin- • Work Flow and Process Tracking • Requirements Analysis – formatic systems, genomic databases • Experiment Tracking, Analysis SRS Delivered and service resources to enable better & Archive • Design & Development understanding of • Sample Management • Testing & Documentation Ocimum Biosolutions underlying mecha- • Hierarchal Location Tracking • Beta Testing  Founded: 2000 nisms of diseases, • Chain of Custody • Final Acceptance Testing  # of employees: 300+ discovery and pri- • Plate Management & Tracking • Go- Live  Locations: MD, India, oritization of gene • Inventory Mgmt & Tracking Deployment timelines vary depending Netherlands targets and bio- • Configurable & Extensible Forms upon the size and scope of the particular  Microsoft solution markers. & Fields client project. Typical implementation time provider: 8 years Biotracker™ is • Instrument Integration is 3 – 6 months on average.  Top Executives: Anu Acha- the only LIMS pur- • Ad-hoc Report Builder Customer successes include: rya, CEO and Subash Lin- gareddy President & CFO posely designed • Cost Estimation of Projects A Microarray & Gene Expression Analysis  Contact Ocimum at out- for Life Science • Standard Reports Core Facility in Asia [email protected] Researchers. The Biotracker™ LIMS has been in produc- Biotracker™ provides integration, explora- critical features tion since 2002 and is currently running tion and analysis of vast quantities of data you should look for in a Life Science in research organizations across pharma- and allow a scalable and flexible storage Research-based LIMS include: ceutical, biotech, academic, and research and retrieval system across our heteroge- Project-Centric LIMS institutes. Biotracker™ is often overlooked neous data repositories. Traditional sample-centric LIMS just do when going through a LIMS selection pro- Biotracker™ at University of New not work well for research environments. cess which tends to focus on traditional Mexico’s Multi-Disciplinary Lab A LIMS for research must provide a flexible LIMS vendors. Researchers then end “After researching multiple LIMS products, data structure that inherently supports up trying to implement a commercial, we chose Biotracker™ due to flexibility a Project/Protocol/Experiment oriented sample-centric LIMS and fail. Life Science needed for a research laboratory”. Barbara environment. Biotracker™ is designed to Research laboratories need Biotracker™ Griffith, Project Director, HSC, UNM operate as researches do and enables you for Core LIMS, Biobanking, Genomics A Top 10 Pharmaceutical Company to derive knowledge from your data. (sequencing, genotyping, expression), The customer needed a solution to replace Flexible LIMS and Proteomics their current biological sample manage- In Research your experiment processes Ocimum Biosolutions’ standard ment and biorepository tracking system. are constantly evolving. Your LIMS must Biotracker™ implementation process Biotracker™ supports the global Molecular be flexible to support your changing needs. follows a modified Waterfall methodology Pathology / Molecular Histology units to Biotracker™ provides an adaptive platform which is described below. Ocimum will, track biological samples and their deriva- to capture your research findings. Rather however, adhere to whatever standards tives maintaining pathology, histology, than dictate the process flow, Biotracker™ or processes that our customer prefers. serology, QC and associate donor’s medi- captures your work in an organized, yet Ocimum has successfully implemented cal and biological information. 

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BioIT Alliance Members http://bioitalliance.org

Aberdean Consulting, LLC Integromics, S.L. Accelrys InterKnowlogy ActiveMotif INVISION IT Systems Affymetrix IO Informatics Agilent Technologies The International Union of Pure and Amylin Pharmaceuticals Applied Chemistry (IUPAC) Applied Biosystems KineMatik Axendia Linguamatics Ltd. Axiom Discovery Inc. Microsoft BIOBASE m-Objects BioDiscovery Molegro ApS Biotique Systems Newtech Global Solutions LLC Blue Reference Inc. NextDocs Corporation CambridgeSoft Corporation nFocus Technologies Inc. Caresoft Inc. Ocimum Biosolutions CeuticalSoft Paradigm Infotech Inc. ChemAxon Persistent Systems Ltd. ChemZoo (ChemSpider) PointCross Clarabridge POINTONE Systems CLC bio PREMIER Biosoft International Capital Technology Information Prodiance Corporation Services (CTIS) Progeniq Pte Ltd. Digipede Technologies ProSanos Corporation discovery biosciences QL2 Dotmatics Ltd. RND Group eXludus SGI FOCUS Biology, LLC SLIM Search Ltd. Gencom Technology Strand Life Sciences GenomeQuest, Inc. Sun Microsystems Gentelligent Inc. Symyx Geospiza, Inc. Syntel GGA Software Services LLC SyynX Solutions GmbH GrapeCity TAKE Solutions GulfStream Bioinformatics Temis Hebrew University of Jerusalem The BioTeam Hewlett-Packard Thermo Fisher Scientific ILink Systems The Scripps Research Institute IMC TranSenda International, LLC InforSense Ltd. Vast Scientific Infosys Technologies Ltd. VizX Labs, LLC Infusion Development Waters

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