demands of lab professionals in applications such as A powerful history: SEQUEST Cluster personal computer. These search times

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1 Superior scalability, flexibility and advanced integration facilitate protein identification database searches ~ BladeCenter at a glance Comprehensive solutions for About greater success The goal of Healthcare and Form Factor Rack/7U, high-availability midplane Once this compute power challenge Life Sciences is to rapidly bring IT Blade bays Up to 14 -way, and up to 7 4-way has been addressed, researchers still technology to customers and Switch modules 4 switch module bays have to efficiently manage the enor- Business Partners in the fields of mous amounts of valuable proteomic pharmaceutical research, biotechnol- data acquired. Healthcare and Life ogy, genomics, health and other life Sciences offers proteomics storage science industries. is a proven infrastructures that leverage its array leader in data integration, super of FAStT products, Linear Tape-Open computing, high performance storage, library products and Tivoli software e-business and information technology suite. These solutions provide research- services. Power Supply Module Up to 4 (hot-swap and redundant 1800W with load balancing and failover capabilities) Cooling Modules hot-swap and redundant blowers standard Systems Management Hardware 1 management module standard, add an optional second module for redundancy ~ BladeCenter HS0 at a glance Intel Xeon up to 3. GHz Number of processors (std/max) 1/ storing and managing this data Long-term projects at Research Up to IDE (or up to hot-swap Ultra30 SCSI drives with optional SCSI Storage Expansion Unit) over the course of many years. Centers and the Deep Computing RAID support Integrated IDE RAID standard on blade server, integrated RAID with SCSI Storage Expansion Unit option ers with an automated manner of Institute foster collaboration with life Copyright Corporation 004 Thermo Electron Corporation joins Healthcare and Life Sciences to accelerate SEQUEST Cluster results Corporation Route 100 Somers, NY U.S.A. Business Partner: Thermo Electron Corp. Printed in the United States of America All Rights Reserved A world leader in hightech instruments, Thermo, the logo, ~, the ~ logo, OnForever, POWER, Tivoli and WebSphere are trademarks or registered trademarks of International Business Machines Corporation in the United States, other countries, or both. Electron Corporation helps life science, laboratory and industrial customers advance scientific knowledge, enable SEQUEST and ProteomeX are trademarks of Thermo Electron Corporation in the United States, other countries, or both. drug discovery, improve And as researchers expand the scope science companies bringing domain of their work, they need to make expertise and innovative technologies project data easily and securely to the development of life science accessible to collaborators and solutions. Intel and Xeon are trademarks of Intel Corporation in the United States, other countries, or both. Director with systems management and trial deployment tools, Director Server Plus Pack optional customers around the world. To meet this need Healthcare and Life For more information Other company, product, and service names may be trademarks or service marks of others. state-of-the-art instrument Sciences can provide a customized To learn more about Healthcare WebSphere implementation. Simple and Life Science Solutions and Printed in the United States on recycled paper containing 10% recovered post-consumer fiber. software to meet the rigorous Limited warranty1 and support 3-year onsite limited warranty Microsoft Windows Server 003, Microsoft Windows 000 Server/Advanced Server, Red Hat Linux, SuSE Linux, Novell NetWare ~ BladeCenter JS0 at a glance PowerPC 970 at 1.6GHz (64-bit) Number of processors Memory bus and easy to use, this innovative solution Business Partners, visit ibm.com/ provides a security-rich Web portal for solutions/lifesciences or contact an the presentation and sharing of data or Healthcare and Life Sciences deliverables among users worldwide. specialist at LS@us.ibm.com. manufacturing processes and protect people and the environment. Thermo Electron s integrated solutions combine systems and advanced demands of lab professionals in applications such as A powerful history: SEQUEST Cluster personal computer. These search times proteomics, drug discovery, and the Cluster ~ 1350 can be further affected by the size of environmental analysis and With the introduction of new tandem the protein database being searched analytical quantification. Based mass spectrometry instruments that and other important parameters. This in Waltham, Massachusetts, have greater sensitivity and faster scan bottleneck must be addressed with a Thermo Electron has revenues speeds, proteomics researchers are high performance computing solution of more than $ billion and finding that complex samples can that can handle this large volume employs approximately 11,000 generate data files that are 5 10x the of data. people in 30 countries worldwide. Healthcare and Life Sciences To learn more about Thermo Electron, 800MHz comprehensive solutions are helping visit Up to IDE more laboratories maximize productiv- Maximum internal storage 80 GB ity and success. size of those to which they ve become accustomed. The resulting SEQUEST Using the framework of parallel virtual database searches, to identify the machine (PVM) programming, SEQUEST Director with systems management and trial deployment tools, Director Server Plus Pack optional proteins and their post-translational Cluster allows for parallel processing, 3-year CRU and onsite limited warranty modifications present in each sample, dramatically reducing database search Limited warranty and support can take up to several days on a times and accelerating protein analysis. SuSE Linux Enterprise Server 8, Turbolinux Enterprise Server 8 gh GH Visit ibm.com/pc/safecomputing periodically for the latest information on safe and effective computing. For a copy of the Statement of Limited Warranty, call Telephone support may be subject to additional charges. For onsite service, sends a technical after attempting to diagnose and resolve the problem remotely.. For a copy of the Statement of Limited Warranty, call Telephone support may be subject to additional charges. For onsite service, sends a technical after attempting to diagnose and resolve the problem remotely. If the problem can be resolved with customer replaceable unit (CRU), then will ship CRU parts to you for your replacement. 5 6

2 SEQUEST Cluster increases the speed and capacity to identify unknown proteins by dividing the database search process into separate tasks and performing them in parallel on the ~ Cluster Once the compute nodes complete their analysis, the results are integrated on the management node and a unified output is generated. More than one year ago, Thermo Electron named Life Sciences its preferred vendor for SEQUEST Cluster solutions, and the two industry giants combined efforts to offer affordable, preconfigured solutions leveraging the Cluster 1350 technology. Together, and Thermo Electron have engaged on more than 100 opportunities worldwide, and the Cluster 1350 has been enthusiastically embraced by proteomics researchers. This original solution, based on the standard x345 (U form) and x335 (1U form) servers, provided several important benefits: Cluster hardware integration at the facility. Typically, customers are shipped several crates of hardware and are forced to build the cluster and make it operational on their own. In contrast, racks, cables and tests the cluster over 48 hours prior to shipping a single crate with the integrated solution. Software integration. taps into the integration capabilities of its worldwide distribution network to offer a preloaded Thermo Electron gold disk image. As a result, researchers no longer need purchase the several necessary software packages and load them in the proper configuration. Three-year worldwide warranty. Covers all components of the cluster including third-party components. This eliminates the need to deal with multiple warranties; supports the entire cluster with a standard next-business-day warranty. Site survey. This includes a complete solutions assurance review (SAR) and hardware setup. An impressive array of diagnostic tools. This includes easy-to-use management software, light path diagnostics, extensive predictive failure analysis, and more. An even more powerful future: SEQUEST Cluster and ~ BladeCenter Thermo Electron and are teaming up once again to facilitate database searches further, integrating the ~ BladeCenter solution into the SEQUEST Cluster. Blades are slim, hotswappable servers that fit into a single chassis, like books in a bookshelf. Each blade is an independent server, with its own processors, memory, storage, network controllers, operating system and applications. The blade server simply slides into a bay in the chassis and plugs into a mid- or backplane, sharing power, fans, floppy drives, switches and ports with other blade servers. The benefits of the blade approach will be obvious to anyone who has to run down hundreds of cables strung through racks just to add and remove servers. With switches and power units shared, precious space is freed up and blade servers enable higher density with far greater ease, when compared with the earlier 1U and U solutions. According to IDC, blade technology is the world s fastest growing server market segment based on server revenue, growing nearly 550% in 003. IDC estimates that blade systems will account for one of every four servers by 007. Recent data from IDC shows that captured 43.5% of the blade server market in the fourth quarter of 003. Making the SEQUEST Cluster more powerful and proteomics more successful The BladeCenter solution has numerous features and benefits that, when combined with SEQUEST Cluster, give proteomic scientists the power and performance they need to speed their research and ultimately reduce the time it takes to bring new drugs and treatment options to market. All the capacity you need, when you need it BladeCenter solutions make adding capacity simple and affordable. BladeCenter s technology features deliver an effective scale-out architec-

3 ture that lets you add server modules quickly using a pay as you grow approach. Outstanding performance density The BladeCenter design enables you to combine up to 14 server blades in a single 7U chassis. This allows up to 84 -way servers in a standard 4U rack. In fact, over a teraflop of compute power can be packed into a single BladeCenter rack. The efficient design features leading-edge cooling technology and the latest Intel Xeon, Intel Xeon MP and PowerPC 970 processors. Affordable availability for your SEQUEST Cluster application Chassis features, such as high-availability midplanes and redundant hot-swap cooling and power help reduce single points of failure. This is part of the OnForever features, designed to deliver outstanding operation and help increase your productivity. Tight integration of key components such as networking services, centralized management and applications to enable high availability. BladeCenter integration of components The BladeCenter integrates the switch and other components into the basic chassis to dramatically reduce the number of cluster components. This results in greater reliability, as there are far fewer items that can break or go down. Further, this integration allows the The JS0 is a crucial part of our ~ BladeCenter offering. By embedding POWER microprocessor technology into our industry leading BladeCenter and offering Linux on POWER enablement right away, we can give customers a full suite of product offerings that no other vendor can match. BladeCenter to use more than 80% fewer cables than would be needed with traditional clusters. This not only allows for a much cleaner solution, but provides for much greater reliability. Advanced manageability Director Director unleashes the power of BladeCenter, giving you comprehensive remote management from a single graphical console. Director, which ships with BladeCenter, automates and simplifies IT tasks, letting you deploy, configure, manage and maintain up to hundreds of blade servers. Advanced management capabilities boost administrator productivity, reduce costs, improve overall productivity and make administration easier. Director and BladeCenter deliver incredible control of -way Intel and -way POWER processor-based blade servers. Shared infrastructure means platform deployment is quicker and more costeffective. Because installing a new blade is fast and easy, expanding capacity for applications like SEQUEST Cluster can be completed in minutes, instead of hours. -Jeff Benck, VP of ~ BladeCenter Group Tools such as Deployment Wizard, and functions such as Automatic Chassis Discovery and Event Action Plans, make infrastructure deployment a snap. The Deployment Wizard allows you to save chassis configurations for easy replication. Another tool, Remote Deployment Manager (RDM), gives you the ability to create, maintain and deploy images from a single drag-anddrop user interface. With the tight integration of storage, networking, servers, the SEQUEST Cluster application and Director s common interface for a rich portfolio of management tools, the BladeCenter design is both intelligent and simple. has created an ideal environment to help maintain your data center. And tools such as light path diagnostics, Predictive Failure Analysis and calibrated vectored cooling can help reduce administration costs. Some of the key optional enhancements in the Director server Plus Pack include Capacity Manager, Software Rejuvenation, System Availability and Rack Manager. 3

4 The ~ BladeCenter HS0 3-bit performance for SEQUEST Cluster The HS0 blades are based on the Intel Xeon and can be configured with one or two processors per blade. Thermo Electron has chosen this industry standard offering to be included in its ProteomeX LTQ Workstation solution. Researchers will be able to purchase the ProteomeX system two quaternary pumps, sophisticated new Finnigan Micro AS proteomics autosampler, 10-port lowvolume switching valve, Finnigan LTQ ion trap mass spectrometer, potent acquisition software, SEQUEST Cluster processing software and a 4-node HS0 BladeCenter Cluster 1350 system via their trusted Thermo Electron sales representative. Larger SEQUEST Cluster HS0 BladeCenter configurations are also available through and certified resellers. ~ BladeCenter JS0 64-bit performance for SEQUEST Cluster The JS0 blades are based on the PowerPC 970 processor and can be configured with either one or two processors per blade. The Medical College of Wisconsin (MCW) has implemented the JS0 as the heart of its new computing infrastructure support system for proteomics research. Working with and Thermo Electron, MCW is the initial customer site to test the SEQUEST Cluster application on the JS0 running SUSE LINUX. We ve used a variety of hardware systems in the past, but we re looking to push the limits of proteomics research and needed a technology platform that could keep up. and the BladeCenter family was the way to go, said Dr. Andrew S. Greene, Professor and Director of the Biotechnology and Biomedical Engineering Center at the Medical College of Wisconsin. With ~ BladeCenter JS0 being based on the POWER Architecture and s commitment to the POWER roadmap, we think that we will have a great future with this platform. Mix-and-match blades for optimal performance The modular design of the BladeCenter enables Intel Xeon-based (two-way HS0 blades) and the PowerPC 970- based (two-way JS0 blades) blade servers in the same chassis. This mixed blade capability helps create workload and configuration flexibility. It even supports multiple operating systems. Applications can be mapped to the hardware architecture that works best, optimizing the overall system. For example, your 3-bit applications can continue to run on the Intel Xeon-based blades, while you add PowerPC 970- based blades for Thermo Electron s SEQUEST Cluster application. Thermo Electron and Healthcare and Life Sciences the experts in protein identification As researchers ramp up their proteomics efforts, they are demanding a faster means for performing protein identification database searches. Healthcare and Life Sciences has partnered with Thermo Electron to offer affordable, preconfigured systems for their SEQUEST Cluster solution for protein identification. Cluster 1350 offerings are available with the original x335 servers (1U form), the 3-bit Intel Xeon-based HS0 BladeCenter and the ultrafast 64-bit PowerPC 970-based JS0 BladeCenter. These solutions can reduce database search times from several days to mere minutes. Using SEQUEST on BladeCenter has shown to be the most efficient way for proteomics researchers to speed up their data analysis without the risk of downtime or the need to be a computer expert. -Lester Taylor, Global Product Marketing Director, Life Sciences Mass Spectrometry, Thermo Electron Corporation 4

5 Superior scalability, flexibility and advanced integration facilitate protein identification database searches ~ BladeCenter at a glance Comprehensive solutions for About greater success The goal of Healthcare and Form Factor Rack/7U, high-availability midplane Once this compute power challenge Life Sciences is to rapidly bring IT Blade bays Up to 14 -way, and up to 7 4-way has been addressed, researchers still technology to customers and Switch modules 4 switch module bays have to efficiently manage the enor- Business Partners in the fields of mous amounts of valuable proteomic pharmaceutical research, biotechnol- data acquired. Healthcare and Life ogy, genomics, health and other life Sciences offers proteomics storage science industries. is a proven infrastructures that leverage its array leader in data integration, super of FAStT products, Linear Tape-Open computing, high performance storage, library products and Tivoli software e-business and information technology suite. These solutions provide research- services. Power Supply Module Up to 4 (hot-swap and redundant 1800W with load balancing and failover capabilities) Cooling Modules hot-swap and redundant blowers standard Systems Management Hardware 1 management module standard, add an optional second module for redundancy ~ BladeCenter HS0 at a glance Intel Xeon up to 3. GHz Number of processors (std/max) 1/ storing and managing this data Long-term projects at Research Up to IDE (or up to hot-swap Ultra30 SCSI drives with optional SCSI Storage Expansion Unit) over the course of many years. Centers and the Deep Computing RAID support Integrated IDE RAID standard on blade server, integrated RAID with SCSI Storage Expansion Unit option ers with an automated manner of Institute foster collaboration with life Copyright Corporation 004 Thermo Electron Corporation joins Healthcare and Life Sciences to accelerate SEQUEST Cluster results Corporation Route 100 Somers, NY U.S.A. Business Partner: Thermo Electron Corp. Printed in the United States of America All Rights Reserved A world leader in hightech instruments, Thermo, the logo, ~, the ~ logo, OnForever, POWER, Tivoli and WebSphere are trademarks or registered trademarks of International Business Machines Corporation in the United States, other countries, or both. Electron Corporation helps life science, laboratory and industrial customers advance scientific knowledge, enable SEQUEST and ProteomeX are trademarks of Thermo Electron Corporation in the United States, other countries, or both. drug discovery, improve And as researchers expand the scope science companies bringing domain of their work, they need to make expertise and innovative technologies project data easily and securely to the development of life science accessible to collaborators and solutions. Intel and Xeon are trademarks of Intel Corporation in the United States, other countries, or both. Director with systems management and trial deployment tools, Director Server Plus Pack optional customers around the world. To meet this need Healthcare and Life For more information Other company, product, and service names may be trademarks or service marks of others. state-of-the-art instrument Sciences can provide a customized To learn more about Healthcare WebSphere implementation. Simple and Life Science Solutions and Printed in the United States on recycled paper containing 10% recovered post-consumer fiber. software to meet the rigorous Limited warranty1 and support 3-year onsite limited warranty Microsoft Windows Server 003, Microsoft Windows 000 Server/Advanced Server, Red Hat Linux, SuSE Linux, Novell NetWare ~ BladeCenter JS0 at a glance PowerPC 970 at 1.6GHz (64-bit) Number of processors Memory bus and easy to use, this innovative solution Business Partners, visit ibm.com/ provides a security-rich Web portal for solutions/lifesciences or contact an the presentation and sharing of data or Healthcare and Life Sciences deliverables among users worldwide. specialist at LS@us.ibm.com. manufacturing processes and protect people and the environment. Thermo Electron s integrated solutions combine systems and advanced demands of lab professionals in applications such as A powerful history: SEQUEST Cluster personal computer. These search times proteomics, drug discovery, and the Cluster ~ 1350 can be further affected by the size of environmental analysis and With the introduction of new tandem the protein database being searched analytical quantification. Based mass spectrometry instruments that and other important parameters. This in Waltham, Massachusetts, have greater sensitivity and faster scan bottleneck must be addressed with a Thermo Electron has revenues speeds, proteomics researchers are high performance computing solution of more than $ billion and finding that complex samples can that can handle this large volume employs approximately 11,000 generate data files that are 5 10x the of data. people in 30 countries worldwide. Healthcare and Life Sciences To learn more about Thermo Electron, 800MHz comprehensive solutions are helping visit Up to IDE more laboratories maximize productiv- Maximum internal storage 80 GB ity and success. size of those to which they ve become accustomed. The resulting SEQUEST Using the framework of parallel virtual database searches, to identify the machine (PVM) programming, SEQUEST Director with systems management and trial deployment tools, Director Server Plus Pack optional proteins and their post-translational Cluster allows for parallel processing, 3-year CRU and onsite limited warranty modifications present in each sample, dramatically reducing database search Limited warranty and support can take up to several days on a times and accelerating protein analysis. SuSE Linux Enterprise Server 8, Turbolinux Enterprise Server 8 gh GH Visit ibm.com/pc/safecomputing periodically for the latest information on safe and effective computing. For a copy of the Statement of Limited Warranty, call Telephone support may be subject to additional charges. For onsite service, sends a technical after attempting to diagnose and resolve the problem remotely.. For a copy of the Statement of Limited Warranty, call Telephone support may be subject to additional charges. For onsite service, sends a technical after attempting to diagnose and resolve the problem remotely. If the problem can be resolved with customer replaceable unit (CRU), then will ship CRU parts to you for your replacement. 5 6

6 Superior scalability, flexibility and advanced integration facilitate protein identification database searches ~ BladeCenter at a glance Comprehensive solutions for About greater success The goal of Healthcare and Form Factor Rack/7U, high-availability midplane Once this compute power challenge Life Sciences is to rapidly bring IT Blade bays Up to 14 -way, and up to 7 4-way has been addressed, researchers still technology to customers and Switch modules 4 switch module bays have to efficiently manage the enor- Business Partners in the fields of mous amounts of valuable proteomic pharmaceutical research, biotechnol- data acquired. Healthcare and Life ogy, genomics, health and other life Sciences offers proteomics storage science industries. is a proven infrastructures that leverage its array leader in data integration, super of FAStT products, Linear Tape-Open computing, high performance storage, library products and Tivoli software e-business and information technology suite. These solutions provide research- services. Power Supply Module Up to 4 (hot-swap and redundant 1800W with load balancing and failover capabilities) Cooling Modules hot-swap and redundant blowers standard Systems Management Hardware 1 management module standard, add an optional second module for redundancy ~ BladeCenter HS0 at a glance Intel Xeon up to 3. GHz Number of processors (std/max) 1/ storing and managing this data Long-term projects at Research Up to IDE (or up to hot-swap Ultra30 SCSI drives with optional SCSI Storage Expansion Unit) over the course of many years. Centers and the Deep Computing RAID support Integrated IDE RAID standard on blade server, integrated RAID with SCSI Storage Expansion Unit option ers with an automated manner of Institute foster collaboration with life Copyright Corporation 004 Thermo Electron Corporation joins Healthcare and Life Sciences to accelerate SEQUEST Cluster results Corporation Route 100 Somers, NY U.S.A. Business Partner: Thermo Electron Corp. Printed in the United States of America All Rights Reserved A world leader in hightech instruments, Thermo, the logo, ~, the ~ logo, OnForever, POWER, Tivoli and WebSphere are trademarks or registered trademarks of International Business Machines Corporation in the United States, other countries, or both. Electron Corporation helps life science, laboratory and industrial customers advance scientific knowledge, enable SEQUEST and ProteomeX are trademarks of Thermo Electron Corporation in the United States, other countries, or both. drug discovery, improve And as researchers expand the scope science companies bringing domain of their work, they need to make expertise and innovative technologies project data easily and securely to the development of life science accessible to collaborators and solutions. Intel and Xeon are trademarks of Intel Corporation in the United States, other countries, or both. Director with systems management and trial deployment tools, Director Server Plus Pack optional customers around the world. To meet this need Healthcare and Life For more information Other company, product, and service names may be trademarks or service marks of others. state-of-the-art instrument Sciences can provide a customized To learn more about Healthcare WebSphere implementation. Simple and Life Science Solutions and Printed in the United States on recycled paper containing 10% recovered post-consumer fiber. software to meet the rigorous Limited warranty1 and support 3-year onsite limited warranty Microsoft Windows Server 003, Microsoft Windows 000 Server/Advanced Server, Red Hat Linux, SuSE Linux, Novell NetWare ~ BladeCenter JS0 at a glance PowerPC 970 at 1.6GHz (64-bit) Number of processors Memory bus and easy to use, this innovative solution Business Partners, visit ibm.com/ provides a security-rich Web portal for solutions/lifesciences or contact an the presentation and sharing of data or Healthcare and Life Sciences deliverables among users worldwide. specialist at LS@us.ibm.com. manufacturing processes and protect people and the environment. Thermo Electron s integrated solutions combine systems and advanced demands of lab professionals in applications such as A powerful history: SEQUEST Cluster personal computer. These search times proteomics, drug discovery, and the Cluster ~ 1350 can be further affected by the size of environmental analysis and With the introduction of new tandem the protein database being searched analytical quantification. Based mass spectrometry instruments that and other important parameters. This in Waltham, Massachusetts, have greater sensitivity and faster scan bottleneck must be addressed with a Thermo Electron has revenues speeds, proteomics researchers are high performance computing solution of more than $ billion and finding that complex samples can that can handle this large volume employs approximately 11,000 generate data files that are 5 10x the of data. people in 30 countries worldwide. Healthcare and Life Sciences To learn more about Thermo Electron, 800MHz comprehensive solutions are helping visit Up to IDE more laboratories maximize productiv- Maximum internal storage 80 GB ity and success. size of those to which they ve become accustomed. The resulting SEQUEST Using the framework of parallel virtual database searches, to identify the machine (PVM) programming, SEQUEST Director with systems management and trial deployment tools, Director Server Plus Pack optional proteins and their post-translational Cluster allows for parallel processing, 3-year CRU and onsite limited warranty modifications present in each sample, dramatically reducing database search Limited warranty and support can take up to several days on a times and accelerating protein analysis. SuSE Linux Enterprise Server 8, Turbolinux Enterprise Server 8 gh GH Visit ibm.com/pc/safecomputing periodically for the latest information on safe and effective computing. For a copy of the Statement of Limited Warranty, call Telephone support may be subject to additional charges. For onsite service, sends a technical after attempting to diagnose and resolve the problem remotely.. For a copy of the Statement of Limited Warranty, call Telephone support may be subject to additional charges. For onsite service, sends a technical after attempting to diagnose and resolve the problem remotely. If the problem can be resolved with customer replaceable unit (CRU), then will ship CRU parts to you for your replacement. 5 6