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The article discusses the increasing ecosystem of commercial initiatives providing a host of cloud-based services and applications. Steve Philpott of Amylin Pharmaceuticals was one of the first to support the transition to cloud computing. It was mentioned one advantage of cloud-based services is its elastic capacity. It was also noted that the relational database service of Amazon.com lets users launch a new database in a matter of seconds.

The article discusses the latest developments in the clinical genomic informatics industry as of March 2011. It cites the launching of two new gene mutation resources, namely, the Human Variome Project (HVP) in Australia by Richard Cotton and the MutaDATABASE, which was conceptualized by Patrick Willems in Belgium. The two resources could complement or compete with David Cooper's Human Gene Mutation Database (HGMD). INSET: The MutaDATABASE.

The article traces the birth and growth of Solexa, a biotechnology company founded by Shankar Balasubramanian and David Klenerman with Mark Osborne and Colin Barnes. It describes the birth of the company in a beer summit at Panton Arms in Cambridge, Cambridgeshire. The circumstances leading to the founding of the company are presented including the functions of each of the key people that subsequently joined the company like Harold Swerdlow and Nick McCooke. The progress of its single-molecule sequencing is discussed as well as its purchase by Illumina.

The article focuses on efforts in crafting tools to provide medical sense to genome sequencing. The genomic medicine module at the pathology department of Beth Israel Deaconess Medical Center is presented along with its open-source genome annotation pipeline. The focus on pathology is explained together with the idea of a whole-genome clinical clearinghouse formulated by mathematician Peter Tonellato. The comprehensive clinical analysis of the genome of Stephen Quake is discussed including the challenge of delivering actionable information to physicians.

The article focuses on the long-term sequencing success of Broad Institute in Cambridge, Massachusetts. The profiles of its key people Chad Nusbaum and Rob Nicol are provided including their functions and responsibilities at the institute. The two-way relationship of the institute with Illumina is explained as well as the sharing of results that started with Solexa. The testing conducted by Nusbaum on any new next generation sequencing (NGS) operation is discussed.

The article focuses on PREDICT algorithm, a three-dimensional (3-D) model of a G protein-coupled receptor (GPCR) devised by Sharon Shacham, senior vice president (VP) for product development at EPIX Pharmaceuticals. PREDICT models various theoretical conformations of the GPCR core from the amino acid sequence of the receptor. The algorithm also allows the research team to build models of related receptors that are believed to be the source of undesirable drug binding, resulting to side effects. INSETS: PREDICTing Success;Molecular Evolution: PRX-00023.

The article focuses on the BioCreative workshops of MITRE Corporation, a nonprofit, public-interest organization that manages three federally funded research and development centers (FFRDCs). According to Lynette Hirschman, they do not make products that they could not compete with since it would affect their primary objective to provide unbiased advice to the government. INSETS: The Language of Text Mining;Commercial/Open Source Pros and Cons.

The article discusses the biopharmaceutical library of the text-mining group headed by William Hayes. The Biogen Idec library has gained a competitive advantage when it transformed into a den of literature informatics and text-mining with some 1,500 professionals including almost 1,000 scientists in research and development. The Query, Update, Organize, Share and Analyze was founded by mathematicians that has the literature retrieval and management aspect, full text search and text mining. INSETS: Sending out an SPSS;The Case for Curation;Full Text Firewall.

Features 50 companies that have driven and continue to drive the future of biomedical research and drug discovery. Accelrys; Affymetrix; Agilent; Beckman Coulter; Bio-Rad Laboratories; Becton Dickinson.

Focuses on the complex chemical syntheses operation of the chemical research center of Tripos in Cornwall, England. Integration of information technology on chemical processes by the company; Information on the Enhanced Chemical Information Management System (ECIMS) created by Tripos in collaboration with Schering AG; Views of Schering vice president Rainer Matternich on the ECIMS. INSETS: Interesting Times;The Right Chemistry.

Features Genizon BioSciences, formerly known as Galileo Genomics, a biotechnology company based in Quebec. Profile of the company; Utilization of the French Canadian gene pool for high-throughput genotyping; Criteria for selecting diseases for its drug development projects; Details of the company's key IT and software suppliers. INSETS: The French Connection;Hooper Dreams;Through the lens.

Deals with the decision of Novartis Institutes for Biomedical Research to relocate its research center at New England Confectionery Co. building in Boston, Massachusetts. Reason the company chose Boston according to global vice president for communications Fintan Steele; Difficulty experienced by Novartis in hiring employees; Information on the functional genomics group formed by Novartis.

The article features Digizyme, a developer of educational and promotional animations, simulations and videos for diverse life science applications. Founder Gaël McGill explains how the idea for the company came from his recognition of the need for graphic design, animation and visualization tools by several industries. The Digizyme platform is powered by Maya software developed by Autodesk.

An interview with Glen de Vries, president of Medidata Solutions Worldwide, a provider of clinical technology solutions that optimize clinical trials from concept to conclusion, is presented. He explains the original goal of Medidata to take data management during a clinical trial to the Web. He clarifies that the company is not a contract research organization (CRO) but one that provides the technology infrastructure that pharma, biotechnology and medical devices will need in the future.

The article focuses on the Carpe Novo software developed by Liz Worthey and a team of programmers for use in a genome sequencing work involving patient Nicholas Volker. It notes that Volcker has been in the hospital for the better part of two years due to a chronic inflammatory bowel disease. Mutation in the X-linked gene XIAP has been identified with the use of Sanger sequencing. It adds that the software has also been used in interpretations of whole-genome sequencing (WGS) in other patients.

The article features DNA Electronics, a biology-information technology (IT) company, which is gaining attention in the next-generation sequencing (NGS) and molecular diagnostics fields. It notes that some key intellectual property (IP) of the company is offering the foundations for semiconductor sequencing platforms. The SNP-DR handheld device can identify deoxyribonucleic acid (DNA) variants from a saliva sample within 20-30 minutes. It relates how Chris Toumazou founded the company in 2003.

The article focuses on the licensing dispute between charge sequencing inventors. Arjang Hassibi, Nader Pourmand and Ron Davis met while they were working on pyrosequencing at Stanford, which is also the time that Hassibi developed a setup that will test if DNA have an associated charge. Pourmand said they are not ignoring the contribution by Hassibi, but his technology is more focused on hydrogen detection and release than the electrical signals.

The article features SomaLogic, which licensed its lung cancer blood diagnostic solution to Quest Diagnostics. SomaLogic chief executive and chairman Larry Gold said their goal is to be a longitudinal proteomic biomaker monitoring company. The company also is developing its Wellness Chip that is a single, simple blood test that contains all the biomarkers of every disease. ALS and Duchenne muscular dystrophy solutions are also being carefully studied by SomaLogic. INSETS: The Strength of SOMAmers;Rule of Four.

The article previews the Integrated Rule Oriented Data System (iRODS) for next-generation sequencing (NGS) applications from Renaissance Computing Institute (RENCI). INSETS: Follow the Rules;iRODS: Wellcome Relief.

The article presents fasp, a communication protocol from Aspera.

The article focuses on Kevin Ulmer and his attempts at the ultimate sequencing solution. It gives a background on the first generation of deoxyribonucleic acid (DNA) sequencing technologies with the roles of biochemist Fred Sanger and physicist Walter Gilbert. Ulmer's work progress and frustrations at his first biotech company SEQ are described along with the fate of his company Pavonis and his role with EXACT Sciences. His return to Sanger sequencing is presented together with another early belief on more interest in obtaining sequence information.

The article features NABsys and the clinical utility of its electronic, single-molecule sequencing. Its strategy to marry the advantages of nanopores with those of sequencing by hybridization is explained along with its five critical metrics for genome sequencing. Emphasis is given to scalability and a clinically relevant sequencing technology. The advantages of the NABsys system are presented along with the different approach it has taken that puts informatics first.

The article features Beijing Genomics Institute (BGI). A profile of BGI is provided including its interface collaboration in America. The benefit of the new facility in Hongkong is cited along with its projected output by end of 2010. The function of a committee of animal, plant and disease experts is presented together with the conditions of BGI on projects taken. Its fee-for-service option is explained including views about potential competition. Mention is also given to its team of young and bright mathematicians and scientists.

The article describes the process that Hugh Rienhoff undertook to determine the genetic cause of his daughter Beatrice's mysterious condition. His involvement in genetics is presented including his starting DNA Sciences. The earlier success of DNA Sciences is provided until its trouble in 2001 when Rienhoff filed the S-1 document. His search for the reason for his daughter's condition is chronicled starting when she was 18 months old with suspected Loeys-Dietz syndrome until his discovery of evidence implicating a mutation in the gene for copine-1.

The article discusses cloud computing or utility computing according to Chris Dagdigian, BioTeam co-founder and technology director. Dagdigian considers Amazon Web Services (AWS) as the cloud. He says he is not talking about SaaS or SalesForce.com or magical cloud terms when he talks about cloud computing. He also relates that there are some interesting pilot projects in private cloud computing.

The article focuses on the informatics solutions developed and used by Infinity Pharmaceuticals for its IPI-504 clinical drug development and trial as well as the lessons learned from the trial. Infinity Pharmaceuticals gives importance to the capabilities of molecular modeling. The firm supports a drug discovery platform and has built a relational database for clinical data and implemented electronic data capture. A transactional database called iTRAC is another application from the IPI-504 Phase III clinical trial for gastrointestinal stromal tumor. INSET: Informatics Infrastructure.

The article features Hans Lehrach, a German molecular biologist and director of Max Planck Institute for Molecular Genetics in Berlin. Developing molecular biology tools and automation, from new gene cloning techniques to chip-based platforms, is Lehrach's specialty. He co-founded Alacris Pharmaceuticals with George Church of Harvard MEdical School. The company turns complex biological data into a form that can be used by the researcher, doctor and patient, through the combined next-generation sequencing, systems biology, and computing horsepower.

The article evaluates the Geniom RT Analyzer automated microarray processing and analysis from febit holding GmbH. INSET: Hope for HybSelect..

An interview with Angela Shen-Hsieh, an architect and founder of Visual i/o, is presented. When asked how she got involved in data visualization, she notes that architects also make pictures of buildings and they are experts in graphical representation. She reveals that her company is targeting bigger pharmaceutical companies but the technology they offer is very horizontal. She explains how their software is deployed within those companies.

The article discusses the highlights of the ninth Advances in Genome Biology and Technology (AGBT) conference held in Marco Island, Florida from February 6 to 9, 2008. Pacific Biosciences sponsored a beachside fireworks display to raise awareness among 600 delegates. An open source sequencing instrument called the Polonator was launched at the conference. David Bentley of Illumina presented the complete assembly of the world's first African genome.

An interview with Rudolph Potenzone, a worldwide industry technology strategist for pharmaceuticals at Microsoft, is presented. When asked about what happened to his former company LION Bioscience, he says he left LION in 2003 to back out of the U.S. activities. He talks about the BioIT alliance and its being close to having 60 members. He also cites some of the other customer needs in life sciences.

The article reports on the development of the company known as Helicos and its single-molecule imaging instrument HeliScope, that measures the florescence of single dye molecules. The HeliScope includes an imaging head, a cooled CCD camera and an XY stage. The imaging head component has four lasers. The CCD camera is optimized for low image acquisition time and the XY stage has the speed of 15 frames per second. INSETS: Clusters and Coordinates;A Frightening Computational Problem.

The article features Tessella, a software consultancy that works on adaptive trial designs in the pharmaceutical industry. One of the company's projects was with Pfizer, on the Acute Stroke Therapy by Inhibition of Neutrophils, which helped them save money on manufacturing a particular drug. Grant Stephen, chief executive officer (CEO) of Tessella says that those planning to venture in adaptive designs must define their objectives for working on the trial. INSET: Trail Blazing Trials.

The article features Jubilant Biosys, a pharmaceutical company based in Bangalore, India. The company has a decade of experience in computational and bio-IT fields and is initiating drug discovery and development activities. It has entered into a partnership with Eli Lilly and continually recruits Indian scientists based in the U.S. to return to India and work with the company. The company started out with 35 staff in 2001 and employs more than 600 as of 2006. INSET: Wyeth's Passage to India..

The article discusses Marshall R. Peterson's plan of building and designing a data center at the Janelia Farm estate with an information technology infrastructure. Howard Hughes Medical Institute acquired the Janelia Farm and turned it into a research campus with a scientific ensemble to drive the data-intensive fields of imaging, visualization and bioinformatics.

Interviews Nick Giannasi, head of informatics for the Bio-Science division at GE Healthcare in the U.S. Relationship with GlaxoSmithKline PLC; Individuals who buy products and services offered by the company, including scientists; Comparison of the DiscoveryLink middleware used by the company from the middleware used by other companies; Views on the business.

Interviews IBM Corp. program director Kristopher Lichter on the supercomputer Big Blue's participation in the National Genographic Project. background of Lichter; Explanation on how IBM Corp. get involved in the project; Reason for the excitement for a purely scientific project; Response inside the IBM Corp. about the project; Nature of IBM's contribution to the project.

The article reports that Japanese pharmaceutical company, Eisai Co. has invested up to 200 million U.S. dollars in H3 Biomedicine, an oncology drug company. H3 co-founder Stuart Schreiber describes the funding model which spared the company of seeking venture finance or short-term licensing deals. Aside from investment, Eisai is also providing ready access to its drug discovery and development resources, with some of its chemists moving to the U.S. to join H3.

The article discusses notable developments in life sciences and information technology (IT) in 2011. Scientists have discovered two black holes with masses several billion times that of the sun and the Kepler 22 planet which orbits with a balmy atmosphere and a prime candidate for life off earth. Biotechnology pioneer Geron went out from the field of human embryonic stem cell that it helped to create while imaging was done on a female brain experiencing orgasm.

The article reports that Accelrys has launched an informatics suite during its European user group meeting in Athens, Greece. Some features of the informatics suite include a chemical registration system, the cloud-based product HEOS and a chemical data cartridge. The product was developed in partnership with SCYNEXIS. Rob Brown, Accelrys' senior director for life science marketing, explains that the suite covers all capabilities that scientists need to cover daily workflows.

The article discusses the genome assembly challenge, the Assemblathon, a competition to identify best practices in the de novo assembly of complex plant and animal genomes. An overview of University of California Davis Genome Center associate director of bioinformatics Ian Korf's discussion of the Assemblation results and inherent challenges in genome assembly at a Webinar is provided. A list of the top five assemblies is presented including Broad Institute and Wellcome Trust Sanger Institute.

The article reports that QuantuMDx (QMDx) medical director Sir John Burn has offered insight at a nanowire technology for rapid DNA genotyping that could be developed to become the world's first handheld DNA sequencer. He presented the disruptive genome diagnostic technology during the International Congress of Human Genetics in Montreal, Quebec. QMDx signed an exclusive license of intellectual property from Nanosys of the diagnostic and sequencing applications of nanowires and nanotubes.

The article reports on the changing landscape of pharmacological services according to Yuri Rozenman of BT Global Services. The management of all patient records for the National Health Service in Great Britain is one of the examples of enterprise communications services offered by BT. It was said that a large amount of BT's core services fall around strategic outsourcing. The team of Rozenman is helping to authenticate drug supplies to prevent counterfeiting of approved drugs.

The article reports on the Sophia Digital Librarian search tool by Sophia Search which thrives on finding ties between documents with no need for any kind of taxonomy. Sophia Search co-founder David Patterson said the search tool is all about content enrichment within repositories. Patterson added that the tool is developed on the firm's patented contextual discovery engine. Sophia Sales Director Jeff Bierach said the firm is targeting more in the life sciences industry and publishing sectors.

The article reports on the support provided by Life Technologies for Genia's nanospore sequencing start-up. Dietrich Stephan of Life Technologies said they have created proprietary innovations around the pore. He believes that one of Genia's differentiators is that most of the company's senior management has roots in the semiconductor sector. One of the firms vying to commercialize nanopore sequencing technology is Oxford Nanopore in Great Britain.

The article focuses on Ed Liu, a medical researcher who will leave the Genomic Institute of Singapore (GIS) to take the post of president and chief executive officer (CEO) of the Jackson Laboratory (JAX) in Maine come January 2012. Goals that Liu has set for himself as he takes the new post are mentioned, one is to push translational research. Liu recalls the offer made to him by JAX which he accepted as he values the freedom of the latter. He also considers Singapore as a research destination.

The article focuses on the software for genome analysis called Variant Annotation, Analysis and Selection Tool (VAAST) developed by University of Utah scientists and software firm Omicia. The software uses individual genome sequencing for the rapid identification of disease-causing mutations. Rapid identification is ensured through the incorporation of variant frequency data in the algorithm. Omicia chief executive officer (CEO) Martin Reese is applying the software to cancer and other areas. INSET: Endeavor Aids Disease Gene Hunt.

The article focuses on the Galaxy open-source platform developed by colleagues Anton Nekrutenko and James Taylor. It notes that Galaxy serves as a platform for ensuring the accessibility of computational tools. The applications of Galaxy are explored in which Nekrutenko mentions that studies that have used the platform range from RNA sequencing to genome mapping. Taylor stresses the need for them to facilitate the growth of the decentralized community beyond the public site.

The article focuses on life scientist Kevin McKernan and his start-up, Medicinal Genomics. It notes that after the departure of McKernan from Life Technologies, his start-up is attracting attention for its sequencing project involving the cannabis genome. McKernan states that he left his former company as he began to be serious about the anti-cancer properties of cannabinoids. Another goal of the start-up involves the incubation of assembly algorithms with a hyper-focus on different organisms.

The article explores the use of flash memory in the University of California, San Diego's San Diego Supercomputer Center, Gordon. Larry Smarr, who spent ten years developing the California Institute for Telecommunications and Information Technology (Calit2), said that the supercomputer center can be labeled as the largest thumb drive in the world. The 20-million U.S. dollar Gordon took advantage of the cheap prices of 10GbE switches, which single port costs less than 1,000 U.S. dollars in 2011. INSET: Groundbreaking Work.