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The Artistry of Molecular Animation >> Cambridge Healthtech Media Group NEXT-GEN TECHNOLOGY • BIG DATA • PERSONALIZED MEDICINE JANUARY 2012 Data Visualization ALL NEW DIGITAL The Artistry EDITION of Molecular Animation >> FEATURE | Drug Safety eClinical Technologies Remedies for Medidata: Integrating Safer Drugs >> Infrastructure First Base for Clinical Good Days and Bad in 2011 >> Trials >> c CONTENTS | January 2012 FEATURE 46 Drug Safety Remedies for Safer Drugs >> UP FRONT 8 Drug Discovery H3 Biomedicine: Health, Hope and Heaps of Japanese Funding >> 12 Data Visualization Picture This: Molecular Maya Puts Life in Life Science Animations >> 18 Genome Informatics Assembly Required: Assemblathon I Tackles Complex Genomes >> 24 High Performance Computing Products, Deployments, and News from Supercomputing 11 >> 26 News Briefs >> 28 INSIDE THE BOX The Unstable Equilibrium of the Bioinformatics Org Chart >> 32 THE BUSH DOCTRINE The Pharmaceutical Safety Data Problem >> 2 JANUARY 2011 Visit Us at www.Bio-ITWorld.com Download a PDF of This Issue CLICK HERE! ARTICLES 36 eClinical Technologies Medidata: Integrating Infrastructure for Clinical Trials >> 42 Diagnostics A QuantuMDx Leap for Handheld DNA Sequencing >> 44 Informatics Tools Accelrys’ Cheminformatics Solution in the Cloud >> KNOWLEDGE CENTER 54 New Products >> 56 Free Trials and Downloads >> 58 Upcoming Events >> 60 Complimentary Resources >> IN EVERY ISSUE 6 FIRST BASE Good Days and Bad in 2011 >> 66 RUSSELL TRANSCRIPT What is (Quantitative) Systems Pharmacology? >> 64 On Deck | 64 Contact Us | 65 Company/Advertiser Index >> CONNECT WITH US! Visit Us at www.Bio-ITWorld.com JANUARY 2011 3 19th International Moscone North Convention Center February 19-23 San Francisco, CA February 19-20 NEW-Symposia Targeting Cancer Stem Cells get Cloud Computing DisplayMolecular of Difficult Targets Med Point-of-Care Diagnostics Next-Generation Pathology inspired Pharma-Bio Partnering Forums Attend. Discover. Apply. February 20 Event Short Courses February 21-23 Spanning five days this year! Core Programs Diagnostics Channel New This Year! Drug Discovery & Development Channel TRI-CON ALL ACCESS PACKAGE Informatics Channel Includes 1 Symposium / Partnering Forum, 2 Short Courses, and 1 Core Program. See website for details. Cancer Channel Organized by Cambridge Healthtech Institute TriConference.com Optimizing Clinical Trials: Concept to ConclusionTM In clinical development, speed means time to market. It means quickly and rigorously building solid evidence while managing limited Speed resources. It means making the world a healthier place now. Medidata’s comprehensive suite of products optimizes your clinical trials from concept to conclusion. That means you make better decisions faster. And that means faster returns. mdsol.com +1.866.515.6044 BUSINESS ANALYTICS | STUDY & PROTOCOL DESIGN | TRIAL MANAGEMENT, PLANNING & BUDGETING | SITE NEGOTIATION RANDOMIZATION & TRIAL SUPPLY MANAGEMENT | EDC/CDM | MONITORING | SAE CAPTURE | CODING | CLINICAL PORTAL Medidata-Solutions-Bio-IT-World-05JAN2012.indd 1 1/5/2012 12:31:01 PM First Base c Good Days and Bad in 2011 By Kevin Davies enthusiasm, that is, I fear, just slightly beyond CONTENTS our scope. t must be so much fun being a physicist right In 2011, Bio•IT World hosted Stephen Wol- now. Scientists have discovered two mon- fram and a record attendance at the Bio-IT ster black holes—the largest on record—with World Expo, and convened its first Cloud masses several billion times that of the Sun. Computing conference, reflecting the rapidly And in the Goldilocks Zone of a nearby gal- growing capacity to spin up supercomputing Iaxy, a planet known as Kepler 22b orbits with a tasks as well as the expanding acceptance of balmy atmosphere of 72° F, a prime candidate the potential of infrastructure-as-a-service. We for life off earth. also enjoyed covering the potential of new tech- At the other end of the matter scale, sci- nologies in the form of “wellness chips” (see, entists have caught their first glimpse of the “Turning Blood into Gold,” Bio•IT World, July Higgs boson, the so-called “God particle.” And 2011) and “SNP-doctors,” (see, “Powering Pre- we are still waiting with baited breath for con- ventative Medicine,” Bio•IT World, September firmation that neutrinos can travel faster than 2011) as well as the creation of the New York the speed of light, as hinted a few months ago. Genome Center (see, “Genome Center for Go- In reflecting on the past year in life sciences tham,” Bio•IT World, November 2011). Some and IT, however, such notable feats are some- of our New Year’s well wishes go to its founders what harder to find. A list of the top ten science in strengthening what must be at times a tem- stories of 2011 in the Guardian, compiled by pestuous alliance of Big Apple egos. veteran science correspondent Robin McKie, includes three of the physical sciences stand- Cancer Connections outs above, but only a couple of items in con- A story that did not receive as much media at- temporary biology. tention as it should was the approval by the One was the rather sad exit of biotechnol- Food and Drug Administration in August ogy pioneer Geron from the human embryonic 2011 of a pair of targeted cancer drugs and stem cell field it helped to create. The other, their companion diagnostics. One was Pfizer’s more cheerily, was the imaging study of a fe- Xalkori, which treats a small percentage of male brain experiencing orgasm, but while im- patients with advanced non-small-cell lung aging is an important technology we cover with cancer (NSCLC) harboring mutations in a gene 6 JANUARY 2012 Visit Us at www.Bio-ITWorld.com called ALK. (A diagnostic test from Abbott question: what did the doctors find in his Molecular reveals the mutation.) The other DNA? While for obvious reasons, Washington c was the melanoma drug Zelboraf (Plexxikon), University could not comment on Hitchens’ which is accompanied by a BRAF mutation prognosis, at a conference last October, Mar- test. dis presented an intriguing case study of a pa- While on the topic of cancer, two papers tient with a long history of tobacco and alcohol published this year by the team of Rick Wilson, abuse, referred to simply as “ESC1” (esopha- Elaine Mardis, Timothy Ley and colleagues at geal cancer patient #1). CONTENTS Washington University in St Louis, illustrated ESC1’s tumor, it turned out, carried muta- the potential of individual genome sequencing tions in a gene called DDR2. A quick PubMed in revealing molecular aberrations in cancer search reveals a couple of interesting facts: patients, even if the ensuing targeted treat- first, DDR2 mutations have been associated ments don’t always prevail or arrive in time. with several metastatic cancers. Second, the Ironically, two of the most famous cancer protein encoded by this gene is a potent target patients to pass away in 2011—Steve Jobs and of Gleevec and related tyrosine kinase inhibi- Christopher Hitchens—both underwent ge- tors. So one can see the rationale for switching nome sequencing. According to Walter Isaa- this patient to Gleevec. ESC1 responded well cson’s best-selling at first, but Mardis stressed that her colleagues biography, Jobs were not managing the patient’s care and did had his genome se- not have up-to-date information. quenced by research- Hitchens, who said cancer was like a “malig- ers from Stanford, nant alien” in his body, died from pneumonia Johns Hopkins, Har- in December at the M.D. Anderson Cancer vard and the Broad Center in Houston, writing columns and meet- Institute. Hitchens, ing deadlines to the end. His death hit me following a recom- harder than Jobs’, I suppose because we had mendation from a COMMONS LICENSE ANDREW RUSK/CREATIVE a few things in common: scotch-loving British person the Daily Christopher Hitchens journalists and authors, both graduates of Ox- Mail headline called an “evangelical Christian ford University. Of course, there the compari- doctor”—perhaps better known as NIH direc- son ends. tor Francis Collins—was sequenced by the St In one of his last interviews, Hitchens told Louis group in early 2011 as he battled stage IV the BBC: “Whatever day came that the news- (metastasized) esophageal cancer. papers came out and I wasn’t there to read Hitchens himself revealed that as a result of them, I’ve always thought that would be a bad the sequencing, he was now taking Gleevec, day—at least for me.” the Novartis drug for leukemia, begging the And us, Christopher. Cheers. • Visit Us at www.Bio-ITWorld.com JANUARY 2012 7 UP FRONT | News c H3 Biomedicine: Health, Hope and Heaps of Japanese Funding [ Drug Discovery ] With a $200 million commitment from Eisai Co., cancer drug start-up has clear path ahead. CONTENTS BY KEVIN DAVIES name Haruo to be included in that. ‘Human, CAMBRIDGE, Mass.—The ‘H3’ in the name of health…’ I definitely believed ‘Haruo’ comes the new oncology drug company H3 Biomedi- last. But it is ‘hope’—a great disappointment!” cine stands for “Human. Health. Hope.” he joked. It might also stand for the heaps of Japa- Eisai is not just writing a handsome check nese investment—up to $200 million—that it but providing ready access to its drug discov- is receiving from Eisai Co., Japan’s fourth larg- ery and development resources. Several Eisai est pharma company. It is an interesting and chemists have already moved to the U.S. to join possibly unique funding model that spares the H3 Biomedicine’s 30 or so current employees in company the travails of seeking venture finance the gleaming new laboratories (see “Lab Life”). or short-term licensing deals, says co-founder H3’s philosophy marries expertise in can- Stuart Schreiber, professor of organic chemistry cer genomics—the forte of co-founder Todd at Harvard University and the Broad Institute. Golub—with discovery-oriented organic syn- One year after H3 Biomedicine’s official thesis, a field in which his Broad Institute col- launch in December 2010, it formally dedicated leagues Stu Schreiber is an authority.
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