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Focus on Best Practices 2013 Compendium from the Bio lIT World Best Practices Awards Program 2013 2013 | Best Practices Compendium | BiolIT World [1] INTRODUCTION Best Practices 2013 2013 Judges The 2013 Best Practices Awards were INTRODUCTION 3 organized by Bio-IT World managing editor KNOWLEDGE MANAGEMENT 4 Allison Proffitt and editor Kevin Davies. Searching for Gold: GSK’s New Search Program that Saved Them Millions Joining the editors in judging the entries GlaxoSmithKline was a distinguished panel of experts: JUDGES’ PRIZE 5 Joe Cerro, SchoonerGroup Genentech Finds Big Savings in Small Places Bill Van Etten,The BioTeam Genentech Stephen Fogelson, Develotron 4 Martin Gollery, Tahoe Informatics CLINICAL AND HEALTH IT 6 PRO-ACT: Bigger and Better ALS Database Open for Mining Phillips Kuhl, Cambridge Healthtech Institute Prize4Life Alan Louie, IDC Health Insights Susan Ward, Consultant INFORMATICS 7 Brenda Yanak, Pfizer From DNA to PDF: Harnessing the Genome and Phenome to Make Better Diagnoses Genomic Medicine Institute, Geisinger Health System - nominated by SimulConsult IT INFRASTRUCTURE/HPC 8 5 The Cloud’s the Limit: Rentable Supercomputers for Improving Drug Discovery Schrodinger - nominated by Cycle Computing EDITORS’ PRIZE 9 GeneInsight: Genetic Knowledge to Action GeneInsight 8 11 HONORABLE MENTION: 10 - 11 Faster, Scarless Assemblies JBI and Amgen - nominated by TeselaGen Biotechnology TrialShare Brings Much Needed Transparency to Clinical Trials Data Immune Tolerance Network - nominated by LabKey Software 2013 BEST PRACTICES OVERVIEW 12 2013 BEST PRACTICES ENTRIES 13 Clinical and Health IT 13 Informatics 65 IT Infrastructure/HPC 155 Knowledge Management 202 2013 | Best Practices Compendium | BiolIT World [2] INTRODUCTION The Bio-IT World Best Practices Awards have been around long enough for us—as editors and judges—to get a little jaded. But instead, our enthusiasm is renewed each year by the excellent entries, innovative ideas, and passion to better our industry. Bio-IT World is honored to be in a position to share these projects with the industry at large. The 2013 awards season was no exception. Our honorees span the whole of the life sciences industry. From an animal work project that saved nearly half a million dollars a year, to a clinical trials data interpretation platform, these truly are best practices for the breadth of the industry. Although every project won’t be applicable to every group, it is our hope that there will be some aspect in each one to emulate and apply for more cost efficient and effective research. The 2014 Bio-IT World Best Practices Call for Entries opens this month, and we have high hopes for the next round of competition. We welcome all collaborations and projects that have advanced the life sciences, and look forward to seeing you at the 2014 Bio-IT World Conference & Expo as we announce the next round of winners. - Allison Proffitt, Editorial Director 2013 Winners BEST Looking to 2014 KNOWLEDGE MANAGEMENT PRACTICES The 2014 Awards will kick off this November when the call GlaxoSmithKline AWARDS for entries goes live. We will collect entries for 4 months before judging begins. JUDGES’ PRIZE 2014 Please visit www.bio-it-world.com/bestpractices for Genentech more information. CLINICAL AND HEALTH IT Prize4Life and the Neurological Clinical Research Do’s and Don’ts for Best Practices Submissions Institute (NCRI) at Massachusetts General Hospital Judging of Best Practices is taken very seriously. While the quality of the winning entries typically shines through, the judges’ task is complicated by a number of INFORMATICS entries that fail to do the underlying quality justice. You can help your chances by Genomic Medicine Institute, Geisinger Health System following some simple guidelines: Nominated by SimulConsult • DO remember the ROI. We cannot judge the potential impact or effect of a IT INFRASTRUCTURE/HPC Best Practice submission if the entry doesn’t explain qualitatively (and ideally Schrodinger quantitatively) how it benefitted the host or user organization. Nominated by Cycle Computing • DON’T repurpose marketing material. Shockingly, some of the entries we receive are poorly disguised press releases. EDITORS’ PRIZE GeneInsight • DO follow the guidelines. We offer specific guidelines on word length, figure limits, etc. for a reason. We can’t make a valid assessment on a two-page entry, nor HONORABLE MENTIONS: can the judges wade through a 20-page thesis. Follow the format. JBI and Amgen • DON’T submit a new product. The competition seeks to recognize partnerships Nominated by TeselaGen Biotechnology and innovative deploy-ments of new technology, not mere descriptions of a Immune Tolerance Network standalone product or resource. Nominated by LabKey Software 2013 | Best Practices Compendium | BiolIT World [3] KNOWLEDGE MANAGEMENT Searching for Gold: GSK’s New Search Program that Saved Them Millions By Matt Luchette | June 5, 2013 2011, the leadership in the GlaxoSmithKline’s R&D department made a troubling realization: their scientists were having a tough time finding their data. By that point, GSK’s research staff was logging all of their experimental results in In electronic lab notebooks. But once the data was saved, the company’s search program, GSKSearch, wasn’t able to parse the records. If researchers in one division wanted to investigate Bio-IT World Editor Allison a compound for clinical development, they had no way of efficiently accessing any studies the Proffitt presents GSK’s company had already done on the compound. And for the data GSKSearch could access, the Andrew Wooster with the program couldn’t recognize many of the chemical, biological, and clinical terms that identified Best Practices Award for specific experiments. Knowledge Management NIKI HINKLE “The search capabilities were not adequate,” said Mirna Samano, the program manager for GlaxoSmithKline’s MaxData strategic program. Hard-to-reach data and archived experiments meant lost time and money for the company, capabilities, including improved text analytics and data extraction with software from NextMove, so Samano and her R&D division set up focus groups with GSK scientists to identify what they and web integration with Microsoft’s C# ASP.NET libraries. The result was a new program needed in order to make the most of their data. that could search through the company’s archived electronic lab notebooks and recognize a vast The message from the scientists was resounding: “Why can’t we have something like Google?” library of scientific terms, bringing once inaccessible data to scientists’ fingertips. To resolve the program, the R&D engineers’ first instinct was to investigate Autonomy, the Samano said the program was an excellent exercise in “how to combine a company’s existing text search program used for GSKSearch, for any limitations or errors in the code. But the tools to accomplish goals.” program was full-functioning and gave robust results. What they realized, though, was that Samano added that while Socrates has been optimized to recognize the company’s chemical the search requirements for their scientists were different than those of a standard text search and biological experiments, in future iterations, she hopes to make the program more useful for engine. They didn’t need Google; they needed a specialized program that could recognize the other areas of R&D, such as clinical and regulatory records. various chemical compounds or drug targets that GSK researchers test every day. Today, Socrates Search has access to over 2 million of the company’s online lab notebooks, has “We needed to help R&D maximize the value of their data,” said Samano. indexed over 70 million unique terms, and supports an average of 500 users every month. GSK The R&D IT engineers set to work developing a new search program that would expand the spent about 1 million pounds (about $1.5 million) on the project, and the company estimates capabilities of GSKSearch. Most importantly, the engineers wanted the program to search the that Socrates Search could save as much as $2 million pounds each year in improved efficiency. company’s entire library of electronic lab notebooks and recognize chemicals through their “The value of the tool is greatly recognized at GSK,” Samano explained. As a director in GSK’s various generic and scientific names, as well as drawings and substructures. In addition, they Animal Research Strategy remarked, “This tool allows us to more fully apply our considerable wanted to add new capabilities, such as recognizing combination drugs, gene aliases, or standard experience, link internal experience, and design more robust experiments.” disease vocabulary, to make searches more streamlined. The program’s capabilities have been recognized outside of the company as well, most Socrates Search, as the project came to be known, was made by combining a number of recently by winning the2013 Best Practices Award for Knowledge Management at the Bio- commercial search programs, many of which were already in place at GSK. Autonomy’s text IT World Expo in April. Winning the award, Samano said, has been instrumental in gaining search and ChemAxon’s JChem Oracle cartridge, which allows users to search for chemicals interest from more colleagues throughout GlaxoSmithKline who would like to take advantage of with their various names or structure, were already a part of GSKSearch, but now had added Socrates’ capabilities. “The project has been a great experience for our team,” she said. n 2013 | Best Practices Compendium | BiolIT World [4] JUDGE’S PRIZE Genentech Finds Big Savings in Small Places By Aaron Krol | July 19, 2013 Genentech’s Mouse Genetics Department in South San Francisco, Dr. Rhonda I was not surprised that Wiler and her team are proving that the simplest investments in IT can yield the biggest returns. there was a positive return on At Dr. Wiler’s department oversees a breeding facility for genetically engineered investment, but was very happily mice, which produces over 40,000 pups a month representing almost a thousand distinct genetic lines.

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