Genetic Engineering & Biotechnology News

MAY15 2017

Genetic Engineering & Biotechnology News (GEN) is the world's most widely read biotech publication. It provides the R&D community with critical information on the tools, technologies, and trends that drive the biotech industry.

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Genetic Engineering & Biotechnology News | GENengnews.com | MAY 15, 2017 | 17 dence related to oncology. "Curation of the Clinical Knowledge- base is semiautomated and undergoes careful review by our dedicated curation team," noted Guru Ananda, Ph.D., scien- tist in the computational sciences group at JAX. "The tool provides connections among variant information, therapies, and literature-based efficacy evidence to justify why a specific variant is associated with a particular therapy." The CKB was originally developed as a resource for cancer gene panel assays offered by JAX, assays that analyze genes identified as clinically relevant or associated with re- sponse or resistance to FDA-approved tar- geted therapies. However, the database is a convenient tool for all oncologists to connect variants with appropriate therapies for an in- formed treatment plan. High-Performance Computing of Big Biodata Petabytes of data stored as 1's and 0's are generated in clinical NGS programs. The immense amount of processing required to analyze the data requires a high-perfor- mance computing (HPC) environment and optimized computing instructions, referred to as a bioinformatic pipeline. If not prop- erly organized, complex pipelines will com- pute at a snail's pace, debilitating NGS data analysis. JAX soon discovered a need for a comput- ing framework that allowed for the develop- ment of multiple, easily maintainable, robust, and reproducible bioinformatics pipelines as the research institution's participation in clinical programs grew. In response, JAX de- veloped Civet, an open-source framework for automation of bioinformatic analyses within a HPC environment. Civet allows pipelines to be easily cre- ated and modified while automatically op- timizing the schedule of computing steps, such as aligning sequencing data to a refer- ence genome or determining copy number variations among sequencing samples. In addition, the framework incorporates trace- ability logs exceeding regulatory standards to ensure that files and libraries used in the execution of each pipeline are tracked and accessible. While Civet optimizes bioinformatic pipelines, helping to achieve faster data processing, ultimately, processing speed is determined by the performance of the HPC environment. HPC uses a network of paral- lel processors that work on multiple bioin- formatic jobs within the pipeline, simulta- neously. Performance is determined by how quickly the pipeline is able to access files located on network-attached storage (NAS). The NAS may be remote to the HPC envi- ronment, causing a significant access time delay, known as latency, and is one of the most substantial problems in the computing of Big Data over the cloud. Cloud computing uses a network of re- mote servers hosted on the internet to store, manage, and process data, rather than a lo- cal server. If all data is stored and processed on the cloud, latency is low. However, this method requires the uploading of massive amounts of data and storage on a third-party vendor cloud system. Another method to limit latency is to build on-premises storage and computing fa- cilities, though this is very costly and difficult to keep up with a growing amount of data. Avere Systems proposes a cloud hybrid mod- el in which data in on-premises NAS is sent to the cloud for processing. Typically, send- ing data to the cloud increases latency due to the physical distance between the NAS and cloud processors, but Avere Systems has a solution for that. "We use a technique called bursting to solve the problem with latency, " explained Scott Jeschonek, director of cloud products at Avere Systems. "Bursting is a type of read-ahead caching using algorithms that learn the access patterns of data transfer from on-premises NAS to the cloud and only transfer relevant data when needed during processing." Avere Systems has optimization solutions for any on-premises or cloud-computing model; however, the hybrid cloud model is an appealing option as it allows for on-site data storage and the cost-saving benefits of cloud computing. Tuesday June 13, 2017 11:00 am ET 8: 00 am PT DURATION 60 minutes COST Complimentary Speakers Advancing Early Cardiovascular Drug Discovery Innovation continues to be a primary driver of value in pharmaceutical research. However, simultaneously, research budgets are coming under ever-increasing pressure. As a consequence, pharma is moving toward a so-called open research model, one that dispenses with recurrent fixed costs in favor of a more flexible and dynamic external "spend." By adopting this model, pharma could tap into innovation outside their walls. In this webinar, case studies will be presented highlighting the value of such collaborations, while focusing on discovery campaigns that employ highly relevant functional assays. Describing how to use an integrated approach that fuses the disciplines of in silico drug design, medicinal chemistry, and discovery biology, the presenters will demonstrate how their unique approach helped them meet key goals during the early discovery process, as well as which factors contributed to their subsequent successes. Making medicines these days cannot be done in isolation. And the story presented in this webinar shows an excellent example of a partnership in action for developing new treatments to support unmet pharmaceutical needs. A live Q&A session will follow the presentations, offering you a chance to pose questions to our expert panelists. Who Should Attend • Drug discovery scientists • Cardiovascular disease investigators • Medicinal chemists • Drug development researchers • CEOs and founders of virtual and startup companies Free Registration! www.GENengnews.com/cardio Webinars You Will Learn • Recent advances in the early drug discovery process • The importance of tight integration of disciplines in addressing challenging targets • How collaboration in early discovery can create high-quality advanced leads Produced with support from Robert S. McDowell, M.D., Ph.D. Senior Vice President, Drug Discovery MyoKardia Kenneth F. Wertman, Ph.D. Senior Vice President Icagen OMICS

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