Informatics Tools for the Big Data Challenge

By Bio-IT World Staff 

 

January 3, 2014 | Now, more than ever, informatics tools are essential to enabling life sciences research. As data volumes grow, the refrain becomes concern about how to work with big data, how to make sense of the wealth. Informatics tools step into that gap making data actionable and manageable. 

 

At this year’s Molecular Medicine Tri-Conference in San Francisco, three days of sessions will focus on a breadth of informatics tools and applications across three programs: Bioinformatics for Big Data; Integrated R&D Informatics and Knowledge Management; and Genome and Transcriptome Analysis. 

 

It will be a wealth of content from a wide range of speakers and viewpoints. Here are just a few of the presentations we’re looking forward to seeing. 

 

Mark Boguski (Harvard Medical School; Beth Israel Deaconess Medical Center) will keynote on Monday discussing customized care in moving systems and bioinformatics toward personalized medicine. Monday, February 10, Noon

 

Martin Gollery (Tahoe Informatics) takes on accelerated data growth with the added complexity of a wide range of disparate data sources that must be integrated and filtered by researchers to build a coherent picture of the system being studied. He’ll look at the different technologies that generate big data in the biomedical arena, and upcoming technologies and the challenges and opportunities that they will present. Tuesday, February 11, 10:30

 

Deepak K. Rajpal (GlaxoSmithKline) will explore how metabolic diseases, especially type 2 diabetes and obesity, are influenced by the microbiome. Various studies have highlighted the role of gastrointestinal microbial communities in metabolic health and disease. He will provide a brief overview of the gut microbiome, its putative role in metabolic diseases and the emerging data in this space. Tuesday, February 11, 12:00 pm

 

Zhiyan Fu (Genome Institute of Singapore) will present a practical case study implementing big data technologies to a mid-size genome center including the challenges of big data life-cycle management in a genome center, how the latest big data technologies are implemented, and the pros and cons of some of the techniques, including Hadoop, HDF5, and different NGS compression algorithms evaluated by GIS. Tuesday, February 11, 2:20 pm

 

Arpit Davé (Bristol-Myers Squibb) will look at how pharma is improving traditional research by enhancing real world data environments. Life sciences organizations have started to change the way they discover, develop, and commercialize medicines to address patient, regulators and payor needs at every stage of the product lifecycle. Real world data (longitudinal and integrated patient information) is the key to answering complex questions in R&D and product commercialization, Davé says. He’ll share his experiences with various data and analytics collaboration models. Wednesday, February 12, 11:20 am

 

Wednesday afternoon’s session, Big Data Driving Personalized Medicine, is full of excellent content. Dalia Cohen chairs the session which features Andreas Kogelnik (Open Medicine Institute) on how OMI is effectively applying a collaborative, "big data" approach to understand and address complex diseases including: Autism, Lyme, Chronic Fatigue Syndrome, Parkinson's, and various cancers; Randy Scott (InVitae) on progress aggregating all of the world’s genetic tests into a single assay; and Iya Khalil (GNS Healthcare) on leveraging advanced analytics and appropriate feedback loops to identify what works on an individual patient level. Wednesday, February 12, 4:00 pm

 

Daniel H. Robertson (Eli Lilly and Company) will provide updates on the Lilly Open Innovation Drug Discovery Program (OIDD) and its network of top global research talent at academic and biotech institutions. Lilly has recently been partnering to deploy additional design tools for OIDD investigators to assist in designing compounds submitted to the assays through this collaboration. Monday, February 10, 12:30 pm

 

Martin Leach (Biogen Idec) will lead a big pharma panel discussion on Monday afternoon highlighting approaches and lessons learned building a comprehensive R&D search capability. Joining him will be John Koch (Merck) and Hongmei Huang (Novartis). Monday, February 10, 3:35 pm

 

At Genentech, Erik Bierwagen and his colleagues have created an integrated informatics system for animal studies from birth to death and beyond. Our efforts span many different disciplines and groups, but share the common effort of integrating data seamlessly. Wednesday, February 12, 5:05 pm

 

Recent genome sequencing projects have revealed a surprising number of unanticipated mutations in genes which modify the epigenome. Peter A. Jones (University of Southern California) has begun to explore the potential effects of these mutations on the epigenome, paying particular attention to the existence and roles of chromatin accessibility in carcinogenesis. He’ll discuss the effects of DNA methylation inhibitors and look into the possibility that drugs can target these changes. Monday, February 10, Noon

 

Chris P. Ponting (University of Oxford; Wellcome Trust Sanger Institute) will discuss experimental approaches being developed to sequence the poly-adenylated transcriptome together with the genome of individual cells. These approaches now enable consideration of the effects of DNA variants on transcript levels in single cells. Tuesday, February 11, 10:30 am

 

Barry S. Taylor (University of California, San Francisco) takes on outlier cancer phenotypes. Little is known about the basis of elusive exceptional responses to cancer therapy. He will describe an outlier phenotype-to-genotype approach that uses both whole-genome and deep targeted sequencing to identify the molecular genetic basis of complete and durable response to both targeted and systemic cancer therapies. He’ll discuss recent work on the use of such approaches coupled to nuanced computational analyses to identify not only individual sensitizing mutations, but also synergistically acting genetic interactions and the contribution of tumor clonality to the durability of treatment response. Wednesday, February 12, 11:10 am