cloud computing


Genomics and the Cloud Going Through “a Second Puberty,” says AWS’ Angel Pizarro

Submitted by Ayanna Monteverdi on Tue, 11/24/2015 - 09:27

Angel Pizarro has watched as genomics and cloud computing have grown up together. Formerly a bioinformatics director at University of Pennsylvania, Angel is now the Technical Business Development Manager at Amazon Web Services.

At U Penn, Angel was part of the shift from setting up one’s own facility with expensive computer equipment for handling the rapid growth of omics data to using a third party service, such as AWS. He says that genomics and the cloud are both going through a "second puberty.” In today's show, Angel explains growing pains involved.

As storage and compute become a non-issue for bioinformaticians, Angel says that the science itself is changing. Questions can be answered more quickly with enormous parallel experimentation. And there are new algorithms being written, optimized for this “bottomless bucket” of compute and storage.

What are the issues for clients doing their "capacity planning," and what are some of the new interesting questions that Angel is hearing from AWS customers? Join us as we probe the future of the twin fields of genomics and cloud computing.

Bioinformatics 3.0: an App Economy with Matt Landry, Biomatters

Submitted by Theral Timpson on Mon, 04/08/2013 - 09:09

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours.

Guest: Matt Landry, CTO, Biomatters
Bio and Contact Info

Chapters: (Advance the marker)

0:37 What is the focus of Biomatters?

4:32 Hack or bioinformatician?

8:52 Are you seeing the commoditization of bioinformatics?

10:38 Bioinformatics 3.0: an app economy

16:49 The state of genomic medicine in New Zealand

21:59 Have you started thinking beyond the cloud?

Matt Landry calls himself a hack rather than a bioinformatician. He's the Chief Technology Officer at Biomatters, a bioinformatics company based in New Zealand that provides an easy-to-use desktop application for biologists. In today's show, Landry explains that coming up with a user friendly platform called Geneious has been the main driver for the company. If you're looking to write your own command line, Geneious is probably not for you, says Matt. He believes that the next phase for bioinformatics will go the user friendly direction and be based on an app model similar to the Apple platform. This makes him very interested in the two cloud based platforms offered by Illumina and now the new one released in beta by DNAnexus.

New Zealand is a country with a small population and a national health service, and Matt comments on the opportunities for genomic medicine in such a country. How do we change the culture of the medical ecosystem, and what comes after the cloud? Matt works out on the front lines and tackles these questions head on.

Appistry Brings Their Cloud Computing to Bio, Sultan Meghji

Submitted by Theral Timpson on Mon, 03/12/2012 - 06:11

Guest:

Sultan Meghji, VP Product Strategy, Appistry Bio and Contact Info

Podcast Sponsor: Ingenuity - iReport, the fastest and most accurate way to get biological meaning from your expression data. Upload your data and get a free iReport analysis summary at www.ingenuity.com/get iReport/

Listen (3:01) Formative years with geneticist father

Listen (4:55) Appistry, new to life science

Listen (7:17) Regulation and security issues

Listen (4:43) Roche move on Illumina

Listen (7:26) We haven't scratched the surface of genomics

Listen (8:12) Human de novo sequencing

Listen (0:46) Emerging sequencing technologies

Listen (6:24) Sequencing still the bottleneck, not analysis

Listen (1:53) No more blockbuster drugs

Sultan Meghji is the Vice President of Product Strategy at Appistry, a company working to develop the infrastructure needed to deliver medically actionable genetic data that can be applied to individual patients. Meghji has spent more than 20 years studying the technical aspects and business applications of high performance computing. He started his career at the National Center for Supercomputing Applications (NCSA), where he developed artificial intelligence systems and Internet technologies. From there, Meghji moved into several IT leadership positions at ABN AMRO, American Express, Monsanto, United Airlines, as well as in academia.

Google Invests in Bioinformatics: Andreas Sundquist, DNAnexus

Submitted by Theral Timpson on Thu, 02/23/2012 - 08:58

Podcast Sponsor: Appistry- Delivering the most cost-effective and the highest quality analytics for your NGS data. Jumpstart your analysis with runs beginning at just $99. Appistry, complex analytics made simple. Guest: Andreas Sundquist, CEO, DNAnexus Bio and Contact Info Listen (9:28) An instant online genomics data center Listen (2:31) Moving bioinformaticians to more interesting work Listen (3:49) From exomes to whole genomes Listen (5:38) Using the cloud Listen (4:35) Mirror of SRA Listen (6:00) Google's investment and the future of bioinformatics Listen (6:12) Is there something in the water at Stanford that creates entrepreneurs? Listen (2:50) Recruiting engineers in Silicon Valley Listen (1:31) Are you the next Sergey Brin? Andreas Sundquist is here to talk about his exciting new company. He’s the CEO and co-founder of DNAnexus, a company receiving a fair amount of buzz since catching a chunk of cash from Google Ventures and TPG Biotech. The company offers cloud based storage and analysis of next-gen sequencing data. Receiving his Ph D in computer science from Stanford, Andreas has published methods for whole-genome mammalian assembly, metagenomics, and population genetics. Andreas talks about his company platform and looks to a time when everyone will have their genome sequenced.

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