Open Source or Commercial? Lasse Goerlitz, CLC Bio, Talks Bioinformatics

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Lasse Goerlitz, VP of Communications, CLC Bio
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Listen (5:16) Highest demand coming from agro

Listen (3:06) What is holding back the adoption of genomic medicine?

Listen (4:03) A commercial platform with plug-ins

Listen (3:37) Open source vs commercial software

Listen (4:40) The all-in-one guys

Listen (5:56) Genomics in Europe

The repeating trend from industry to industry is for software to go from fragmented, custom applications toward larger dominant platforms. It's still the early days for bioinformatics, and just who the dominant platforms of the future will be remain unknown. Will they be open source, public platforms or commercial platforms?

CLC Bio, a bioinformatics company has been working on the solution for eight years now and hopes that their platform which works with many different plug-ins will become number one for biologists around the world. In today's show, CLC's VP of Communications, Lasse Goerlitz, talks about their platform and trends in genomics. Currently their heaviest users are in ag bio, but the demand from the clinic is rising. We conclude with a discussion of differences between Europe and the US in the genomics space.

Bioinformatics 3.0: an App Economy with Matt Landry, Biomatters

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Guest: Matt Landry, CTO, Biomatters
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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.

Ingenuity Nabs Genome Scientist, Nathan Pearson

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Nathan Pearson, PhD, Principle Genome Scientist, Ingenuity Systems Bio and Contact Info

Chapters: (Advance the marker)

0:42 What does it mean that you left Knome for Ingenuity?

7:02 How important is it that we have common ontologies?

13:00 What is your first goal at Ingenuity?

15:24 What will it take to get the ultimate end user buying?

18:54 Is sequencing good enough?

20:48 Where will Ingenuity make most headway going forward?

26:50 Thoughts on ENCODE and junk/not junk?

31:35 BONUS A student of Jonathan Eisen

Long time player in bioinformatics and database cultivation, Ingenuity Systems recently announced a new Principal Genome Scientist, Nathan Pearson. Nathan is known for joining Ozzy Osbourne and his wife on stage for a TED talk after interpreting the rock star's genome at Knome. What does this move mean for Ingenuity and for Knome? As I wrote in a recent blog, Pearson feels he'll make more headway moving to a platform further upstream. "For me," he says in the interview, "it's a chance to put my shoulder behind a platform that has a really high ceiling for bringing genomes into everyone's life in a more substantive way". Though new on the job, Pearson is comfortable explaining his first goal at Ingenuity, and tackling the big question of what will it take to get the end user, i.e., patients in the clinic, buying genomic medicine. At the end we catch Nathan talking about the person who influenced him to be a scientist, evolutionary biologist, Jonathan Eisen.

Editor of Bio-IT World Shares Overview of Bioinformatics in 2013

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Kevin Davies , Editor-in-Chief, Bio-IT World Bio and Contact Info

Listen (3:41) What must we all know about bioinformatics?

Listen (12:30) The explosive genome interpretation space

Listen (3:27) What will success in this space look like?

Listen (3:38) The Clinical Genome Conference expanding

Listen (6:18) What does it mean that CHI bought out the Genetic Conference?

Kevin Davies is the founding editor and current Editor-in-Chief of Bio-IT World. Reporting regularly on all things bioinformatics, he joins us to share his thoughts on the field. This last year has seen a flowering of new companies offering genome interpretation and reporting, a space Davis says is "the most interesting to me personally." But what will success for these early entrants look like?

DTC genomics has changed drastically since Davies covered the field in his 2010 book, The $1,000 Genome. Is the world of DTC genomics over? And what does it mean that CHI, conference producer and owner of Bio-IT World, bought out the Consumer Genetics Conference last year?

Looking at the Big Picture in Bioinformatics with Christophe Lambert, Golden Helix

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. . . and by Biotix - makers of A BETTER TIP(TM) for Next Gen Sequencing


Christophe Lambert, PhD , CEO, Golden Helix, Inc Bio and Contact Info

Listen (6:56) Beware the lure of solving tough problems for a small market

Listen (8:32) Is Illumina competing with their customers?

Listen (9:37) If the end user isn't buying, no one is selling

Listen (6:36) Learning from our GWAS mistakes

Listen (4:14) Where has Golden Helix found success?

Today we transition from our series on sequencing to one on bioinformatics. Christophe Lambert is the CEO of Golden Helix, a bioinformatics company based in Bozeman, Montana. With some degrees in computer science, Lambert saw early on the potential for IT in bio and began Golden Helix back in 1998, the same year Ingenuity Systems was founded. A research internship led to some funding from Glaxo Welcome and Lambert says he "started writing code in his bedroom" with no one to talk to but his wife.

Lambert's fourteen years in the business combined with his ability to think systematically has given him an insightful perspective on the industry. He's one of the few in this exploding field who acknowledges that the industry is quite small, not yet really making it to the clinic. "When the end user is not buying, no one is selling," he says in today's show. Lambert's impulse is to always look at the macro picture, probing why the science isn't there yet and what societal issues are holding back genomic medicine. I tried to pull him back a bit and get more information on Golden Helix, but half way through the interview, I just went with him. I highly recommend his blog at This Montana Canadian has something to say.

Speeding Data Transfer with Dawei Lin, UC Davis

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Dawei Lin, PhD, Director of the Bioinformatics Core at UC Davis Genome Center Bio and Contact Info

Chapters: (Advance the marker)

0:50 Set up first bioinformatics server in China

3:15 From 26 hrs to 30 seconds: a new high speed connection with China

11:52 Training the next generation of bioinformaticians

25:47 Empowering the masses to understand their own biological data

30:02 BGI and genomics in China

35:15 Know thyself

37:43 EXTRA: Molecular modeling with legos

Dawei Lin set up the first bioinformatics server in China back in 1995. And things have come full circle this past summer, as he was involved in setting up a new high speed connection between China and the Genome Center at UC Davis where he is Director of the Bioinformatics Core. Dawei worked with BGI to set up the connection. We ask him about the company and about genomics in China.

It's Dawei's passion to know himself that brought him to working with biological data.

$1,000 Genome No Good

There comes a time when powerful memes that have become widespread begin to lose their value. Is it that time for ‘The $1,000 Genome?’ Mark Boguski thinks so. At the first annual Clinical Genome Conference in San Francisco this week, Dr. Boguski from Harvard Medical School said that the term is actually fallacious. The price of sequencing has come down.

India's Rising Star in Bio-IT: Prahalad Achutharao

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Prahalad Achutharao, CEO Geschickten Biosciences Bio and Contact Info

Listen (4:51) How is the genomics revolution progressing in India?

Listen (2:51) Geschickten providing knowledge of knowledge

Listen (4:15) First to talk about cloud computing for life sciences

Listen (7:34) Leveraging big data experience outside of biology

Listen (4:01) IT has given India a great push as a nation

Listen (1:04) What should Americans know about India and the future?

Recently awarded the 2012 Indian Leadership Award for Industrial Development, Prahalad Achutharao is one of India's rising stars in IT. Particularly in bio-IT. The first to talk about cloud computing in the life sciences, Prahalad and his colleagues at Geschickten are leveraging deep experience handling big data for bioinformatics. We talk to Prahalad about what Geschickten brings to the table in NGS data storage, analysis and interpretation and also about the progress of the genomics revolution in India.