big data


Delivering Genomic Medicine: Challenges in Data Visualization and Reporting - Panel Event Set for June 5th in Oakland

Mendelspod and Chempetitive Group are pleased to team up and bring you another evening of networking with a panel discussion, "Delivering Genomic Medicine: Challenges in Data Visualization and Reporting." Join us after work in Oakland on Thursday, June 5th for drinks, bites and discussion.
 

Myths of Big Data with Sabina Leonelli, Philosopher of Information

Guest:

Sabina Leonelli, Philosopher, University of Exeter

Bio and Contact Info

Listen (6:44) Not a fan of the term Big Data

Listen (4:20) Something lost in bringing data together from various scientific cultures

Listen (3:36) Are data scientists really scientists?

Listen (4:11) Controversies around Open Data

Listen (3:03) Data systems come with their own biases

Listen (6:22) Message to bioinformaticians: Come up with the story of your data

Listen (1:15) Data driven vs hypothesis driven science

Listen (2:46) Thoughts on the Quantified Self movement

For the next installment in our Philosophy of Science series, we look at issues around data. Sabina Leonelli is a philosopher of information who collaborates with bioinformaticians. In today's interview, she expresses her concerns about the terms Big Data and Open Data.

"I have to admit, I'm not a big fan of this expression, 'Big Data,'" she says at the outset of the show.

Using data in science is, of course, a very old practice. So what's new about "big" data? Sabina is mostly concerned about the challenges of bringing data together from various sources. The biggest challenge here, she says, is with classification.

"Biology is fragmented in a lot of different epistemic cultures . . and each research tradition has different preferred ways of doing things," she points out. "What I'm interested in is the relationship between the language used and the actual practices. And there appears to be a very strong relationship between the way that people perform their research and the way in which they think about it. So terminology becomes a very specific signal for the various research traditions."

Sabina goes on to point out that the nuances of specific research traditions can be lost as data is integrated with other traditions. For instance, most large bioinformatics databases are done in English, whereas some of the individual research data may have been originally done in another language.

This becomes especially important with the new movement toward Open Data, where biases are built into the databases.

"The problem resides with the expectation that what is 'Open Data' is all the data there is," she says.

In fact, the data in Open Data tends to come from databases which are highly standardized and often from the most powerful labs.

How can bioinformaticians deal with these challenges? Sabina says researchers should be more diligent about creating "a story" around their data. This will help make the biases more transparent. She also says that a lot of conceptual effort must go into creating databases from the outset so that the data might be used for yet unknown questions in the future.

We finish the interview with her thoughts on the Quantified Self movement.

Podcast brought to you by: Chempetitive Group - "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."

5 Myths of Genomic Medicine

No topic has been more popular at Mendelspod than that of genomic medicine.  This is partly an editorial decision.  But it also comes to us from every direction.  And it is very exciting to hear stories of new knowledge about human biology being translated into precision healthcare.  We have featured the major players in the NGS tools industry and some of the newcomers working on “next next gen”.  We’ve featured data analytics companies and some of the new genomic interpretation and reporting groups who are setting up shop.  We have interviewed professors talking about their latest discover

Big Data Takes the Stage at Stanford

We're currently developing a series on big data here at Mendelspod.  So we jumped at the chance to attend the first 'Big Data in BioMedicine Conference' put on at Stanford in conjunction with the University of Oxford.  The conference gave a great overview of the topic, reaching not only into all that omics data, but health IT and public health as well.  

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

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

Guest:

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?

Speeding Data Transfer with Dawei Lin, UC Davis

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

Guest:

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.

Appistry Brings Their Cloud Computing to Bio, Sultan Meghji

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.



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