bioinformatics


Training the Next Generation of Bioinformaticians: Russ Altman, Stanford

Guest:

Russ Altman, Dept Chair, Bioengineering, Stanford University

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Listen (5:32) A bioinformatician bottleneck?

Listen (4:19) Does the engineer or coder have enough basic biology?

Listen (5:04) Have we been overly reductionist?

Listen (5:16) Beautiful but useless algorithms

Listen (4:13) New breakthroughs in natural language processing

Listen (3:39) A new regulatory science

For our last episode in the series, The Bioinformatician Bottleneck, we turned to someone who has not only done lots of bioinformatics projects (he's been lead investigator for the PharmGKB Knowledgebase) but also one who is training the next generation of bioinformaticians. Russ Altman is Director of the Biomedical Informatics program at Stanford. He's also an entertaining speaker who's comfortable with an enormous range of topics.

It's been some time since we had Russ to the program, so we had some catching up to do. What are his thoughts on the recent philosophy of science topics we've been discussing? Are the new biologists becoming mere technicians? What is meant by open data? Etc. He warns of being too black and white when it comes to reductionism or antireductionism. And agrees that the new biologist needs quite a bit of informatics training. But he's not worried that all bioinformaticians have to be better biologists, saying that there's a whole range of jobs out there.

What's Russ excited about in 2014? The increased ability to do natural language processing, he says.

"We have 25 million published abstracts that are freely available. So that's a lot of text. Increasingly we're having access to the full text and figures. I think we're near the point where we'll have an amazing capability to do very high fidelity interpretation of what's being said in these articles," he says in today's interview.

Russ finishes up by talking about a new West Coast FDA center in which he's involved. The center is focused on a program for a new emerging regulatory science, which he defines as the science needed to make good regulatory decisions.

"This area of regulatory science," he says, "has great opportunity to accelerate drug development and drug discovery."

I saw Russ at Stanford's Big Data conference after our interview and asked him at what age he decided against Hollywood and for going into a life of academia and science.

"Who says I did?" he retorted without hesitation.

Podcast brought to you by: Roswell Park Cancer Insititute, dedicated to understanding, preventing and curing cancer for over 115 years.

Myths of Big Data with Sabina Leonelli, Philosopher of Information

Guest:

Sabina Leonelli, Philosopher, University of Exeter

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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."

Bioinformatics Pioneer, Martin Reese, on Scaling Up Human Genome Interpretation

Guest: Martin Reese, Co-founder, President & CSO, Omicia

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Chapters: (Advance the marker)

0:40 How did you get started in bioinformatics?

3:04 What is the biggest challenge with human genome interpretation?

8:01 Diagnosing Ogden Syndrome

13:30 What sets Omicia apart?

18:08 Who is ordering your tests?

23:29 FDA letter to 23andMe unfortunate

25:47 What's your main objective for 2014?

Martin Reese's career in bioinformatics began in 1993 when he attended a lecture in Heidelberg, Germany entitled "Genome Informatics." Reese, a German, then switched his studies from medical informatics to bioinformatics and moved to Berkeley where he worked on assembling the genome for the Human Genome Project. In 1996, he started a company with his Ph D advisor, David Haussler (of Genome Browser fame), called Neomorphic, part of the first commercialization of bioinformatics.

Martin is now the president of Omicia, a company he founded to take on the challenge of scaling up human genome interpretation.

How far have we come in the clinical interpretation space? Martin says that in 2013, 80% of human genome interpretation was done for research and 20% for the clinic. In the next 3-5 years, he predicts those percentages will switch to 20% for research and 80% clinical.

Martin says that one of the biggest challenges for human genome interpretation is easy-to-use visualization tools. For this reason, he's been a fan of the DTC company, 23andMe, and felt that the FDA's letter to the company was "very unfortunate."

"[23andMe] educated the whole population about genetics," he says in the interview, "and they tried to make the reports easily understandable and manageable by a regular person. . . . The easier we make the reports, the better doctors can understand them."

Just who is ordering reports from Omicia, and what is the company's objective in the year ahead? Join us for an insider's take on clinical genomics.

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Is this the Omics-to-Clinic Site We've All Been Waiting for?

Guest: Jonathan Hirsch, Founder, President, Syapse

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Chapters: (Advance the marker)

0:50 Why is Syapse the right solution?

6:12 What are you providing that hasn't already been there?

12:50 "Versioning" and preparing for FDA approval

15:44 How are you driving adoption of your service?

20:30 Scaling with a configurable platform

22:00 When will we see clinical sequencers?

26:14 What does genomic medicine look like in five years?

28:02 A PCORI grant

There are roughly two types of bioinformatics site offerings, "infrastructure" and "analytical" solutions. In our first interview of the year we focus on a new company offering an infrastructure solution, one that covers the end-to-end flow of omics into the clinic. Jonathan Hirsch is the President and Founder of Syapse and says his company is providing some services that have not been available before, particularly in the area of clinical reporting.

Recipient of a recent PCORI (Patient Centered Outcomes Research Initiative) Grant that is funded by the new ACA, Syapse is already offering their services to diagnostics labs who need a solution for reporting to physicians.

"We're in a very interesting place," says Hirsch in today's interview, "where the physicians are actually driving the adoption of IT solutions. And that's the trend that we're playing off."

How will the site scale, and how does Hirsch see genomic medicine in five years? Join us as we begin the year looking deeply into the adoption of personalized medicine.

Note: Hirsch will join Mendelspod Host, Theral Timpson, on two panel discussions on bioinformatics infrastructure later this month:

Jan 28th: PMWC 2014, Mountain View, California at 10:45 am (see details)

Jan 30th: Evening Event at Tres Lounge in San Francisco at 5:00 pm (see details)

An Industrial Revolution of Digital Healthcare: Interview with Sultan Meghji

Guest:

Sultan Meghji, Founder, Reformation Medicine

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Listen (4:20) The end of technology as a specialty

Listen (4:12) Sequencing devices still a bottleneck for clinical genomics

Listen (4:39) How to become a bioinformatician in six months

Listen (4:39) Basic scientists vs. technicians

Listen (8:19) Going through the Industrial Revolution of digital health

Listen (5:05) Do you think about bioethics?

Listen (4:49) Yes to regulation, and yes to access for everyone

Data scientists like Sultan Meghji are a highly valued species in today's world. Beginning his career at the National Center for Supercomputing Applications (NCSA) where he worked on original internet technologies, Sultan has used his expertise in several industries, including finance, air transportation, and now biotechnology.

We've had Sultan on for a couple shows already, and his broad experience and far reaching vision made him an obvious choice for our series, The Bioinformatician Bottleneck.

"We could graduate ten times what we're graduating every year for a decade, and I still wouldn't be convinced that we have enough [bioinformaticians]," he says in today's interview.

What to do about it? Sultan has suggestions, one of which is to have a "Khan Academy style program for How to Become a Bioinformatician in 6 Months." What about the years it takes to train great basic scientists in an age when biologists are already being called "mere technicians?" Sultan says technicians can handle much of the work of commercializing research.

Sultan goes on to suggest there are other important bottlenecks, including the sequencing tools space. Does he stop to think about bioethics? And is he for or against FDA regulation of personal genomic information? Today's show is far reaching and centered around Sultan's goal of bringing genomics to the masses.

"It's almost like the Industrial Revolution of digital healthcare," he says. "We're going to call it something else, but . . .at some point my blood, or some part of me, is going to go into a diagnostic black box, and out is going to come some recommendation that a doctor didn't actually look at. And I'm going to take it to the bank."

Podcast brought to you by: Roswell Park Cancer Insititute, dedicated to understanding, preventing and curing cancer for over 115 years.



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