Coast To Coast Bio Podcast

In episode 16 we discuss a recent meeting that Deepak attended, the vagaries of crystallography, infrastructure buildouts, announcements by Nature and Innocentive and scalability (and a secret outtake) Show notes Sawzall Jimmy Lin USC gets a grant for grid computing Innocentive and Nature team up ChemSpider coming to a phone near you Scaling at Twitter … Continue reading Episode 16: Crowdsourcing and scaling →

On Episode 15, Hari and Deepak discuss a great TED talk by Sir Tim Berners-Lee on how the web needs to be about data, databases and APIs that allow the data to talk to each other .  CC0 is finally out and Deepak tells us why this is important. Show notes Tim Berners-Lee at TED … Continue reading Episode 15: Tim Berners-Lee and Harold Varmus →

Episode 14 was quite a blast.  We talk about the popularity of R, and new, ambitious and heavily hyped projects by Stephen Wolfram and Stephen Friend Show notes How Google and Facebook use R MachetEC2 is an EC2 AMI for data analysis Stephen Wolfram’s Wolfram|Alpha promises to impact the way we query data and look … Continue reading Episode 14: Of Wolfram|Alpha, Sages and Statistics →

This started off as a regular episode in which we were going to discus a few stories. But a talk given by Joel Dudley, resident Bioinformatics specialist in the Butte lab at Stanford, which Shirley Wu blogged about was just too good to miss. The issues raised in this blog post were so close to … Continue reading Episode 13: Better engineering in Bioinformatics. Joel Dudley as blogged by Shirley Wu →

In Episode 12 , Hari who had just finished a remote data run collecting diffraction data at the Berkeley synchrotron talks about his experiences; Google and IBM team up to bring health information management to your handheld; and then we have a brief chat about whether web concepts should necessarily mirror their pre-web avataars. Show … Continue reading Episode 12: Remote synchrotron operation, reinventing the wheel on the web, and your Google heartbeat →

In episode 11 of Coast to Coast Bio, Deepak and Hari debate big data, talk about what skills a bioinformatician should have, microblogging’s successful entry at PLoS, and even talk about how Google shut down the WWW Show notes Big data: Shoot first, ask questions later Attila asks about bioinformatics skills Friendfeed in PLoS Google … Continue reading Episode 11: Arguing big data and bioinformatics skills →

In episode 10 of Coast to Coast Bio, Hari and Deepak talk about ScienceOnline09, discuss living code, and sing the praises of Git, Friendfeed and Twitter Show Notes ScienceOnline09 Bora’s blog Anton Zuiker’s blog Social Networks in Science Science blogging networks The Edge annual question Evernote welcomes Google Notebook users Living Code And we forgot … Continue reading Episode 10: Of conferences and living code →

Episode 9 of Coast to Coast Bio finds Deepak and Hari kicking off a new year by recording a podcast together over some good red wine. Topics discussed include using GitHub as a a knowledge resource backend, remote desktops, Haskell, and various other random topics. Show Notes Jon Udell interviews Jeff Jonas  on the interviews … Continue reading Episode 9: One coast →

In Episode 8 of Coast to Coast Bio, the final episode for 2008, Hari and Deepak have a long, spirited, discussion about a recent talk by Sydney Brenner. Here are the show notes for this episode Sydney Brenner does not quite like Systems Biology Loose Ends Greg Petsko article “When Bubbles burst” ( Subscription required) … Continue reading Episode 8: Twenty minutes of Brenner →

In Episode 7, Deepak and Hari discuss Steven Chu’s selection as the Secretary of Energy, the Uniprot architecture, Open Notebook Science and issues with the Encylopedia of Life. Here are the shownotes Steven Chu is the new Secretary of Energy Synthetic Biology: Drew Endy debates Jim thomas at the longnow foundation seminars on longterm thinking … Continue reading Episode 7: Scientists in the cabinet, useful chemistry and reference architectures →

There were some technical difficulties with the recording, so we apologies for some of the quality issues Our weekly chat this week tries to explore web services like Embrace a little more and then goes into the Nature Precedings article on Instaseq, the Google powered bioinformatics search engine.  We talk about the excitement we feel … Continue reading Episode 6 : Web services, Instaseq and a blogging genomicist goes mainstream →

We talk about a few submissions at The Elsevier grand challenge , after which we launch into a brief discussion of the Embrace registry for bioinformatics web services (at some point we need to talk about the greater Embrace project) . Along the same vein we discuss a cool new use of annotation to teach … Continue reading Episode 5 : Grand challenges, javascript frameworks and collaborative annotations →

After a week long hiatus prompted by failing hotel internet connections and sleep deprivation following a two-day synchrotron run , we return with an episode filled with discussion ranging from specialized hardware solutions for millisecond scale molecular dynamics simulations to collaborative personal genomics and  astronomical galaxy calling Here are the shownotes: First cut (video) of … Continue reading Episode 4 : From map-reduce for molecular dynamics to galaxy zoo →

In Episode 3 of Coast to Coast Bio we talk about everything from the tension between experimentalists and bioinformaticians, Zotero vs. ThomsonReuters and even Michael Crichton The following links were discussed on the podcast this week Science in the Open talks about how good data models  and  well-posed questions lead to good code and the … Continue reading Coast to Coast Bio podcast #3 →

We’re back. In episode 2 we talk about topics ranging from next-gen sequencing to structured data. Specific sites or stories discussed include Nautilus: Next-generation sequencing poster and podcast Glue Is DAS the answer Git ( and esp Git from the bottom up a free pdf that explains the underlying magic) Toby Segaran: Personal data integration … Continue reading Coast to Coast Bio podcast: Episode 2 →

Alright here goes..We (i.e Deepak and Hari) had been thinking about starting a podcast for a while and we finally figured the best way to start is to simply dive in and get cracking. The audio quality isn’t quite there yet, but we’ll get things more streamlined as we streamline our workflow In this episode … Continue reading Announcing the Coast to Coast Bio podcast →