Coast to Coast Bio Podcast

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 for information.

“Sage” is a $5 mil funded organization founded by (former) Merck’s Stephen Friend and Eric Schadt to create a scientific commons platform to do better genomics inspired drug discovery research

We talk about the great success of Galaxy Zoo and how the next phase of the project is using Amazon Web Services to scale better

Mendeley aims to be the “Last.fm of Research papers” according to Ricardo Vidal, who recently signed on as community Liaison

Links of the week

Hari continues with his python kick with Scipy.org

Deepak was checking out freemat.org an open source matlab clone that packs quite a punch

 

 Coast to Coast Bio podcast #14 [43:50m]: Play Now | Play in Popup | Download

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Please give us your feedback either in the comments or by emailing us at hari — at — bioscreencast [dawt-com]

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 our heart that we spent all of 45 minutes talking about them .

Show notes

The shortest shownotes this far:

Joel Dudley on software engineering in Bioinformatics

Shirley wu : Tips and tricks for software engineering n Bioinformatics

 

 Coast to Coast Bio podcast #13 [50:26m]: Play Now | Play in Popup | Download

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Google Summer of code needs BioInformatics mentors and volunteers  

Links of the week ( thanks wlad for pointing our the omission)

Deepak was digging the datasets at the infochimps and  Hari likes Matplotlib 

You can always send us podcast ideas by tagging items in delicious with for:c2cbio

Please give us your feedback either in the comments or by emailing us at hari — at — bioscreencast [dawt-com]

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 notes

Remote synchrotron operation

Google takes your pulse

Webcentric software – telegraphs and telephones ( a post by Rich Apodaca )

Links of the week

NextBio

Breaking eggs and making omelets a blog on multimedia and ffmpeg

 

 Coast to Coast Bio podcast #12: Play Now | Play in Popup | Download

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 our weekly links.  Ah well

You can always send us podcast ideas by tagging items in delicious with for:c2cbio

Please give us your feedback either in the comments or by emailing us at hari — at — bioscreencast [dawt-com]

 

 Coast to Coast Podcast #10 [48:20m]: Play Now | Play in Popup | Download

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 with innovators : A recommended listen from Deepak

Git contributing to Bioinformatics Zen : How Bioinformatics zen uses github

Jean Clause Bradley reviews a book on Open education for Nature Magazine

Getting Value out of friendfeed : How Friendfeed enables science , Jean Clause Bradley collects real world examples

A brief mention of Learn you a Haskell and how functional programming can make you a better imperative programmer.

kodos regexp debugging for python and other languages

Nxclient from Nomachine : Hari blogs about bringing supper zippy remote desktops to the X-server and client

We also have a new feature. Our link of the week

Deepak’s Link: Hacker News
Hari’s Link:Daily Python URL

 

 Standard Podcast [35:12m]: Play Now | Play in Popup | Download

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)

Resolver One an ironPython spreadsheet  and Haris HelloWorld where he plays around with sequence data ( screencast link)

Jamis Buck on DSLs

GitHub Pages

Pawel Szczesny on Visual Analytics

 

 Coast to Coast Bio Podcast #8 [46:51m]: Play Now | Play in Popup | Download

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 to see that Matt Wood the head of production software at the Sanger Institute is blogging for the O’Reilly Radar, discuss cheminformatics, Git and Github, and finally end with the Ten Commandments of protein folding courtesy of Bosco (we do not apologize for being structure geeks). And here are the shownotes

• Uniprot architechture
• Instaseq: a Google powered Bioinformatics search
• Embrace and other service registries
• Matt Wood’s blogging on the O’Reilly Radar
• From SVN to Git/Github
• Boscos Ten commandments of protein folding

 

 Standard Podcast [32:50m]: Play Now | Play in Popup | Download

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 undergraduates bioinformatics principles and finally cover Sproutcore, a javascript frame work that could make rich internet apps even richer.

The Elsevier grand challenge: What researchers are promising to build using data APIs made available by Elsevier. Specifically talk about Rod Pages effort

Plos Biology : Metagenome annotation using a distributed grid of undegraduate students

The Embrace registry: a collection of life-science web services with built-in service testing. We also touch upon the Embrace Grid, which we will need to revisit some day.

Sproutcore and Cappuccino: Taking Javascript libraries to the next level

 

 Coast to Coast Bio podcast #5: Play Now | Play in Popup | Download