Coast to Coast Bio Podcast

In Episode 24, Hari and Deepak talk about advances in publishing, incremental science,

Show notes

Cell Beta prototypes

• Martin Fenner on the Article of the Future

PLoS makes a move

Links of the week

Hari: ReportLab
Deepak: Pro Git

Editors note: Due to recording issues some discussion at the end had to be edited out. We apologize for the abruptness

 

 Coast to Coast Bio podcast #24 [40:45m]: Play Now | Play in Popup | Download

You can always send us podcast ideas by posting items to the Friendfeed room or 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 23, Hari and Deepak fend of car alarms, go into deep ratholes, and talk a lot about programming and data visualization

Show notes

The canonical model of software development

Web-centric curriculum

• MIT Open Courseware

Introduction to scripting in Ruby for biologists

Indexing and searching NCBI genes with Apache Lucene

• Apache Jackrabbit
• Solr
• Mahout

Rise of the data scientist

50 great examples of data visualization

• Flare
• Processing

wellformed.eigenfactor.org

Beautiful Data: The Stories Behind Elegant Data Solutions

Links of the week

Hari: Summon (thread on Friendfeed)

Deepak: your.flowingdata.com

 

 Coast to Coast Bio podcast #23 [57:02m]: Play Now | Play in Popup | Download

You can always send us podcast ideas by posting items to the Friendfeed room or 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 22 Hari and Deepak talk about various events in the bay area and podcasts of interest, about putting science in our lives, funding the science we do, and scratch their heads over crazy articles on the drugs of the future.

Show notes

Scifoo is here again

• Preceded by SciBarCamp – Palo Alto

Stack Overflow is a huge influence

• As is net@night

Put a little science in your life

• Bernoulli’s principle
• Astroparticle physics
• Deepak thinks Shirley Wu has the best blog out there for communicating science while Hari loved her open letter to Oprah

James Hendler on the NSF, funding and panels

Digital Chemistry leaves us scratching our heads and Derek Lowe as well

Welcome to the streamosphere

Links of the week

Hari: PyCon Schedule

Deepak: TechZing; Rotamerically Induced Perturbations

 

 Coast to Coast Bio podcast #22 [59:15m]: Play Now | Play in Popup | Download

You can always send us podcast ideas by posting items to the Friendfeed room or 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]

We have missed recording c2cbio the last few weeks but we are happy to be finally interviewing Ricardo Vidal.  Apart from blogging on his My Biotech Life blog , Ricardo recently started as “community liason” at Mendeley. We talk about  Mendeley, the social aspects of sharing and tracking what we are reading and whats on the horizon for the platform . We then go onto chat about the usual c2cbio mix , synthetic biology , science blogging in a post-twitter  world, how blogging still opens doors and other things online-science.

Interview Recorded on Thursday,  June 26th 2009

Show Notes:

Ricardos blog :My Biotech life

Mendeley social software for managing and sharing research papers

Ricardos interviews with Victor Henning one of the co-founders of Mendeley

 

 Episode 21 : Ricardo Vidal [53:56m]: Play Now | Play in Popup | Download

You can always send us podcast ideas by posting items to the Friendfeed room or tagging items in deliciouswith for:c2cbio

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

In a long overdue episode 20, Hari and Deepak talk about a lot of old topics.  Old since the podcast was recorded a while ago, but some of the discussion is still pertinent.  Hari blames writing papers and Deepak blames all the interest in cloud computing.

Show notes

Wolfram|Alpha

Learning from StackOverflow

Royal Society acquires ChemSpider

Cheminformatics with Hadoop and EC2

Chemcaster

Janelia Farms – The whiskey portion of the show

Links of the week

Hari: Free programming books

Deepak: tricki.org

 

 Coast to Coast Bio podcast #20 [43:47m]: Play Now | Play in Popup | Download

You can always send us podcast ideas by posting items to the Friendfeed room or 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 19, Deepak and Hari talk about Synthetic Biology, Grand Challenge Winners and Protein Engineering.

Show notes

A synthetic biology company bites the dust

iGEM closes doors to amateurs

• Howtoons
• BioBricks Foundation
• Drew Endy and Jim Thomas and the synthetic biology debate 

Protein Power

Reflect

• Ubiquity

Active Research

This Week in Virology

Pierre does Hadoop; on a laptop

Jaunty Jackalope

Google Code supports Hg

Ensembl Genomes

Links of the week

Hari: 25 great free resources for making charts

Deepak: Develop.Github

 

 Coast to Coast Bio podcast #19 [59:14m]: Play Now | Play in Popup | Download

You can always send us podcast ideas by posting items to the Friendfeed room or 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]

Trying to do the TWiT thing and find a funny headline.  Let’s see if this sustains.  In this, the longest episode of c2cbio yet, Hari and Deepak talk about crowdsourcing, JoVE, managing patient records and a bunch of other little things

Show notes

There are crowds, and then there are crowds

• John Wilbanks’ E-Tech talk
• CCP4 bulletin board
• Computational Chemistry List
• The structure of scientific revolutions (It was on a Science podcast, not Scientific American)

Can someone confirm that JoVE has gone closed access?

• JoVE
• John Wilbanks on JoVE and open access

Managing your own patient record

Python moves to Hg

ZFS

The end of SGI

Links of the week

Hari: PyCon Videos

Deepak: Passenger PrefPane

 

 Coast to Coast Bio podcast #18: Play Now | Play in Popup | Download

You can always send us podcast ideas by posting items to the Friendfeed room or 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 17, we have a very spirited discussion on the role of libraries in research, about Summer of Code and data-driven analytics

Show notes

Nescent has the list of the bioinformatics project proposals for the Google Summer of Code 2009

• Donnie Berkholz

Libraries of the Future debate on FriendFeed

• Libraries of the Future debate
• Peter Murray-Rust on Libraries of the Future
• Christina Pikas responds

The unreasonable effectiveness of data: Alon Halevy, Peter Norvig, and Fernando Pereira at google discuss natural language processing vs more complex models that harness huge pools of data.

Are your coding skills current ? Whats hot in the coding language world ? TIOBE has the list.

Exciting news in the Python world after Pycon 2009, Unladen swallow: A team of five engineers announces a project to increase the speed of Cpython five fold using  LLVM

On the Ruby front, we have ActiveResearch, a gathering of science geeks at RailsConf and Paulo Nuin has a Ruby in Bioinformatics Blog

Links of the week

Deepak likes the concept behing the news stories site: http://thesciencebehindit.net/

Hari was checking out Jessenollers blog for some pythonic wisdom

Incidentally, we now have a Friendfeed room where we can carry on with this and other conversations

 

 Coast to Coast Bio podcast #17 [54:22m]: Play Now | Play in Popup | Download

You can always send us podcast ideas by posting items to the Friendfeed room or 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 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 using Scala

• Tiago on using Scala for Bioinformatics

Database sharding

• Amazon’s Dynamo
• Project Voldemort
• Tokyo Cabinet

Links of the week

Eli Bendersky

Spectral Game

 

 Coast to Coast Bio podcast #16 [46:26m]: Play Now | Play in Popup | Download

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]

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

• Paul Miller’s blog post
• Hans Rosling’s Ted talk

Harold Varmus on the Daily show : How we need to focus on science and fundamental research

• Natali del Conte’s Kepler misstep

Zeroing in on the public domain attribution with CC0

• CC0

Sleeping with the enemy? Friendfeeders sound off on collaborations with Microsoft and we chime in

• The post that started off the brouhaha

Links of the week

Deepak: Build SNP reports with Promethease

Hari: Blogging crystallography Stephen Curry blogs  on NNB and  Ted Ericksons P21212.com (check out the cool video links  to movies made by James Holton)

Footnote: Hari goes ga-ga over the Kindle

 

 Standard Podcast [42:16m]: Play Now | Play in Popup | Download

—-

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]