c2cbio

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

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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

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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

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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

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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

Hari’s post on code-itch

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

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 slashes the web

Links of the week

Deepak: eScienceNews

Hari: Voidspace

Producers note: There was some background noise from Hari’s apartment.  Took a lot of it away but it’s there in a few places and has minor impacts on audio in a few places

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 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]

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

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

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 (mp3)

Design and implementation of the UniProt website

Crowds, solubility and the future of organic chemistry

Announcing the ChemSpider Journal of Chemistry

EOL is not delivering

Sorting a million 32-bit integers in 2 MB of RAM using Python