Episode 21 : Interview with Ricardo Vidal , a triple time zone pajama party

June 28th, 2009

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

 
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Episode 20: Man, it’s been forever

June 14th, 2009

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

 
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Episode 19: Karmic Chlamydial Koalas

May 3rd, 2009

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

Protein Power

Reflect

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

 
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Episode 18: I touched an electric organ

April 12th, 2009

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

Can someone confirm that JoVE has gone closed 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

 
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Episode 17: Libraries, swallows and pythons

April 5th, 2009

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

Libraries of the Future debate on FriendFeed

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

 
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Episode 16: Crowdsourcing and scaling

March 26th, 2009

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

Database sharding

Links of the week

Eli Bendersky

Spectral Game

 
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Episode 15: Tim Berners-Lee and Harold Varmus

March 19th, 2009

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

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

Zeroing in on the public domain attribution with 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: Of Wolfram|Alpha, Sages and Statistics

March 12th, 2009

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

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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Episode 13: Better engineering in Bioinformatics. Joel Dudley as blogged by Shirley Wu

February 27th, 2009

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 

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Episode 12: Remote synchrotron operation, reinventing the wheel on the web, and your Google heartbeat

February 12th, 2009

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

     
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