c2cbio

In the first episode of 2011, Deepak and Hari talk about new endeavors by MacMillan, about post-publication peer review, about computational science and good software, and get all giddy about virtual machines and javascript drawing programs.

Show Notes

Digital Science

Article by Declan Butler

Trial by Twitter

Annotatr

J-STOR

Crossref

Principles of Computational Science

Software Carpentry

ExPASy

PDB

Pubchem

WebGL and Chemwriter

Jolecule

Link of the week

Deepak: Vagrant

Hari: Pubchem sketcher (paper)

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Chris Lasher did ask, so we deliver

In this information packed episode we catch up, talk about blogging, podcast, other content and whether we are moving away from them.  We also talk about Arsenic life, automated deployment, and various sundry matters

Shownotes

This Week in Virology

The Pipeline

AppleTV

Roku

Quora

BioStar

MajorGroove

Micro Instances

AWS Console

Boto

Chef

We are all devops: Jacob Kaplan Moss at the Boston Django meetup. Video recording and post courtesy P.K.Shiu

Puppet

Cfengine

Vagrant

Homebrew

Cinderella

Jacob Kaplan-Moss on Devops

Devops

Heroku-MongoHQ app from Neal Saunders (blog post)

Ion Torrent Grant Challenge

Jimmy Lin’s Data Intensive Text Processing with MapReduce

Cloud9

Tom White’s Hadoop: The Definitive Guide

Schatz Lab

Arsenic Life Paper

Carl Zimmer

Rosie Redfield’s original post

Rosie Redfield’s Comments on response

Deepak’s blog post (1, 2)

Open Research Computation

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Editors note: We’ve had some trouble keeping c2cbio up lately, so this episode is very late.

In Episode 34, we recover from technology gremlins to talk about Craig Venter and the synthetic genome, about open data for malaria, about the UC library system taking on NPG and about being a programmer in academia

Shownotes

Craig Venter and man-made genomics

Guardian

Wired

Nature

GSK, malaria and CC0

The NPG, UC dustup (pdf)

Slashdot

Programming, Bioinformatics, and academia

and talking about data management

Links of the week

Deepak: http://rubyquicktips.tumblr.com/

Hari:  http://code.google.com/p/cinfony/

This was our first time recording three weeks in a row and we are thrilled to be back on this horse.  Of course, it took another 2+ weeks to publish the podcast (Deepak takes all blame)

The recently concluded Sage Congress seems to have been quite an event. Everyone who attended said it would take them months to grok everything that was talked about. Deepak clues us in on everything Sage and Serene.

Hari gets all excited with the cloning of the Trp-channel possibly behind infra-red vision in Snakes. Drug Safety information is 140 characters or less, sound ridiculous? . Game theory meets open access science among scientists – The prisoners dilemma recast as the scientists dilemma an interesting look at the choices facing pre-tenure academics- we discuss.

Producers Note: Deepak left his monitors on during the recording, which is why you can hear a little bit of lag on Hari’s audio

Shownotes

Sage Congress

Josh Sommers’ talk

Trp-channels and snakes: David Julius’s lab shows us the channel that mediates heat sensing in rattlesnakes (PMID 20228791)

Deepak’s prank

Hari’s retaliation

The FDA and Twitter

The Scientists Dilemma at Depth First

Managing projects (on BioStar)

Links of the Week

Deepak: GenePattern

Hari: CanvasMol

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

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In episode 32, we talk about careers in academia and industry; spend a lot of time talking about open access journals, including Nature Communications; comment on data access and don’t completely agree on peer review.

Production notes: Still not happy with the production quality.  Need to dig into what’s happening.  Might need to reduce recording levels for starters

Show notes

Andy Leifer from Aravi Samuels lab at Boston Barcamp 2010

Nature Communications

University clings on to Tree Ring data

Peer Review: The never ending story

Biotorrents (paper, web)

Links of the week

Deepak: Khan Academy

Hari: Project Euler

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

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We start of with our new unilateral intro and a discussion of all things new; jobs, podcast mics, conferences and talks.

In our science section we discus the recent storm in a teacup over the BRCA patents from Myriad being overturned by a federal court judge in New York. The YAGS acronym was coined by Jonathan Eisen in response to an article by Carl Zimmer about why new genome sequencing announcements dont make for exciting science. In our community section we discus a blog post from Cameron Neylon about Institutional openness and then talk about the sciencemag spotlight featuring Jean Claude Bradley, Jonathan Eisen and Carl Boettiger.

Apologies for the sometimes funky audio.  The usual pipeline didn’t do it’s trick

Show notes

BRCA patents , what now?

Yet-another-genome syndrome, Carl Zimmer

Deep sequencing of dogs (the Chihuahua thing might be an urban legend, or so Google says)

The Personal & the Institutional

Scientists embrace openness (Friendfeed thread)

A great forum question about biologists and programming

Links of the week

Deepak: Galaxy Cloud

Hari: The Kojo learning environment

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, by emailing us at hari — at — bioscreencast [dawt-com] or messaging @c2cbio on Twitter

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Welcome to the first episode of 2010, and hopefully back to being somewhat regular. In this episode we talk about what we’ve been up to and some exciting career changes. We talk about trends in next-generation sequencing, about the latest research on Thalidomide and about geeks and labels. We talk about new sites to ask questions about science, and about blog carnivals, and we talk about those those cool geo-data APIs and mashups.

Show notes

Sequencing in 2010

The anti-geek manifesto

Also see this Science is Unintuitive

Homing in on Thalidomide

The abstract

Lots of Stackexchange bio-related sites

Biostar

Major Groove

Chempedia Labs

NMR Wiki

Blog carnivals are back. Our interest, Iddo Friedberg and the Bioinformatics Blog Carniva. Hari in particular latched on to this quote by Maria Hodges“The advice given to pre-tenure scholars was consistent across all fields: focus on publishing in the right venues and avoid spending too much time on public engagement, committee work, writing op-ed pieces, developing websites, blogging, and other non-traditional forms of electronic dissemination (including online course activities)”

Deepak is jealous of geo

Links of the week

Deepak: Instapaper

Hari: Tutvid.com

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, by emailing us at hari — at — bioscreencast [dawt-com] or messaging @c2cbio on Twitter

After an almost two month hiatus prompted partly by a crashing unsaved Audacity session and a lost hard disk, we get back to podcasting with a new format.  This format we hope will add some biology back into our mix while we retain most of our usual geekery .

Beginning with episode 29 we will have three sections: The first section we have titled Science, here we will talk about published and reported scientific developments.  In the second section called Community spotlight, we will talk about interesting discussions on the Friendfeed life-scientists room  and  other Life-science blogs. Finally we have our section on things programming and the usual geeky “stuff”.

So Accordingly…we start episode 29 with some excuses that may explain our absence , then go on to introducing the new format . In the Science section we talk about how far the Mamalian Gene Consortium got and then chat about the aftermath of gene mapping companies like deCode, that finally closed their doors. As our community spotlight , we chose the interesting discussion about the many science based social networking sites that seem to have gone all quiet. Finally , we talk about the launch of chempedia and how the stack exchange ( or stackoverflow) model may be a needed twist to improve scientific  communication.

Keith Robinson writes at the Omics Omics Blog about “his most expensive paper” ever

What after deCode : Keith Robinson at the Omics Omics blog

Prompted by Cameron Neylon the Friendfeed life scientists room weighs in on some of the social networking sites they use

Rich Apodaca on  bringing the stack exchange engine to Chemists and Chemistry .

Chempedia is awesome: Check it out!

Links of the week:

Hari : DNA origami and Cadnano :http://www.cadnano.org

Deepak: A new Java web framework :playframework.org

Atom starts off by filing his Hadoop world report and then we launch into a discussion of Django, Tornado and how functional programming is probably the messiah that will lead us as we transition to the realtime web. Finally we talk about what all of this means for life science developers.

[Recorded on October 4th 2009]

Deepak Singh and Hadoop World.

Snakes on the web-Jacob Kaplan Moss:What sucks about web development and will Django and Python rise to the challenge.

Tornado and Nginx and Epoll

The new PUBMED interface

Rich Apodaca: Restful chemical tracking system

LOTW:

Developing Emol : Showmedo videos

Karmasphere studo for Hadoop

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 emerge from an hiatus with a programming heavy chat: Deepak and Hari start off discussing Haris recent programming experiences as he wrote an app to create protein crystallization grids. Are we there yet?- We discus Rich Hickeys talk at the recently concluded JVM language summit  and slide further into other things code and coding. Finally we discus Greg Petskos recent commentary about Twitter in Genome Biology.

GridZilla

Freindfeed  helped seed a fruitful online collaboration Pierre Lidenbaum and Andrew Su and the creation of the Gene wiki.

Rich Hickey at the JVM Languages Summit 2009, video coming up at InfoQ

Simon-Peyton Jones: Haskell and Erlang growing up together, slides

Deepak @ Hadoop world 2009: Hadoop for Bioinformatics

RHIPE

Cascading, ETL and other stuff

Greg Petskos take on Twitter.

Links of the week:

Deepak: Hurl it an Http curl rails app

Hari: Real World Haskell

Recorded on : September 20th 2009

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]