Coast to Coast Bio Podcast http://www.c2cbio.com A podcast about biology, programming and everything in the middle Sun, 30 Jan 2011 06:21:43 +0000 en-US hourly 1 http://wordpress.org/?v=3.5.1 Licensed under a Creative Commons Attribution license hari@bioscreencast.com (Deepak Singh & Hari Jayaram) hari@bioscreencast.com (Deepak Singh & Hari Jayaram) 1440 http://c2cbio.s3.amazonaws.com/CoastToCoastLogo3.png Coast to Coast Bio Podcast http://www.c2cbio.com 144 144 Geeking about biology and programming The Coast to Coast Bio podcast is brought to you by Deepak Singh and Hari Jayaram, who get together every week to riff about topics ranging from biology to programming and everything in between. bioinformatics,programming,technology Deepak Singh & Hari Jayaram no no Licensed under a Creative Commons Attribution licensebioinformatics,programming,technologyScience & Medicine/Natural SciencesTechnologyhari@bioscreencast.comDeepak Singh & Hari Jayaramhttp://creativecommons.org/licenses/by/3.0/ Episode 36: The USB slot on the left side http://feedproxy.google.com/~r/c2cbio/~3/0nW-fDfOynk/ http://www.c2cbio.com/2011/01/29/episode-36/#comments Sun, 30 Jan 2011 05:12:16 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=259 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

Link of the week

Deepak: Vagrant
Hari: Pubchem sketcher (paper)

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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]]> http://www.c2cbio.com/2011/01/29/episode-36/feed/ 1 1:03:02 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 No[...] 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) 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 We now have a Facebook Fan page. Please join us there podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2011/01/29/episode-36/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_36.mp3 Episode 35: The Grinch didn’t steal c2cbio http://feedproxy.google.com/~r/c2cbio/~3/vAkM51NSBoI/ http://www.c2cbio.com/2010/12/24/the-grinch-didnt-steal-c2cbio/#comments Sat, 25 Dec 2010 04:57:52 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=253 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

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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]]> http://www.c2cbio.com/2010/12/24/the-grinch-didnt-steal-c2cbio/feed/ 0 0:58:14 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 matt[...] 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 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 We now have a Facebook Fan page. Please join us there podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2010/12/24/the-grinch-didnt-steal-c2cbio/http://static.c2cbio.com/Coast_to_Coast_Bio_podcast_35.mp3 Episode 34: Technology gremlins http://feedproxy.google.com/~r/c2cbio/~3/bUeBpUEOm8Q/ http://www.c2cbio.com/2010/07/07/episode-34-technology-gremlins/#comments Wed, 07 Jul 2010 16:43:53 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=249 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

Links of the week

Deepak: http://rubyquicktips.tumblr.com/
Hari:  http://code.google.com/p/cinfony/

]]> http://www.c2cbio.com/2010/07/07/episode-34-technology-gremlins/feed/ 0 1:02:45 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 lib[...] 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/ podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2010/07/07/episode-34-technology-gremlins/http://static.c2cbio.com/Coast_to_Coast_Bio_podcast_34.mp3 Episode 33: Sage, Snakes and Pharma Tweets http://feedproxy.google.com/~r/c2cbio/~3/9E8lyVdt68s/ http://www.c2cbio.com/2010/05/18/episode-33-sage-snakes-and-pharma-tweets/#comments Wed, 19 May 2010 05:48:08 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=244 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

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
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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]]> http://www.c2cbio.com/2010/05/18/episode-33-sage-snakes-and-pharma-tweets/feed/ 0 0:59:22 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 a[...] 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 Please give us your feedback either in the comments, by emailing us at hari — at — bioscreencast [dawt-com] or messaging @c2cbio on Twitter We now have a Facebook Fan page. Please join us there podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2010/05/18/episode-33-sage-snakes-and-pharma-tweets/http://static.c2cbio.com/Coast_to_Coast_Bio_podcast_33.mp3 Episode 32: Careers, open access publishing and peer review http://feedproxy.google.com/~r/c2cbio/~3/AAV6jFFD0ZM/ http://www.c2cbio.com/2010/04/25/episode-32-careers-open-access-publishing-and-peer-review/#comments Mon, 26 Apr 2010 00:09:42 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=239 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

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

Please give us your feedback either in the comments, by emailing us at hari — at — bioscreencast [dawt-com] or messaging @c2cbio on Twitter

We now have a Facebook Fan page. Please join us there

]]> http://www.c2cbio.com/2010/04/25/episode-32-careers-open-access-publishing-and-peer-review/feed/ 0 1:00:10 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 n[...] 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 Please give us your feedback either in the comments, by emailing us at hari — at — bioscreencast [dawt-com] or messaging @c2cbio on Twitter We now have a Facebook Fan page. Please join us there podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2010/04/25/episode-32-careers-open-access-publishing-and-peer-review/http://static.c2cbio.com/Coast_to_Coast_Bio_podcast_32.mp3 The rigs http://feedproxy.google.com/~r/c2cbio/~3/Q5d0R_8Xc2U/ http://www.c2cbio.com/2010/04/18/the-rigs/#comments Sun, 18 Apr 2010 20:12:56 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/2010/04/18/the-rigs/ Hari’s rig

Deepak’s rig

]]> http://www.c2cbio.com/2010/04/18/the-rigs/feed/ 0 http://www.c2cbio.com/2010/04/18/the-rigs/ Episode 31: Genes, patents and open science http://feedproxy.google.com/~r/c2cbio/~3/OdpHIWeh_5A/ http://www.c2cbio.com/2010/04/18/episode-31-genes-patents-and-open-science/#comments Sun, 18 Apr 2010 19:59:58 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=224 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

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

We now have a Facebook Fan page. Please join us there

]]> http://www.c2cbio.com/2010/04/18/episode-31-genes-patents-and-open-science/feed/ 0 1:00:18 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 c[...] 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 We now have a Facebook Fan page. Please join us there podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2010/04/18/episode-31-genes-patents-and-open-science/http://static.c2cbio.com/Coast_to_Coast_Bio_podcast_31.mp3 Episode 30: There and back again http://feedproxy.google.com/~r/c2cbio/~3/SGlzasG_apQ/ http://www.c2cbio.com/2010/03/28/episode-30/#comments Sun, 28 Mar 2010 15:29:21 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=220 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
  • Homing in on Thalidomide
  • Lots of Stackexchange bio-related sites
  • 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

    ]]>     http://www.c2cbio.com/2010/03/28/episode-30/feed/ 0 1:00:18 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 re[...] 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 podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2010/03/28/episode-30/http://static.c2cbio.com/Coast_to_Coast_Bio_podcast_30.mp3     ScienceOnline 2010: Podcasting in Science http://feedproxy.google.com/~r/c2cbio/~3/chg4I90neFM/ http://www.c2cbio.com/2010/01/29/scienceonline-2010-podcasting-in-science/#comments Sat, 30 Jan 2010 03:09:36 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=217 At ScienceOnline 2010, Deepak and Dr. Kiki moderated a session on Podcasting in Science.  Video from the session is embedded below

    ]]>     http://www.c2cbio.com/2010/01/29/scienceonline-2010-podcasting-in-science/feed/ 0 noGeeking about biology and programmingDeepak Singh & Hari JayaramThe Coast to Coast Bio podcast is brought to you by Deepak Singh and Hari Jayaram, who get together every week to riff about topics ranging from biology to programming and everything in between.bioinformatics,programming,technologyhttp://www.c2cbio.com/2010/01/29/scienceonline-2010-podcasting-in-science/http://www.youtube.com/p/102BD0B4C30F5324&hl=en_US&fs=1     Back with a new format : episode 29 http://feedproxy.google.com/~r/c2cbio/~3/k9wj5nenFk0/ http://www.c2cbio.com/2009/11/29/back-with-a-new-format-episode-29/#comments Sun, 29 Nov 2009 13:09:49 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=207 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

    ]]>     http://www.c2cbio.com/2009/11/29/back-with-a-new-format-episode-29/feed/ 0 0:55:06 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[...] 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 podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/11/29/back-with-a-new-format-episode-29/http://static.c2cbio.com/Coast_to_Coast_Bio_podcast_29.mp3     Episode 28: c2c-programming? – Hadoop , Django , Scala, Tornado : A programming heavy session http://feedproxy.google.com/~r/c2cbio/~3/szAt58Ynlh0/ http://www.c2cbio.com/2009/10/18/episode-28-c2c-programming-hadoop-django-scala-tornado-a-programming-heavy-session/#comments Mon, 19 Oct 2009 03:22:21 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=199 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]

    ]]>     http://www.c2cbio.com/2009/10/18/episode-28-c2c-programming-hadoop-django-scala-tornado-a-programming-heavy-session/feed/ 0 0:46:33 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 [...] 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/10/18/episode-28-c2c-programming-hadoop-django-scala-tornado-a-programming-heavy-session/http://harijay_c2cbio.s3.amazonaws.com/episode28-c2cbio.mp3     Episode 27 : After a Hiatus http://feedproxy.google.com/~r/c2cbio/~3/sd6SJ0WeuSY/ http://www.c2cbio.com/2009/09/30/episode-27-after-a-hiatus/#comments Wed, 30 Sep 2009 11:15:22 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=190 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

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

    ]]>     http://www.c2cbio.com/2009/09/30/episode-27-after-a-hiatus/feed/ 0 0:48:24 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 recen[...] 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/09/30/episode-27-after-a-hiatus/https://code-itch.s3.amazonaws.com/episode27-c2cbio.mp3     Episode 26: Google, PLoS and NCBI get into bed together http://feedproxy.google.com/~r/c2cbio/~3/r96Qolra1a4/ http://www.c2cbio.com/2009/09/03/episode-26/#comments Thu, 03 Sep 2009 13:00:57 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=186 Deepak and Hari talk about an actual use of Google Knol, discuss surveys and somehow end up talking about YAML

    Show Notes

    Jekyll

    PLoS works with Google and NCBI to launch PLoS Currents: Influenza

    An inside/outside view of US science (sub required … sorry)

    How XML threatens Big Data

    Links of the week

    Hari: Zebra Crossing
    Deepak: Flightcaster (Should have been two months not weeks)

    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]

    ]]>     http://www.c2cbio.com/2009/09/03/episode-26/feed/ 0 1:04:24 Deepak and Hari talk about an actual use of Google Knol, discuss surveys and somehow end up talking about YAML Show Notes Jekyll PLoS works with Google and NCBI to launch PLoS Currents: Influenza The Knol NCBI Rapid Research Notes Google blog post [...] Deepak and Hari talk about an actual use of Google Knol, discuss surveys and somehow end up talking about YAML Show Notes Jekyll PLoS works with Google and NCBI to launch PLoS Currents: Influenza The Knol NCBI Rapid Research Notes Google blog post An inside/outside view of US science (sub required … sorry) How XML threatens Big Data JSON Apache Thrift YAML Links of the week Hari: Zebra Crossing Deepak: Flightcaster (Should have been two months not weeks) 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/09/03/episode-26/http://static.c2cbio.com/Coast_to_Coast_Bio_podcast_26.mp3     Episode 25: Quarter Century http://feedproxy.google.com/~r/c2cbio/~3/M21jgx0ML4s/ http://www.c2cbio.com/2009/08/25/episode-25/#comments Wed, 26 Aug 2009 06:57:09 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=184 We celebrate our 25th episode by talking about our favorite podcasts (and I did get This Week in Science mixed up with Dr. Kiki’s Science Hour), Facebook acquiring Friendfeed, the Push Button Web

    Show Notes


    Facebook acquires Friendfeed

    The Push Button Web

    Google buys On2

    Science and JoVE join hands

    Training new digital curators

    Scientists as better programmers

    How computing has changed biology

    Links of the week

    Hari: Pubsubhubbub
    Deepak: Posterous

    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]

    ]]>     http://www.c2cbio.com/2009/08/25/episode-25/feed/ 1 0:52:38 We celebrate our 25th episode by talking about our favorite podcasts (and I did get This Week in Science mixed up with Dr. Kiki’s Science Hour), Facebook acquiring Friendfeed, the Push Button Web Show Notes Facebook acquires Friendfeed The Pu[...] We celebrate our 25th episode by talking about our favorite podcasts (and I did get This Week in Science mixed up with Dr. Kiki’s Science Hour), Facebook acquiring Friendfeed, the Push Button Web Show Notes Facebook acquires Friendfeed The Push Button Web Pubsubhubbub Google buys On2 Science and JoVE join hands For example Training new digital curators Scientists as better programmers How computing has changed biology Links of the week Hari: Pubsubhubbub Deepak: Posterous 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/08/25/episode-25/http://static.c2cbio.com/Coast_to_Coast_Bio_podcast_25.mp3     Episode 24: Science is built on incrementalism http://feedproxy.google.com/~r/c2cbio/~3/dYp_ycASOfM/ http://www.c2cbio.com/2009/08/16/episode-24/#comments Sun, 16 Aug 2009 07:13:41 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=182 In Episode 24, Hari and Deepak talk about advances in publishing, incremental science,

    Show notes

    Cell Beta prototypes

    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

    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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    ]]>     http://www.c2cbio.com/2009/08/16/episode-24/feed/ 1 0:40:45 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[...] 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 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/08/16/episode-24/http://static.c2cbio.com/Coast_to_Coast_Bio_podcast_24.mp3     Episode 23: So why were you talking about iPhones? http://feedproxy.google.com/~r/c2cbio/~3/hhxGUAihceY/ http://www.c2cbio.com/2009/07/26/episode-23/#comments Sun, 26 Jul 2009 18:59:34 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=173 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

    Introduction to scripting in Ruby for biologists

    Indexing and searching NCBI genes with Apache Lucene

    Rise of the data scientist

    50 great examples of data visualization

    wellformed.eigenfactor.org

    Beautiful Data: The Stories Behind Elegant Data Solutions

    Links of the week

    Hari: Summon (thread on Friendfeed)

    Deepak: your.flowingdata.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 or by emailing us at hari — at — bioscreencast [dawt-com]

    ]]>     http://www.c2cbio.com/2009/07/26/episode-23/feed/ 0 0:57:02 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 scr[...] 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 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/07/26/episode-23/http://d3cwx9mdvjohat.cloudfront.net/Coast_to_Coast_Bio_podcast_23.mp3     Episode 22: Hey dad, how does this plane fly? http://feedproxy.google.com/~r/c2cbio/~3/C62Frwm9hR4/ http://www.c2cbio.com/2009/07/18/episode-22/#comments Sun, 19 Jul 2009 06:44:17 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=167 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

    Stack Overflow is a huge influence

    Put a little science in your life

    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

    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]

    ]]>     http://www.c2cbio.com/2009/07/18/episode-22/feed/ 1 0:59:15 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 Scifo[...] 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 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/07/18/episode-22/https://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_22.mp3     Episode 21 : Interview with Ricardo Vidal , a triple time zone pajama party http://feedproxy.google.com/~r/c2cbio/~3/XA17gu9vDfA/ http://www.c2cbio.com/2009/06/28/episode-21-interview-with-ricardo-vidal-a-triple-time-zone-pajama-party/#comments Sun, 28 Jun 2009 17:04:09 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=150 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

    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]

    ]]>     http://www.c2cbio.com/2009/06/28/episode-21-interview-with-ricardo-vidal-a-triple-time-zone-pajama-party/feed/ 1 0:53:56 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  M[...] 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 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/06/28/episode-21-interview-with-ricardo-vidal-a-triple-time-zone-pajama-party/http://code-itch.s3.amazonaws.com/episode21-c2cbio.mp3     Episode 20: Man, it’s been forever http://feedproxy.google.com/~r/c2cbio/~3/7Pw5yMEjziw/ http://www.c2cbio.com/2009/06/14/episode-20/#comments Mon, 15 Jun 2009 00:32:20 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=146 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

    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]

    ]]>     http://www.c2cbio.com/2009/06/14/episode-20/feed/ 0 0:43:47 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 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 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/06/14/episode-20/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_20.mp3     Episode 19: Karmic Chlamydial Koalas http://feedproxy.google.com/~r/c2cbio/~3/mTduLVlQU-M/ http://www.c2cbio.com/2009/05/03/episode-19-karmic-chlamydial-koalas/#comments Sun, 03 May 2009 07:59:17 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=141 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

    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]

    ]]>     http://www.c2cbio.com/2009/05/03/episode-19-karmic-chlamydial-koalas/feed/ 0 0:59:14 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[...] 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 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/05/03/episode-19-karmic-chlamydial-koalas/https://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_19.mp3     Episode 18: I touched an electric organ http://feedproxy.google.com/~r/c2cbio/~3/Y-BmcuiaNoE/ http://www.c2cbio.com/2009/04/12/episode-18/#comments Sun, 12 Apr 2009 15:20:44 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=132 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

    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]

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    ]]>     http://www.c2cbio.com/2009/04/12/episode-18/feed/ 1 0:00:01 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 n[...] 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 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/04/12/episode-18/https://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_18.mp3     Episode 17: Libraries, swallows and pythons http://feedproxy.google.com/~r/c2cbio/~3/KZbv7-REfpU/ http://www.c2cbio.com/2009/04/05/episode-17/#comments Mon, 06 Apr 2009 00:08:00 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=127 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

    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]

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    ]]>     http://www.c2cbio.com/2009/04/05/episode-17/feed/ 4 0:54:22 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[...] 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 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/04/05/episode-17/https://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_17.mp3     Episode 16: Crowdsourcing and scaling http://feedproxy.google.com/~r/c2cbio/~3/3E61lOmCNEM/ http://www.c2cbio.com/2009/03/26/crowdsourcing-and-scaling/#comments Fri, 27 Mar 2009 06:26:19 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=125 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

    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]

    ]]>     http://www.c2cbio.com/2009/03/26/crowdsourcing-and-scaling/feed/ 0 0:46:26 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 f[...] 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 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/03/26/crowdsourcing-and-scaling/https://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_16.mp3     Episode 15: Tim Berners-Lee and Harold Varmus http://feedproxy.google.com/~r/c2cbio/~3/3sn8J-4OQFM/ http://www.c2cbio.com/2009/03/19/tim-berners-lee-and-harold-varmus/#comments Fri, 20 Mar 2009 04:16:51 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=115 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

    —-

    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]

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    ]]>     http://www.c2cbio.com/2009/03/19/tim-berners-lee-and-harold-varmus/feed/ 1 0:42:16 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 [...] 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 —- 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/03/19/tim-berners-lee-and-harold-varmus/https://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_15.mp3     Episode 14: Of Wolfram|Alpha, Sages and Statistics http://feedproxy.google.com/~r/c2cbio/~3/BGi7o0MIHB8/ http://www.c2cbio.com/2009/03/12/of-wolframalpha-sages-and-statistics/#comments Fri, 13 Mar 2009 05:25:21 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=107 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

    —-

    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]

    ]]>     http://www.c2cbio.com/2009/03/12/of-wolframalpha-sages-and-statistics/feed/ 1 0:43:50 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 Wolfr[...] 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 —- 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/03/12/of-wolframalpha-sages-and-statistics/https://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_14.mp3     Episode 13: Better engineering in Bioinformatics. Joel Dudley as blogged by Shirley Wu http://feedproxy.google.com/~r/c2cbio/~3/_zsHK0WYk7E/ http://www.c2cbio.com/2009/02/27/episode-13/#comments Fri, 27 Feb 2009 15:38:53 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=100 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

    —-

    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]

    ]]>     http://www.c2cbio.com/2009/02/27/episode-13/feed/ 5 0:50:26 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 iss[...] 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 —- 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/02/27/episode-13/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_13.mp3     Episode 12: Remote synchrotron operation, reinventing the wheel on the web, and your Google heartbeat http://feedproxy.google.com/~r/c2cbio/~3/q7b6y-Gjjy4/ http://www.c2cbio.com/2009/02/12/episode-12/#comments Fri, 13 Feb 2009 05:41:26 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=95 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

    ]]>     http://www.c2cbio.com/2009/02/12/episode-12/feed/ 0 0:00:01 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 brie[...] 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 podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/02/12/episode-12/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_12.mp3     Episode 11: Arguing big data and bioinformatics skills http://feedproxy.google.com/~r/c2cbio/~3/25k3pRoEB20/ http://www.c2cbio.com/2009/02/05/episode-11/#comments Fri, 06 Feb 2009 06:18:02 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=92 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]

    ]]>     http://www.c2cbio.com/2009/02/05/episode-11/feed/ 0 0:00:01 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 [...] 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/02/05/episode-11/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_11.mp3     Episode 10: Of conferences and living code http://feedproxy.google.com/~r/c2cbio/~3/jV8oiw-jI58/ http://www.c2cbio.com/2009/01/29/episode-10/#comments Thu, 29 Jan 2009 07:35:07 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=86 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

    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]

    ]]>     http://www.c2cbio.com/2009/01/29/episode-10/feed/ 1 0:48:20 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 Scie[...] 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] podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/01/29/episode-10/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_Podcast_10.mp3     Episode 9: One coast http://feedproxy.google.com/~r/c2cbio/~3/9VhJa9WxNOk/ http://www.c2cbio.com/2009/01/15/one-coast/#comments Thu, 15 Jan 2009 20:43:03 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=81 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

    ]]>     http://www.c2cbio.com/2009/01/15/one-coast/feed/ 1 0:35:12 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 othe[...] 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 podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2009/01/15/one-coast/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_Podcast_9.mp3     Episode 8: Twenty minutes of Brenner http://feedproxy.google.com/~r/c2cbio/~3/uYrmFBTJ1fk/ http://www.c2cbio.com/2008/12/24/episode-8/#comments Wed, 24 Dec 2008 17:44:54 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=70 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

    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

    ]]>     http://www.c2cbio.com/2008/12/24/episode-8/feed/ 1 0:46:51 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 Loo[...] 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 podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2008/12/24/episode-8/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_Podcast_8.mp3     Episode 7: Scientists in the cabinet, useful chemistry and reference architectures http://feedproxy.google.com/~r/c2cbio/~3/9X6r7HqGgeY/ http://www.c2cbio.com/2008/12/17/episode-7-scientists-in-the-cabinet-useful-chemistry-and-reference-architectures/#comments Wed, 17 Dec 2008 16:00:10 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=65 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

    ]]>     http://www.c2cbio.com/2008/12/17/episode-7-scientists-in-the-cabinet-useful-chemistry-and-reference-architectures/feed/ 2 0:40:28 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 [...] 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 podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2008/12/17/episode-7-scientists-in-the-cabinet-useful-chemistry-and-reference-architectures/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast%20_7.mp3     Episode 6 : Web services, Instaseq and a blogging genomicist goes mainstream http://feedproxy.google.com/~r/c2cbio/~3/P78IQUME5YM/ http://www.c2cbio.com/2008/12/11/episode-6-web-services-instaseq-and-a-blogging-genomicist-goes-mainstream/#comments Thu, 11 Dec 2008 07:45:15 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=54 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

    ]]>     http://www.c2cbio.com/2008/12/11/episode-6-web-services-instaseq-and-a-blogging-genomicist-goes-mainstream/feed/ 2 0:32:50 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[...] 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 podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2008/12/11/episode-6-web-services-instaseq-and-a-blogging-genomicist-goes-mainstream/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_6.mp3     Episode 5 : Grand challenges, javascript frameworks and collaborative annotations http://feedproxy.google.com/~r/c2cbio/~3/6rMmx9UYUKE/ http://www.c2cbio.com/2008/12/03/episode-5-grand-challenges-javascript-frameworks-and-collaborative-annotations/#comments Thu, 04 Dec 2008 03:46:46 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=51 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

    ]]>     http://www.c2cbio.com/2008/12/03/episode-5-grand-challenges-javascript-frameworks-and-collaborative-annotations/feed/ 1 0:00:01 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 sam[...] 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 podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2008/12/03/episode-5-grand-challenges-javascript-frameworks-and-collaborative-annotations/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_5.mp3     Episode 4 : From map-reduce for molecular dynamics to galaxy zoo http://feedproxy.google.com/~r/c2cbio/~3/vsYjgl8AaX8/ http://www.c2cbio.com/2008/11/26/episode-4-from-map-reduce-for-molecular-dynamics-to-galaxy-zoo/#comments Wed, 26 Nov 2008 17:08:10 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=44 After a week long hiatus prompted by failing hotel internet connections and sleep deprivation following a two-day synchrotron run , we return with an episode filled with discussion ranging from specialized hardware solutions for millisecond scale molecular dynamics simulations to collaborative personal genomics and  astronomical galaxy calling

    Here are the shownotes:

    First cut (video) of Deepaks talk on big data and open science at  Virginia Tech ( abstract)

    D.E Shaw research group and map-reduce for molecular dynamics

    NCI Cancer Molecular Analysis Portal and the BigHealth Consortium

    Galaxy zoo : a collaborative galazy annotation project has its first publications

    Whats new in Mathematica 6 (and 7)

    ]]>     http://www.c2cbio.com/2008/11/26/episode-4-from-map-reduce-for-molecular-dynamics-to-galaxy-zoo/feed/ 1 0:00:01 After a week long hiatus prompted by failing hotel internet connections and sleep deprivation following a two-day synchrotron run , we return with an episode filled with discussion ranging from specialized hardware solutions for millisecond scale mo[...] After a week long hiatus prompted by failing hotel internet connections and sleep deprivation following a two-day synchrotron run , we return with an episode filled with discussion ranging from specialized hardware solutions for millisecond scale molecular dynamics simulations to collaborative personal genomics and  astronomical galaxy calling Here are the shownotes: First cut (video) of Deepaks talk on big data and open science at  Virginia Tech ( abstract) D.E Shaw research group and map-reduce for molecular dynamics NCI Cancer Molecular Analysis Portal and the BigHealth Consortium Galaxy zoo : a collaborative galazy annotation project has its first publications Whats new in Mathematica 6 (and 7) podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2008/11/26/episode-4-from-map-reduce-for-molecular-dynamics-to-galaxy-zoo/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio_podcast_4.mp3     Coast to Coast Bio podcast #3 http://feedproxy.google.com/~r/c2cbio/~3/_lrWjpDaaos/ http://www.c2cbio.com/2008/11/12/coast-to-coast-bio-podcast-3/#comments Wed, 12 Nov 2008 19:26:24 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=35 In Episode 3 of Coast to Coast Bio we talk about everything from the tension between experimentalists and bioinformaticians, Zotero vs. ThomsonReuters and even Michael Crichton

    The following links were discussed on the podcast this week

    Science in the Open talks about how good data models  and  well-posed questions lead to good code

    and the Saunders principle wherein Bioinformaticians struggle with inconsistent formats , prompting code-itch (Hari) to complain that Bioinformaticians have to grin and bear it!

    Zotero the open bibliography management firefox extension is being sued by Thomson  the creators of EndNote .

    Delicious Networks and  Connotea : Social bookmarking and content discovery ( side note : a few screencasts about connotea )

    Duncan Hull reviews the many social Bibliography apps

    The podcast can also be found on iTunes

    ]]>     http://www.c2cbio.com/2008/11/12/coast-to-coast-bio-podcast-3/feed/ 1 0:00:01 In Episode 3 of Coast to Coast Bio we talk about everything from the tension between experimentalists and bioinformaticians, Zotero vs. ThomsonReuters and even Michael Crichton The following links were discussed on the podcast this week Science in t[...] In Episode 3 of Coast to Coast Bio we talk about everything from the tension between experimentalists and bioinformaticians, Zotero vs. ThomsonReuters and even Michael Crichton The following links were discussed on the podcast this week Science in the Open talks about how good data models  and  well-posed questions lead to good code and the Saunders principle wherein Bioinformaticians struggle with inconsistent formats , prompting code-itch (Hari) to complain that Bioinformaticians have to grin and bear it! Zotero the open bibliography management firefox extension is being sued by Thomson  the creators of EndNote . Delicious Networks and  Connotea : Social bookmarking and content discovery ( side note : a few screencasts about connotea ) Duncan Hull reviews the many social Bibliography apps The podcast can also be found on iTunes podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2008/11/12/coast-to-coast-bio-podcast-3/http://c2cbio.s3.amazonaws.com/Coast_to_Coast_Bio%20podcast_%20Episode_3.mp3     Coast to Coast Bio podcast: Episode 2 http://feedproxy.google.com/~r/c2cbio/~3/wqMRSDq4Ry4/ http://www.c2cbio.com/2008/11/05/coast-to-coast-bio-podcast-episode-2/#comments Wed, 05 Nov 2008 18:11:57 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=28 We’re back. In episode 2 we talk about topics ranging from next-gen sequencing to structured data.

    Specific sites or stories discussed include

    Nautilus: Next-generation sequencing poster and podcast
    Glue
    Is DAS the answer
    Git ( and esp Git from the bottom up a free pdf that explains the underlying magic)
    Toby Segaran: Personal data integration

    Please feel free to send us your feedback as well as your thoughts and ideas. If there is something you feel we could talk about, you can bookmark it on delicious with the tag for:c2cbio

    The Coast to Coast Bio podcast is also available via iTunes

    Reblog this post [with Zemanta]
    ]]>     http://www.c2cbio.com/2008/11/05/coast-to-coast-bio-podcast-episode-2/feed/ 2 0:00:01 We’re back. In episode 2 we talk about topics ranging from next-gen sequencing to structured data. Specific sites or stories discussed include Nautilus: Next-generation sequencing poster and podcast Glue Is DAS the answer Git ( and esp Git fr[...] We’re back. In episode 2 we talk about topics ranging from next-gen sequencing to structured data. Specific sites or stories discussed include Nautilus: Next-generation sequencing poster and podcast Glue Is DAS the answer Git ( and esp Git from the bottom up a free pdf that explains the underlying magic) Toby Segaran: Personal data integration Please feel free to send us your feedback as well as your thoughts and ideas. If there is something you feel we could talk about, you can bookmark it on delicious with the tag for:c2cbio The Coast to Coast Bio podcast is also available via iTunes podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2008/11/05/coast-to-coast-bio-podcast-episode-2/http://c2cbio.s3.amazonaws.com/Coast%20to%20Coast%20Bio%20podcast_%20Episode%202.mp3     Announcing the Coast to Coast Bio podcast http://feedproxy.google.com/~r/c2cbio/~3/y-QqUcW4180/ http://www.c2cbio.com/2008/10/29/announcing-the-coast-to-coast-bio-podcast/#comments Wed, 29 Oct 2008 20:58:44 +0000 hari@bioscreencast.com (Deepak Singh & Hari Jayaram) http://www.c2cbio.com/?p=5 Alright here goes..We (i.e Deepak and Hari) had been thinking about starting a podcast for a while and we finally figured the best way to start is to simply dive in and get cracking. The audio quality isn’t quite there yet, but we’ll get things more streamlined as we streamline our workflow

    In this episode we talk about the plethora of wikis out there , when databases aren’t really databases , a brief foray into writing python extensions for Mindtouch Deki and Biocarta, a graphical user contributed pathway archive.

    The format of the podcast will evolve over time as we settle into a routine and schedule. Our current plan is to publish a new episode every week and talk about matters somewhere in the continuum between biology and programming

    Other links mentioned in the podcast

    Stack Overflow podcast
    GDGT Podcast
    FLOSS Weekly
    Dan Ingalls
    Net at Nite
    E. Coli Hub
    Topsan
    Java Posse
    The Battle between Nature and Encyclopedia Britannica
    The Genes Wiki project
    Matt Wood

    ]]>     http://www.c2cbio.com/2008/10/29/announcing-the-coast-to-coast-bio-podcast/feed/ 1 0:34:06 Alright here goes..We (i.e Deepak and Hari) had been thinking about starting a podcast for a while and we finally figured the best way to start is to simply dive in and get cracking. The audio quality isn’t quite there yet, but we’ll ge[...] Alright here goes..We (i.e Deepak and Hari) had been thinking about starting a podcast for a while and we finally figured the best way to start is to simply dive in and get cracking. The audio quality isn’t quite there yet, but we’ll get things more streamlined as we streamline our workflow In this episode we talk about the plethora of wikis out there , when databases aren’t really databases , a brief foray into writing python extensions for Mindtouch Deki and Biocarta, a graphical user contributed pathway archive. The format of the podcast will evolve over time as we settle into a routine and schedule. Our current plan is to publish a new episode every week and talk about matters somewhere in the continuum between biology and programming Other links mentioned in the podcast Stack Overflow podcast GDGT Podcast FLOSS Weekly Dan Ingalls Net at Nite E. Coli Hub Topsan Java Posse The Battle between Nature and Encyclopedia Britannica The Genes Wiki project Matt Wood podcast Deepak Singh & Hari Jayaram no no http://www.c2cbio.com/2008/10/29/announcing-the-coast-to-coast-bio-podcast/http://c2cbio.s3.amazonaws.com/c2cbio_ep1.mp3     Deepak Singh & Hari JayaramnonadultGeeking about biology and programming