Episode 8: Twenty minutes of Brenner

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

Episode 7: Scientists in the cabinet, useful chemistry and reference architectures

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

Episode 6 : Web services, Instaseq and a blogging genomicist goes mainstream

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

Episode 5 : Grand challenges, javascript frameworks and collaborative annotations

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

Episode 4 : From map-reduce for molecular dynamics to galaxy zoo

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)

Coast to Coast Bio podcast #3

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

Coast to Coast Bio podcast: Episode 2

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
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

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Announcing the Coast to Coast Bio podcast

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
Java Posse
The Battle between Nature and Encyclopedia Britannica
The Genes Wiki project
Matt Wood

A podcast about biology, programming and everything in the middle