c2cbio

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

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

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)

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

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

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