September 2007
33 posts
Wolfram Blog: The Math(ematica) behind... →
“A Web app developer worth his salt won’t go near HTML or JavaScript until...”
– Ahead of the Curve | Tom Yager | InfoWorld | Never send an HTML hacker to do a developer’s job | August 29, 2007 03:00 AM | By Tom Yager
Ahead of the Curve | Tom Yager | InfoWorld | More... →
“Systems Biology-a discipline so sprawling and unwieldy as to merit comparison to...”
– James Watson -in his biography as quoted on Corie loks blog
The Rich PDB interface explained →
It was a while back that I caught the video on the PDB site which explained all the functionalities that its search interface has. Thanks to the screencast I became a much more efficient querier of the PDB, especially after they adopted the new ( now almost three years old) interface.
I strongly believe that screencasting can play a role in helping us all search better.
Since I work on...
Why I dont like Facebook →
Allright ..treat this as a post designed to elicit comments or its just me venting !Why I dont do Facebook by meFirstly : The adds ! They are bloody annoying: I dont know why the adds on facebook annoy me more than the adds on Youtube . But they DO.My first few logins were greeted with jarring adds with models in various stages of undress! I am no prude but thats very intrusive ,...
Google unveils Presently:
And now we present... →
“Q: who do they admire outside of their own company. David Filo: Steve Jobs. Chad...”
– TC40 Keynote Speakers: Humble Beginnings
Is Apple killing Java in favor of Objective C →
I have very often expressed my frustration at how far behind Apple is, in bringing out a mac version of Java 6. The deveoper preview is stuck , with the last beta dated at Sept 2006. Along these lines, apple stopped updating the Quicktime for Java API for the last many releases, with new functionality only available from the objective-c library .
Recently at the Oreilly Ignite II event, one of...
Why are our bioinformatics workflows so... →
Why are our bioinformatics workflows so complicated!
Last week to answer one question I had to resort to information from several sources . A lot of them contributed immense value to my “workflow” and were also either difficult to perform or very easy. For a start I have ranked them in terms of both Value ( 1 for no value to 10 for a lot of value) to ease of use ( 1 for very complicated to 10...
Maybe scoble was right-human annotated search and... →
Deepak at bbgm and Simon Brocklehurst pointed me to the uproar that scobles post a few months back caused. In his post Robert scoble said search engines like Mahalo and not google are the future of the internet . I am beginning to agree with some of what he said.
I want to explain myself with the following example. I have been reading up a lot on two subjects , one is ffmpeg the open source...
The RESTful NCBI query →
I first caught this on Pierres blog.
NCBI it turns out can be queried along REST principles ( hence the RESTful in the title). Ever since learning about REST-based URLs , I always wished that many web APIs implemented the ideology in their design. I was excited to learn how easy and intuitive it becomes to query a database using REST principles.
Gone are queries that looked like
...
NCBI oddities →
I have often blogged about my trials and tribulations with the NCBI database.This morning I was trying to locate all the kappa light chain genes from the NCBI database.
I tried the following search
Immunoglobulin kappa mouse in the Genome database subsection.
The results I got were a curious mix of microbe genomes ranging from Aspergillus Niger to Salmonella enterica. Maybe I left my search...
“The 2004 quake measured 8.9 and struck under the sea near the northern Sumatran...”
– BBC NEWS | Asia-Pacific | Powerful quake shakes Indonesia
Ignite Boston - Tweaking, mixing competition and... →
As you probably saw from my post on processing, ignite-boston II was a blast. I was there talking about opening up science and bioscreencast.com. The talks at this Ignite were really interesting .
I especially liked the one by Ned Gulley from Mathworks who spoke of “Tweaking” a wiki-like matlab based programming contest. Tweaking is a great concept that effectively mixes collaboration with...
Video in Science - my foray into the SecondLife... →
Well I had talked about how Deepak went to SciFoo recently. It turns out that some of this years SciFoo alumni led by the indomitable Jean Claude Bradley (JCB or Horace Moody ) started the “metaverse” version of these sessions on the Nature Island on Second Life called Second Nature.
In keeping with the “non conference” format of the original, session themes at SciFoo Lives On are decided on by...
Processing and Visualizing Data →
I first heard of processing , from a post on Natures Nacent blog in which Euan Addie talked of how terrible visualization tools in the bio-space are.
I heard Ben Frys talk at the Ignite Boston event where he introduced processing to the audience and also gave a breathtaking demo ( despite the contrast issues that the venue had) of the app. Especially amazing was his visualization of the HapMap...
Sequence first ask questions later? →
I am little confused after reading about the metagenomics approach that identified the causative agent for the colony collapse disorder which Deepak and myself blogged about.
After trolling through pubmed , it seems like a number of the honeybee potential pathogens were already quite well known. The Kashmir bee virus and the Israeli acute Paralysis virus were also lurking among bee populations....
Metagenomics gives clues to a three year problem... →
Just yesterday I was reading about how metagenomics is proving to be a better choice for many questions than many traditional DNA amplification centric molecular techniques like many microarray and other PCR based approaches.
Metagenomics , which is a fancy way of saying ” sequence everything ” directly from the sample and then figure out what that everything is , now has another feather in its...
454 Finds Virus Clue to Disappearing Bee Disorder... →
Bioclipse2 - BioclipseWiki →
http://images.google.com/imgres?imgurl=http://www.s... →
Model of Entrez Databases →
How to Build a Craig Venter -- Cohen 2007 (904): 1... →
Google GPhone To Be First JavaFX Phone? at Simon’s... →
Science Library Pad: schoolteacher's balloon... →
“Affymetrix introduced the Genome-Wide Human SNP Array 6.0, which includes about...”
– Life Science Technologies: Microarray Technologies: Bench to Bedside
“Newer DNA sequencing technologies now threaten to do to microarray technology...”
– Life Science Technologies: Microarray Technologies: Bench to Bedside- Emma Hit in the Science Magazine
“Nature receives approximately 10,000 papers every year and our editors reject...”
– Overview: Nature’s trial of open peer review
eSciDoc from the Max Planck Society and FIZ... →
“Rakerman Yellowjacket: I found a lot of things were getting mixed together -...”
– Science Library Pad
“The current study sought to empirically ascertain the type of information youth...”
– Personal information of adolescents on the Interne…[J Adolesc. 2007] - PubMed Result