Monthly Archives: April 2007

Blogs that make me think- or a post from a fan

Deepak , who introduced me to blogging recently added me onto his list of “Thinking bloggers”. I am honored to be part of a list on bbgm that contains four veteran bloggers and I am sure being his friend has a lot to do with it.

I feel compelled to propagate the”meme” ( a term about which I knew nothing about till I read it on bbgm) .

SO , If I am to list the blogs or bloggers that inspired me the list would go like this..

1)Jon Udell : I started reading his columns in infoworld many years ago. But it was reading through reading his blog posts that got me interested in Screencasting ( he is the originator of the term) , XML , the seminars on long term thinking and about 95% of the things that take up my “free” time.

2) Chris Geminiani at Juice analytics: Deepak first blogged about this company on his bbgm blog. Following which I also heard one of its founders interviewed by Jon Udell. Following these postings,I was hooked. Juice’s approach to analytics using Excel has made me start appreciating the power of analytics (for eg check out this post analysing the above podcast interview)

3)Jean Claude Bradley: Early on Jean Claude Bradley commented on one of my posts, following which I checked out his useful chemistry blog. His championing of the power of the wiki , his approach to chemistry education and dedication to open-science are inspirational. Jean Claude Bradley also introduced be to youtube as a means of science popularization.

4) Pierre Lidenbaum at Yokofakun: I started reading his blog after using his pubmed2connotea greasemonkey script. Pierre bioinformatics posts excite the wannabe coder in me.

5 &6 ) For the last blog, I would like to trackback to two blogs that are examples of science blogging at its best. They are the John Hawks anthropology blog and Damian Allis’s blog, also tagged by Deepak. Both of these blogs make me want to be a better “scientific” blogger and were instrumental in making me take the blog plunge. I particularly enjoyed readings John Hawks coverage of the “hobbit man” findings and the visual appeal of Damians Allis’s blog ( I confess I am no computational chemist).

Before I go I will repeat here the rules of the Thinking blog tagging chain ,copied from Deepaks post:

(1) If, and only if, you get tagged, write a post with links to 5 blogs that make you think; (2) Link to this post so that people can easily find the exact origin of the meme; and (3) Optional: Proudly display the ‘Thinking Blogger Award’ with a link to the post that you wrote.


Membrane Protein Crystallization Analytics

I am starting to really like analytics. I started following the developments in the “analytics movement “after reading about companies like juice analytics , swivel , gapminder and “many eyes” at the bbgm blog. Along these lines Nature magazine also recently carried a news and views piece on IBMs many-eyes and the opportunities it afforded for scientific collaboration.

As a person closely involved in membrane protein purification , characterization and crystallization , I am always on the lookout for information related to the various aspects of doing membrane protein biochemistry . The very good compilation of membrane proteins of known structure compiled by Steven white at U.C Irvine was always my go-to place for information about membrane protein structures . But talking of analytics , I recently came across the very appropriately named “Membrane protein databank” which has a lot of compiled and elegantly displayed statistics on every aspect of membrane proteins structural biology ranging from the the expression systems and source organisms used to the detergents , additives and phasing methodology used for structure solution.

The MPDB seems to be a manually curated database which relies on the efforts of its creators to keep it up-to-date and accurate. As we all get increasingly open to sharing data pre and post publication . It will be exciting to see compilations like the MPDB emerge in the empirical and trial and error world of protein expression and crystallization trials . The advantages of using web2.0 frameworks to share and store information of the kind contained in the MPDB is exciting.

I cant wait for the day that a live RSS feed on my personalized google homepage informs me of the fact that Tim Toolman from the University of Xtal has crystallized a CLC channel from Halothermotrix orenii by expression in archaeoglobus fulgidus and it simultaneously updates a live graph of the many parameters used in these experiments probably available as a desktop widget on my google toolbar.