Category Archives: bbgm

Back on the NCBI horse

I have been working a lot with alignments in Jalview and had blogged about how Google can find Uniprot IDs better than NCBI ..well it turns out that NCBI did indeed have most of the Uniprot sequences I was looking for. The fault was mine! for not using the correct form of uniprot id..

The catch
I had to say just Q57T52 instead of the Q57T52_SALCH and Q325Y4 instead of Q325Y4_SHIBS

Which brings to me to one incredible thing about google. The google suggest and spelling correction. NCBI recently added the spelling correction feature. But still does not have something that would have told me that I should try Q57T52 instead of the old style Q57T52_SALCH uniprot id query.

So all in all out of the 742 sequences that the manually curated PFAM database had used in its voltage_clc gamily alignment. I could find almost 640 of them at the NCBI using the NCBI web service. All it took was understanding the existence of the deprecated uniprot id.

When I similarly tested the EBI web service for the same 742 sequences, only 582 sequences were obtainable in the uniprotxml format from the uniprotkb database.

As a final try , looking for some of the sequences that were missing in the better performing NCBI database , by doing a google search returned a match in the first few results. So google still is quite amazing in its ability to index even probably poorly page-ranked words like Q40LF7_DESAC. Surely the day they take on bioinformatics in a formal way will be a fun day to look forward to.

references : bbgm on a Google for Bioinformatics

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Error Bars and experimental Biology – and the bbgm podcast

I will try to keep this post real short.

The Journal of Cell Biology carries a very useful article on error bars in experimental biology. Sadly the article is only available with a subscription, but Here is a link to the abstract on pubmed and the full text is available free at this link. The article talks about error bars in different context and how they should be used. Targeted at the non-statistics geek the article is easy to follow and quite useful.

My good friend Deepak who got me into blogging , recently started podcasting. Like his excellent blog the bbgm podcast is mostly about technology and computing and other things biotech . Deepak is extremely well plugged-in to the web 2.0 world and his podcast is fun medley of the things that catch his attention and the biotech-Bio IT business world . Recently he interviewed me on the fifth edition of his podcast. It was a lot of fun and I did get to talk a little about screencasting which is what we have been spending a fair amount of time on. He also got me hooked onto the TED talks, I would recommend these very enthusiastically. I was fascinated by a TED talk about photosynth and seadragon by Blaise Aguera Y arcas from Microsoft. I am very excited at the “how” , of this technology since it shares many similarities with single particle image processing and electron cryomicroscopy.

Check out the bbgm podcast here.

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.