Under the hood web 2.0- PUBMED and RSS

Snap poll: Did you know that PUBMED and a lot of the NCBI gives you the ability to create custom RSS feed around just about any query

My Answer : Yes I do ..but I learnt about this feature very recently, and I have been using PUBMED for years. You can watch how this feature works from this screencast .

The reason I bring this up is my observation that the NCBI and the EBI have been putting in a lot of energy at staying current while  preserving their orginal interface. Under the hood at the NCBI you can find features like MY-NCBI which has some killer personalization options ( to borrow a web 2.0 buzzword) . The NCBI forms have started to use more and more javascript and things  have started to look “more ajaxy” . Even the collections option just about ensures that I dont use connotea as often ( other than when I want to share collections on the web).

The point is that the bio-search space has and continues to see variations to the theme of search. A lot of these offerings seem to be mere duplications of functionality already present at the EBI and NCBI. While this is a good thing and only through such attempts will we arrive at a “Google”( in the verb sense) for biosearch.

I sometimes wonder if it would just be more worthwhile for atleast the career scientists among us, to learn how to use NCBI and EBI first. Then maybe private research dollars could be diverted to tackle the harder problems in bio-search .

References: Helia seraches PUBMED/MEDLINE

I feel Chicken Gunya? Can social networks help track emerging diseases

I remember being particularly amazed at Jonathan Harris and Seepandar Kamwars  “We feel fine”  visualization based on extracted statements from blog posts around the world. Reading about the re-emergence of dengue fever , chicken-gunya , west-nile and other viruses across South Asia, I started wondering if there are ways of keeping track of emerging pathogens using the many social networks that span the Globe.

In many countries there is no paranoia associated with sharing health information like there exists in the developed world. Even if the paranoia exists like it does in the US. We are curiously caught in a world where people reading my blog are more likely to know I have contracted the flu than any two of my healthcare providers who need that information to treat me better.

While the debate on the best way to handle health information online continues, I was wondering how open I would be to sharing information about what afflicts me, if there was a societal benefit to be derived from it. It could something as simple as monitoring allergy symptoms around where I live or something fancy like tracking an emerging pathogen.

Imagine all of us updating a common channel with “de-personalized” information on what afflicts us globally.   I can imagine the system to be something like this ..I  could “submit” to this service information about what ails me ..and the machine could obfuscate my details , preserving only things like my approximate geographical area and my age and sex and add it to this health information social network.

If implemented well could  possibly then have daily visualizations along the lines of  “We feel fine” to possibly something like  “We feel chicken Gunya”

Of $6 web hosts and dying web apps

Just yesterday I was reading tiagos blog where he requested hosting for a computational intensive bioinformatics web-app that he wrote. The application queries and sytematizes mitochondrial genome information from entrez databases, and I assume would be quite useful to animal geneticists and ecologists. Tiago is physically moving institutes and his blog posts talks of his fears of how the app might die if his personal computer goes down.

In one of my personal projects , I have been wrestling with cloning kappa light chains from several monoclonal antibodies that I generated. The cloning required a good knowledge of the anitbody light and heavy chain leader sequences . Several papers I was reading reference the Kabat and Wu database, which catalogs the thousands of sequences of antibodies and other immunological proteins from mouse and humans . Sadly the links to the Kabat and Wu database in some of these papers does not point to any meaningful location. The resulting google and pubmed searches to find this lost data greatly increased the time and effort required to design my cloning experiments.

Which brings me to my question.

In an era when we have free wiki hosting , 4 GB free email access , supercomputers that power maps , gigabyte large free image sharing applications, $6 per month, terabyte bandwidth web hosting. Why are we still so far from an advertisement supported “free” app host for meaningful scientific data ?

Perhaps its because only a few thousand people who are saving a rare turtle species somewhere on this planet will find tiagos web-app useful..Surely thats not yet worth enterprise level attention, or maybe we should all just write our web apps to run off facebook!

Video in Science – my foray into the SecondLife metaverse

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 the attendants , in this case on the wiki that serves as its permanent home outside of Second Life. Yesterdays session was on the role of “Video in Science” and of course we were there with Deepak as Whitewizard Chemistry and myself as Vishwaroop Baroque.

As I awkwardly bumped into the attendees thanks to my terrible gaming skills , the whitewizard chemistry told the audience about bioscreencast.com. This was followed by a talk by JCB on “YouTube and the Sciences” and finally one from someone at the SciVee project.

This was my first time in Second Life. I entered as a skeptic, since I always thought second Life is just a toy for gaming geeks and uber nerds. But I must say the poster session was just like the real thing with some added benefits. Like in the real thing, the questions made the poster session come alive but this time you get a text transcript of all conversations that took place and an overall rich experience. Not to mention the fact that the poster lives on on the NPG island and does not end up in my lab storage area ( read trash can).

I came away convinced that activities like this have a great value in enriching the online scientific experience.

Bertalan, one of the attendees, live blogged the event. You can catch also read about the goings on at Deepaks bbgm blog and of course on the bioscreencast.com blog.

A full text transcript is available on Jean Claude Bradleys blog

Bioscreencast.com – Screencasting for the Life Sciences

For the last many months five of us have been toiling away at building a tool for the life sciences. I am very excited to announce bioscreencast.com , our attempt at building a community for the Life Science sciences.

As biology gets more and more complex. We all found that we were forced to wear many hats. The march of genomics into every area of life science, forces us to learn new skills everyday.  There is no denying , how every life scientist has to become very well versed with computational data analysis. The lines between the former day computational biologists , bio-informaticians , statisticians, crystallographers, theoreticians and bench life scientists are blurring everyday.

Bioscreencast.com is our attempt at building a community that can share its knowledge through the powerful medium of screencasting.

This is just a beta and needless to say we need you to give us all the feedback you can.  So Dive in , check out our blog and let us know what you think.

References:

Bioscreencast.com Blog

Another post from one of us (Deepak Singh)

And last but not the least The Bioscreencast.com website .

Nature precedings : A great offerring from the NPG stable

Nature just launched Nature precedings , a home for Pre-publication research and preliminary findings. Within seconds of browsing through its very intuitive interface I immediately got the purpose of this offering from Nature Publishing group.

The way it works is simple- you can upload content in the form of word documents , powerpoint files and pdf files and it gets released to the community after a preliminary check for appropriateness of content and suitability for the nature precedings audience. Signed up users can then vote on the content ( a la Digg) and it gets moves up or down its category. All of the content is also search-able and link-able and citeable.

As the help pages suggest, I hope the site serves , in the least as a repository of supplementary material and science findings related to published work anywhere, which can then be commented on and discussed.

More interestingly the FAQ page, informs us that the Nature publishing group Journals do accept material that is in the un-peer-reviewed form and that has appeared in the preprint form : So if i get together a manuscript , I can first post it on Nature precedings and then send it for consideration to Nature for review separately and nature would still consider it ( if it meets its other criteria of course).

So this site could be a great place to establish the provenance of ideas, i.e I have a great new finding , I am gutsy enough to write it up in some form , post it on Nature precedings ..and then a few months later send the finished work to a print journal like a Nature publishing group journal that would accept it.

With all of this Nature precedings has the great potential to become an online repository of pre-print findings , supplementary material and other content of use to the science community…I really cant wait for the first paper to make it from Nature Precedings to the real thing , Nature itself with a citation that first appeared online!.

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University-knowledge beyond authority

I have recently started attending the Berkman Centre Thursday Blog group meetings. The meetings which are open to the general public were started many years ago by Dave Winer and colleagues and are loosely structured to discuss topics related to blogging, the social web and also recently ( since I have been attending) entrepreneurial activity in the web 2.0 space from local startups .

At the meeting I heard from Mike Walsh of a conference to be organized by the center titled , University- knowledge beyond authority.
The conference aims to “generate questions, insight and solutions from diverse perspectives across the landscape of University, with a focus on the role of University as an institution.We seek to establish University as a collective force much like ‘Government’ or ‘Private Enterprise’ in its ability to negotiate and compromise for our needs in the digital environment.”

The conference has several sessions dealing with topics ranging from fair use , open-access to discussing the relationships between “University” and library and the RIAA.

The concept of University it seems is to organize thought and opinion on these topics from an educational perspective. Since I know very little about the complex world of licensing , and the DMCA is almost a four letter word to me, it will be fun to listen to how this concept of University evolves at University.

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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.

Compiling search strategies in the biosciences

 This morning I spent nearly two hours trolling through the various biological databases trying to find some information but in the end my searches drew a blank. I grew dejected at having wasted all that time only to find nothing.

I then read Jon Udells blog post “Hunting the elusive search strategy” .  In this post , he talks about how some of us are  good searchers vs other people who are not.  He also says

“Effective search depends on reservoirs of tacit knowledge and unconscious skill. Some people possess much deeper reservoirs, and/or can tap into them more effectively, than others. That makes them valuable.”

Some have the ability to compile and relate matches and near matches on the fly  during a search to interactively synthesize a search strategy. Assuming this ability is learned and not innate, the post says it will be very useful to compile effective strategies to understand what is it that makes a good search strategy.

Jon Udell started a tag called searchstrategy on del.icio.us to compile his list.   I too started one on del.icio.us called ncbi-serach-strategy to hopefully compile my own list that will be more bioscience specific. Maybe by such tag aggregation , we can all start to learn at what is it that makes a good search strategy.

I would definitely recommend reading Jon Udell’s post and the comments therein , and also hope this practice of compiling search strategies catches on  as we all learn to handle the gigabytes of omics information.

refs : Google Hacks

 Search , in this Omics age

See “Search in this Omics age”

The coming deluge: Google buys jotspot

Just caught this on the Google blog . Google buys jotspot. I have previously talked about the wonders of jotspot and the ability to virtualize , collaborate and share using the service and other Wikis like backpackit. With Google acquiring jotspot , I am sure we are very close to seeing a fully integrated experience with shared documents, spreadsheets and enterprise wiki features from the google-jotspot team.

Maybe I might just move my “self ELN” away from backpackit to the new Jotspot. For now Jotspot has disabled further registrations and sent its users an email explaining that

“Google shares JotSpot‘s vision for helping people collaborate, share and work together online. JotSpot‘s team and technology are a strong fit with existing Google products like Google Docs & Spreadsheets and Google Groups.”
All of this signal Googles move into the ongoing wave of enterprise wiki service applications.

refs: Moving ELNs offsite

Update: Clearly the acquisition of Jotspot by google has everyone very excited . Check out the responses here