Since a lot of what I have been doing lately is computation and x-ray crystallography, I spend a lot of time leafing through manuals and program documentation for software that is the bread-and-butter of any crystallographic analysis.
Be it cns , coot , phaser , solve-resolve , refmac , pymol , molmol etc etc . they all contribute one small piece of the structure solution puzzle.

Although the online manuals are still are an important source of program information, a cool new development in the online crystallography world are the many new wikis that were started in the last year.

Mostly based on the mediawiki platform, these wikis are constantly updated with crystallographic tips and tricks and plain old documentation by everyone from the creators of these powerful packages to seasoned users and even beginners.

Like many micro-communities on the web, crystallographers have long gathered around the many email-centric news groups. The membership for some of these groups probably numbers in the thousands . Interestingly, some of these wikis were seeded after discussions on these newsgroups. And its quite often that one sees a email discussion summarized as a wiki article. Having just spent three hours to debug the installation of a new crystallographic package, I couldnt be happier.

For a summary of these crystallographic wikis check out this link

It was a while back that I caught the video on the PDB site which explained all the functionalities that its interface has. It was nice to see the video uploaded on Bioscreencast.com.

It would be a huge understatement in this genomic age to say that Biology now largely resides in the database. Be it PUBMED or FlyBase We have databases which range from the all encompassing to the niche. While many are automatically put together, a significant number of them are manually curated.

As Jon Udell wrote in his article on search strategies, the tacit skill required to query these databases is something that not all of us possess. Some of us are better queriers than others. Screencasts, which are basically movies of your computer screen are a very effective way of communicating user database interactions.

At Bioscreencast.com we made it a point to have a category called “Database and Biosearch”. Like the screencast from the PDB we are happy to have contributions from other Databases like the new Uniprot to niche ones like the Membrane Protein Databank.

It will be great to see more of such screencasts, from curators and end users alike.

Ben fry one of the co creators of processing a grpahical visualziation app gave a great talk at the recent Ignite Boston event organzied by Oreilly.

He showed a few examples of its power and relative ease of use . Specially breathtaking was its use in visualizing the HapMap data including the one featured on the Nature cover above.

Ben is currently working on a Book called Visualizing data which is available as a rough cut through Oreilly.

I definitely plan to start playing around with the processing environment. As Euan Addie said on the Natures Nascent blog The way we present genomic and proteomic data on the web sucks and apps like processing are a great step forward.

So this might seem a common theme in my few posts on NNB. But reading all the posts about scifoo here on nature network and elsewhere in the weblog world has made me resolve to get more involved in what I believe in . The power of web 2.0 and other technologies to transform science and scientific communication.

So with this post I hope to resurrect my dormant blog.

Things that caught my attention apart from the scifoo posts above

• Rosie Redfields post on microarray analysis

• The amazing “ted-talk from Jonathan Harris”http://www.ted.com/talks/view/id/144 on the I feel fine project and the Universe project.

• This comes from scifoo. The eigenfactor project. I especially liked the page explaining their methods.

I would definitely check out Jonathan Harris’s work. The visual and data presentation aspects of it along with the social possibilities of his technology are indeed stunning examples of great technology.

That could very well be a Newspaper headline in SecondLife in the future.

So what is second life? Well here is an excerpt from the SecondLife website.

“Second Life is a 3-D virtual world entirely built and owned by its residents. Since opening to the public in 2003, it has grown explosively and today is inhabitedby a total of 1,305,952 people from around the globe”

SO why would anyone want a Secondlife. Well when I first asked myself this,the answer I gave myself , was to live out an alternate reality. Say, what If I wanted to be a pro wrestler or even worse a drug peddler, Secondlife would certainly afford me that virtual opportunity. Considering that fact , although I have never been a Gamer, it made sense that this alternate Universe made drew a lot of Gamers especially of the role playing kind. The Secondlife platform has enjoyed much success and achieved such a high level of adoption that its currency the Linden dollar has a real world value that surpasses a few real currencies (250 Linden is now 1 USD). Now I don’t understand economics but how this is at all possible, I think would be worth studying.

Along the way, I heard that corporations and other real world organization also started jumping onto the SecondLife bandwagon. This makes sense: If a million people inhabited this alternate world. They obviously represented a captive market. Importantly, although the inhabitants included everyone from knights on horses to wizards and pimps, it was quite likely that everyone wanted a Real-world computer or an Ipod!
Also a Secondlife billboard or Superbowl probably would not cost millions. There is also value we are told in having people “interact” with your products and provide feedback , although how this is better than a well designed website I don’t know. Some corporations like IBM are also exploring using Secondlife as a virtual meeting place. Now I have never spent any time on internet chat-rooms, but watching this screencast from John Udell at InfoWorld convinced me that the whole idea of a “meeting” on SecondLife in its present state required a different kind of attention span not to mention keyboard savvy!.

Regardless, I had almost decided on signing on and getting a secondlife avatar when I read on The Nascent blog that Nature magazine too has set up its outpost on SecondLife called SecondNature. All of a sudden I realized, that I could finally someday hope to live that fantasy of having a cover paper in SecondNature or even better maybe one day actually receive a SecondNobel prize. Now that is an avatar I would pay many a Linden Dollar for, not to mention give-up my prospective career as a pro-wrestler.

My newest addiction is netcasts. These are basically mp3 files that were previously called podcasts. These files get automatically downloaded to an mp3 player of your choice when you subscribe to them using an appropriate client.

In short think of podcasts or netcasts as “on-demand” radio shows available for free as downloadable mp3 files.

Common mis-conceptions:

1. You don’t need an ipod to listen to a podcast.
2. You don’t even need a stand alone mp3 player to listen to a podcast
3. All you need is something that plays mp3 files like your computer that you are reading this post on.

In my case, to fuel my addiction I decided to use the 40 min it takes to get me to drive to work to catch up on the things I like catching up on i.e science and technology.

I bought myself a relatively cheap mp3 player ( like any used one from ebay or an ipod shuffle which costs just $70 ).

I then use firefox and my personalized google home page as my netcast client and download the files when I see them onto my mp3 player.

I also bought myself a real cheap FM transmitter ($15). This is basically a device that converts any audio signal to an FM radio signal that you can then receive on your car stereo. Think of these as modern versions of you “tape adapter kits” but now all you need is a car equipped with an FM radio.

So every morning as I drink my tea I download that mornings podcast onto my mp3 player and then plug it into my FM transmitter device which I have fixed in my car . And before I start my commute, I just hit play. So depending on the day of the week I get to catch up on the latest in Nature magazine, Science magazine or this week in tech or the dozens of other podcasts out there.

I put together a screencast ( Not another cast! type) explaining how to use firefox and google to get at podcasts and be informed when they are updated. You can save the file by checking it out on youtube by clicking this link or hold down shift key and click this link and view the wmv file it once it is downloaded to your PC, since it is not streaming video.

I recently was very fortunate to attend one of the Howard Hughes Science meetings. One of the matters discussed at the meeting was a proposed HHMI mandate to have all investigators deposit their papers at pubmed central in order to make them freely searchable by internet search engines, since all the content therein is open-access.

Of course the need for this is obvious considering the fact that the public funds most of our research and that most of it is locked away behind subscription only access. On a related note, we all know how often we have struggled to find relevant papers using the PUBMED search interface and hoped that Google would “do a google” on the NCBI PUBMED database. Well it turns out that open-access will basically facilitate that since the search-bots can now troll through all that content.
Following the discussion I did mention connotea to quite a few attendees specifically hoping to convince them of the benefits of “social bookmarking” and how it helps find new content.

I was quite surprised to find that most of them had never heard of social bookmarking , del.icio.us or connotea ( or was I surprised to find that none of them were web2.0 geeks like myself).

Flash forward to this morning when I was naively trying to find myself a review on membrane protein expression using a PUBMED search. After numerous tries with what I hoped were relevant keywords on NCBI-PUBMED , I drew a blank and fortunately had my sister who researches the field send me some references. As I do often nowadays, I promptly started compiling them into a connotea tag titled .

Then later, I read the post on Rod Pages blog about matching up two keywords using connotea and more importantly linking them to the original reference to create a “new database” using connotea: Which made me think , if only more social bookmarkers a.k.a taggers started using connotea then eventually it will become ( as intended by connoteas creators) a good “searchable” repository of published papers annotated and tagged by experts.
Considering how few people at the Hughes meeting had heard of connotea, I really wished ( for entirely selfish reasons) that more of them (being experts in their respective fields) did also use connotea.
And so I hope that regular connotea users take it on themselves to proselytize connotea a la the proverbial afternoon knock on your door courtesy the Jehovahs witness.

So hopefully , the next time you hear a knock on you lab door it might just benefit all of us that you open the door.

See:
HHMI meeting agenda
Nascent post on linking Treebase and taxon Ids using connotea
Wikipedia entry on Jehovahs Witness
My HHMI meeting connotea tag

Well after a summer of conferences ,days spent away from the lab and countless days spent dealing with crashed computers and fried hard-disks. I am finally set to start blogging here on Nature Network Boston.
This blog will mostly be about technology of the computer sort and how it relates to doing better science. Being a practicing biochemist and an X-ray crystllographer , the posts may be coloured by my professional interests.

Also considering I spend a large fraction of my free time keeping up with the goings on in the web2.0 world , a lot of the posts may focus on technologies that helps one be more productive in everyday research activities.

I do have a proclivity for long winded posts on my other blog ( shameless plug – see http://harijay.wordpress.com ) and I will really try to be more concise here , so I shall end here on this intoductory post.

Heres to blogging on NNB.