And one more year is done

December 24, 2008

2008 has come and is almost gone and it’s time to shut down bbgm to do some housecleaning while all of you are out for the holidays, except Pierre of course, who will be writing some cool code. Dec 31 marks three years of bbgm as a self hosted blog, and every year brings with it something new and different. This year has been no different.

I started off the year hoping to do a lot of video, screencasts, and incorporating all of that into bbgm, but that never materialized, mostly due to a lack of time, but also my style, where I tend to just throw stories together when I feel like it. I still hope to do incorporate more video, but not quite sure about how that might happen, and time is an even more precious commodity these days.

But, while the video thing didn’t quite pan out, nor did my hopes of actively doing some “hobby science” and programming, many other things did pan out in what ended up being a very eventful year. Some highlights

I changed jobs
Hari and I finally started a podcast
Chris Lasher and co invited me to Virginia Tech to give a talk
I got interviewed by Jon Udell
Started recording music again
… and finally did something with deepaksingh.net

I will also remember 2008 as the year of the microcommunity, perhaps best personified by The Life Scientists on Friendfeed and The Biogang. Being part of those groups, and others, is a privilege, educational and a whole lot of fun.

One interesting observation. Even though blogging has slowed down for various reasons, I still seem to be averaging about 30 posts a month. In the era of Friendfeed, not too shabby. Either that, or it just shows how much I used to blow some months ago.

Thank you for reading, listening and watching. Have a great Christmas, New Years, etc etc

See you on the other side

Posted by Deepak Singh | Filed Under Admin, Self

Coast to Coast Bio 8 and a screencast from Ensembl

December 24, 2008

A new podcast, the final episode for 2008, of Coast to Coast Bio is now available. You can always subscribe on iTunes.

Up on Bioscreencast, you can see a screencast providing an overview of the new Ensembl website

Posted by Deepak Singh | Filed Under Audio/Video

From merging rivals to code repositories

December 23, 2008

Image via WikipediaInteresting development today. Ruby on Rails and Merb have decided to merge rather than duke it out in the blogosphere as they had been doing? What does it mean? Well, Ruby and Ruby web frameworks are likely to be an increasingly visible part of the scientific software world in the coming years, so any news about the dominant Ruby web framework and a young hotshot alternative with some pretty smart people behind it merits attention. But I also found it interesting that two groups that seemed to genuinely get on each others nerves sat down together and decided to see how they could come up with a solution that should, hopefully benefit the general community.

The first thing that came to my mind was, why couldn’t AMBER and CHARMM have done this many years ago? They are similar enough in their history. Which also got me thinking about code in science. Wouldn’t it be nice to see the source for CHARMM or AMBER or NAMD on Github or someplace like that. You can have a core team managing patch reviews and formal point releases and then people forking out code to build their own specific apps. Given the history of that field and the kind of expertise required to develop such codes, perhaps the decisions made all those years ago were the right ones, and subsequent direction has been driven by a number of other reasons, but I’d really like to see scientific code on open code repositories. And wouldn’t it be nice to have something like the Apache foundation, where certain core projects could be brought to incubate and grow.

OK, it’s the holiday season. I am allowed to have my flights of fancy.

Posted by Deepak Singh | Filed Under Business

DSLs and scientific programming

December 21, 2008

I hope we can talk about this on Coast to Coast Bio tonight. In my exploration of proper programming and Ruby, I’ve seen a lot of discussion around Domain Specific Languages, and to try and understand the role that DSL’s could play in scientific programming.

The Wikipedia article on DSL’s starts with the following

The term domain-specific language (DSL) has become popular in recent years in software development to indicate a programming language or specification language dedicated to a particular problem domain, a particular problem representation technique, and/or a particular solution technique.

Alright, in other words, the Matlab language, the Mathematica language, or closer to home the CHARMM scripting language are all examples of DSLs. The other day I blogged about Kappa, which is a DSL as well. So what’s so special about them and why do they come up a lot in the Ruby community, and I suspect others as well. In fact a couple of months ago (and I am still long overdue on writing at more length on this subject), I got very intrigued by SimTK. More on this in a bit

To some extent, it’s probably fashionable to do so. On the other hand, I see the value in using a general language, like Ruby, to generate a “language” targeted at solving a particular problem. I think that’s the key and what would be interesting to explore, especially in building DSLs for scientific programming and computing. Let’s go back to SimTK. which Shirley (or should I say Dr. Wu) described to me as a “code repository and project management tool”. But there is a second aspect to the project, the simulation toolkit, which allows you to build purpose-driven applications like OpenSim, or OpenMM (which might be a DSL in itself). Now, having not jumped into SimTK, I am not completely sure if the framework qualifies as a DSL, but they have used a general programming language to construct a system for a specific set of problems.

So where am I going with all this? Well, we have languages like Ruby and Python, both of which have pretty strong metaprogramming capabilities. In fact, people are already looking at such problems as evidenced by Tiago’s blog posts. How mainstream will these DSLs that are written using Ruby, Python etc get? We don’t really have a vibrant scientific programming community (they tend to be a little silo-ed), and there are few avenues for scientific programmers to come together in a general sense, so we end up with multiple “specialized” DSLs for things like molecular modeling. But these are early days, so you never know where things will end up.

What I would like to do is re-visit this post in a few months when I have done a better job wrapping my head around DSLs and metaprogramming, cause I haven’t quite yet

Posted by Deepak Singh | Filed Under Modeling & Simulation, Programming, Science

Web as platform: Twittering for stocks and proteins

December 20, 2008

Image via WikipediaContinuing to clear out my inbox, aka my brain, before I shut down for the year.

The other day I was listening to Technometria, with Eric Norlin as the special guest. The episode, about The Implicit Web touched upon a lot of interesting topics. Among other things they talked about Stocktwits, which I’ve been meaning to look into for a while, just cause some of the people using it are smart folks, but I wasn’t quite sure how it worked.

The service positions itself as a “social, stock microblogging service”, which uses Twitter as a content production platform, and then adds on to it a stock-centric structure. This immediately appealed to me, since it’s an excellent example of the data finds the data, then people find the people. I believe the way it works is around stock symbols, being able to track them via the Twitter API. What especially made me think about this were Pierre’s blog post and tweets about using Twitter for bioinformatics. This fits into some general paradigms as well, those around harnessing information streams.

One reason I don’t necessary buy into dedicated scientific social networks is that for many tasks, existing frameworks, e.g. Twitter, FriendFeed, LinkedIn, etc do a pretty good job of harnessing collective intelligence since we already have such rich information streams. Other communities have done a pretty good job of leveraging these platforms, perhaps we’ll start seeing the science types do so as well.