Category Archives: Uncategorized

Good old fashioned email centric community

I Just caught an article on techcrunch. It was titled Facebook Fatigue? Visitors Level Off In the U.S.The article spoke of a coolling down of visitor traffic on facebook . Facebook, the internets big social phenomenon of 2006-2007 whose founders keep holding out from selling their internet property pending higher and higher evaluations, it seems is in trouble.It turns out Facebook is no exception to the fall in traffic once a social networking site gets too popular . As has been observed in the internet social networking ecosystem,once a website becomes mainstream and common place it either becomes a victim of its own success and fades away into nothingness or becomes so much a part of your everyday existence that its no longer exciting but very usefull. All of this begs the question, is facebook useful. Before you read any further.  I must confess I hated facebook from the get go.
 Yes! I do have a functioning presence on the medium and I do politely accept friend requests. But from the very start I found Facebook annoying, confusing and downright useless. Nothing made me want to jump onto the naysayer bandwagon more than playing a game of 20 questions every time  I visited the site. I will not repeat myself , and get right back to answering the question. Did I ever find facebook useful. Well maybe! but it definitely wasn’t worth the pain of feeling that If I click the wrong option box ..all my information gets sold to an add selling bot.  I always preferred and still prefer the “privacy” of email or the “convenience” of sharing a link to my picasa album ..over the 20 question and click-a-box-too-many  game that every facebook app made me go through everytime I wanted to be social.

Visiting  facebook convinced me that these games are only played by people who are used to jostling with crowds at the local club ( akin to  answering all those questions, responding to pokes and writings on my wall) or having their clique that they keep in touch with constantly. Fortunately for me ( my point of view) I never needed that level of interaction and so facebook was never for me, and so for me it was useless!Facebook made me realize how warm a personal email can be over a writing on someones wall.  Thank you facebook for making me realize how valuable and indeed immensely social the email centric communities I participate in are. I have gotten more value from checking and respondint to my email since I realized this fact.  Facebook made me love my gmail account and yes .

In case you have feelings about write on my facebook wall..because chances are I will never read it

Apple breaks its Java silence

Apple finally said something about Java in leopard..Its upto 10% faster, has a lot of under the hood improvements and 64 bit support . Way to go apple. I had remarked about how apples silence on staying up with the Joneses on java support was the only thing making me rethink my switch to the mac . But its announcements like these that convince me I did make the right choice after all.

My Vote for Java6 on leopard-13949712720901FOROSX

As a lot of you may know. Leopard does not include Java 6. While Apple going slow on Java comes as no surprise , Apples slowness on this front has prompted at least James Gosling to abandon the Apple Mac as a Java development platform.

I came across this internet campaign to cast a vote for Java 6 on leopard.

So here goes.. I feel that apple should continue to support Java fully  and in a timely manner. What better way to get developers onto their preferred cocoa frameworks than making sure they use macs to do all their other non cocoa development.  So apple please add back Java to the develop on leopard pages and hire all the engineers required to get Java 6 on the mac  in a timely manner. I am 13949712720901FOROSX

Ignite Boston – Tweaking, mixing competition and collaboration

As you probably saw from my post on processing, ignite-boston II was a blast. I was there talking about opening up science and The talks at this Ignite were really interesting .

I especially liked the one by Ned Gulley from Mathworks who spoke of “Tweaking” a wiki-like matlab based programming contest. Tweaking is a great concept that effectively mixes collaboration with competition. In traditional code-jams and programing contests groups usually work in relative isolation to submit their best code for any given task which is then ranked at the very end and a winning group declared. In Tweaking all user entries are publicly displayed throughout the week that the contest runs. All entrants can modify and adapt each others code to move up the ladder. As each tweaked entry is submitted a secret test routine dynamically ranks the entry and it moves in the ranking. In Tweaking even single tweaks which result in a leap in functionality can move an entrant up the rankings and this opens up a whole trajectory for code improvement for all participants.To mix the wiki like collaborative element with code competitions seems to be a great way to enrich the coding experience for everyone.

Ned spoke of a series of projects , including one on SARS phylogeny and a lattice model protein folding simulation which tingled my structural biology neurons. Neds paper on tweaking talks about how tweaking is not only a fun learning experience for all participants, but also an interesting study into the nature of collaboration and the interplay of motivation , reward , collaboration and competition. If only all science projects worked like Tweaking.

Image Credit: Mathworks Tweaking protein folding competition

Ned blogs at the Starchamber, a blog whose Resident buzzwords are : synthetic biology, ambient displays, swarm robotics, wise crowds.

Put your brain to use: Galaxy Zoo

I caught this on Natures Nascent blog. Like re-CAPTCHA which I had blogged about before. This project uses the human brain to classify galaxies. You know the types , spiral , elliptical , merging etc etc.

The way it works is fun , you sign up, go through the tutorial , take the test ..If you get 8 out of 15 correct, you can start classifying galaxies. No worries, if you dont pass the can just take it again , till you earn your stars .

Once you do , you can start classifying galaxies

A few things about the project capture my interest.

As as far as the codeitch, itch goes ..its amazing how much better the human brain is ,at recognizing patterns like the ones in the spiral galaxy above and telling it apart from an elliptical one. I know image processing algorithms are getting better and better as the days go ( I had my beginings in structural biology with 3d reconstruction of viruses from projection images and some single particle reconstruction)..but the human brain it seems still takes the prize…

The second amazing thing is , the galaxy zoo in just two days , classified a million images with community participation. And their servers are struggling to meet the load.
A big hurrah for public participation and open science indeed.

Powered by ScribeFire.

Image link from the Sloan Digital survey 

Out of the cradle and into a beta-

I am very excited to announce the coming to fruition of a project that five of us have been working on for the last few months.Its a site based on screencasts called You can read more about the site on our bioscreencast blog post and at my Omics world blog.

The entire site was coded into life by one person, our head web geek and javascript junkie, Suresh.

As a wannabe coder, I came away amazed at the sheer power of the many open source libraries out there, the robustness of mysql databases, the sheer elegance of css..the swiss army knife like ffmpeg , the clumsiness of php, the list goes on. What made the whole process doubly enjoyable was that all five of us are relative web newbies.. and learning how these things work along the way was a lot of fun.

Watching Suresh work his web magic has made me want to learn more of the six technologies I want to master, and I have also added a few more to the list( more on this in future posts)

Just thought Id give my plug for I hope the life scientists out there ,  like the site,  and all of you will keep your feedback coming.


The Bioscreencast website

The Bioscreencast Blog

One of our co-conspirator Deepaks intro post

The entire site was coded and crafted by one person, our head geek Suresh .

Photosynth-seadragon and single particle imaging

As a a graduate student I had worked on a project where I used single particle imaging techniques to image the structure of a small viral protein. The protein particle fortunately has some symmetry, and using single particle image reconstruction techniques I could obtain a three-dimensional model of the particle from two dimensional projection images taken on an electron microscope.

After deepak got me hooked on to the TED talks , I caught a talk by Blaise Aguera Y Arcas on Microsofts new application called photosynth.

In the talk Blaise Arcas describes how they were able to put together a very high resolution almost three dimensional composite of the Notre Dame Cathedral assembled from tagged images on flickr.

Their software was able to accurately find the register for thousands of images from this tagged set and assemble it into the final composite. Check out the video above to get an appreciation of the complexity of the application. While I am hardly an expert in image processing, the algorithmic complexity of the application boggles my mind. Particularly impressive are the sections in the video where he talks about photosynth finding the register of images in the actual assembled composite despite them having people , hands and other obstacles obscuring the view of the cathedral.

I also caught some of the discussion on microsofts channel 9 on the technology. I sure would like to know the concepts they used to put-together such an amazing app. I also wonder of any of these concepts can help improve image reconstruction techniques in use in the single particle bio-imaging field.

Screencast centric java eclipse blog

Trolling through the google search results for javafx the new “flash competitor” from sun , I came across this cool screencast centric code blog.

Its called The blog uses the wink tool to create audio-less screencasts which are in flash and show at a very good resolution on the browser page. The topics covered are java and eclipse centric.

Though I am a convert to netbeans , I like the overall style of the blog and the content featured. I have been playing around with wink and really like its feature-set. Maybe codeitch will feature some wink based screencasts while I attempt to converge on a platform to deliver my screencast centric code content  . The only problem is that since I don’t use my own hosting provider , its hard to embed my screencasts the way  has. But maybe there just might be a way to have my cake and eat it too.

Brightcove-great for screencasts

I am a strong proponent of screencast based teaching and learning. For the most part I have been using youtube to host screencasts. Typically these were recorded using ISHOWU on my mac using the H.264 codec/format and then uploaded onto youtube either directly or after converting to ( ipod capable) m4v . The results of these you probably see on my early screencasts on codeitch and at The Omics world.

I was introduced to a brightcove via a webcast forwarded to me by Deepak, which talked of their enhanced flash codec ( from on2 technologies) and decided to give it a try.

I uploaded the same screencast onto brightcove and youtube. In the past , youtube tended sometimes to garble the first few seconds of my video if I went directly from H.264 to youtube-flash and so I also uploaded a version where I went from H.264 to m4v (ipod) and then uploaded that file to youtube.

Brightcoves transcoding did an excellent job and you can almost read the text on my deliberately high resolutio screen capture. I will definitely use brightcove for all my future screencasts both here and at The Omics world. Hopefully the folks at will start supporting the brightcove plugin soon which will allow it to play within this blog page , till then just click on this link or see it in action on my tumblrlog. Feel free to right mouse click on the video and explore the options the brightcove player gives you from right inside the player window. No more looking for  information on crowded youtube pages.

Ignite Boston – I cannot wait

Deepak has blogged about Ignite Seattle an informal gathering organized by Oreilly in Seattle geared towards the local tech crowd. I always wondered why Boston does not have an Ignite event as well considering its huge tech population.

Well I just heard on the Berkman Thursday meetings blog that Oreilly is organizing an Ignite Boston event on May 31st, 2007. These meetings sound like they are a lot of fun and I am glad Boston finally has one.
It will be fun to get another opportunity to meet the local tech crowd.I cant wait !