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Why scripting is not as simple as… scripting

If you haven’t read the transcript of Sean Eddy‘s recent talk “On High Throughput Sequencing for Neuroscience“, go ahead and read it. It’s full of many observations and insights into the relationships between computational and “wet” biology, and it is very well-written. I agree with many of his points, for example, that sequencing is not […]

A Simple Genome Annotator?

A question to genome annotators out there. I need a simple genome annotator for annotating bacteriophage genomes in an undergraduate course. Until now, we used DNAMaster but for various reasons  I would like to move away from that. Here’s what  I need for class: 1. Annotate a single assembled linear chromosome, about 50,000 bp, 80-120 genes, no […]

DNA half life, and my dream of an Allosaurus Army

Let’s get this clear: Tyrannosaurus rex, the best selling figurine of class reptilia is not my favorite bad-ass top-of-the-food chain predator. Come on. Did you see its arms? I mean…   As a kid, I always thought the Allosaurus was much cooler. For one thing, it was on the cover of my favorite dinosaur book, “The […]

Should research code be released as part of the peer review process?

So there have been a few reactions to my latest post on accountable research software, including a Tweeter kerfuffle (again). Ever notice how people come out really aggressive on Twitter? Must the the necessity to compress ideas into 140chars. You can’t just write “Interesting point you make there, sir. Don’t you think that your laudable goal would […]

Biocuration 2012

  Great meeting:  Biocuration 2012, Georgetown University, DC.  When I leave a meeting with my head exploding with new ideas and a need to try them all out at once, I know I got my money’s worth, and then some. Even a three hour flight delay followed by discovering my car with a dead battery […]

Operating systems and sandwiches

Ubuntu Linux: “You can have your sandwich any way you like, but recently we started wrapping it in this really ugly wrapper. Still yummy though, and you can ask for a different wrapper. But you have to ask”. Mac OSX: “We only serve ham & cheese on white bread. If you don’t like it, go […]

It was 20 years ago today

…Tim Berners-Lee taught the world to play.   Well, actually, he posted the following on the Usenet group alt.hypertext. For those of you who are too young to remember Usenet, think of it as a working version of Google+.  Scroll down to message 3, in which the first web-page server is announced.

Tweets from AFP/CAFA 2011

The AFP/CAFA 2011 meeting was held on July 15 and July 16. Yes, it was a huge success, and I’m not just saying that beacuse I am one of the organizers.  I will write up something more comprehensive soon; in the meantime, here are my tweets from the meeting. I am learning a lot about […]

ISMB 2011 tweets

ISMB this year had quite a few twiterrers. Hashtag: #ISMB. I tried to collect all the #ISMB tweets, so I wrote my own twitter scavenger script, but it seems to go only 3 days back.  I am not sure if this is a Twitter feature, or something with the library I am using (tweepy) or […]

Google+ at first blush: too complex and too simple

  I have recently been invited to Google+, (thanks Ruchira!)  and as social timesucks go, it is quite enjoyable.  Here are my first impressions about g+. In a nutshell: g+’s attempt at compartmentalized communication is laudable, but falls short of the mark. Mainly because, no social network can emulate the real-life way we communicate (or not) with […]

That being said, I still want a Google+ invite…

… because, um, I dunno. Just too nerdy I guess. Click here to send me one, if you are so inclined: http://is.gd/Ag43 Thanks! .

Alan Turing’s 99th Birthday

I can’t bring myself to say Happy Birthday Alan Turing, for Turing was definitely not a happy man towards the end of  his life. All his contributions science and society amounted to naught when he was persecuted for his homosexuality, eventually driving him to suicide. What that brilliant mind could have contributed to society beyond his 42nd year, […]

Quick Fix: ssh timeouts

  It is very annoying when you leave an ssh window open to your server with something running, go to lunch, come back to see this: Read from remote host my.stupid.server.uni.edu: Connection reset by peer. Connection to my.stupid.server.uni.edu closed.   So here are two fixes. The first is server side. ssh to your server, and […]

Social media used to track disease outbreak

  There are some interesting developments regarding the February outbreak of Legionelliosis which was traced to the Playboy mansion. Reminder: over 120 delegates of the DOMAINFest in Santa Monica, California came down with symptoms of a respiratory illness. The convention included a trip to the Playboy mansion, which later was suspected as the outbreak source. […]

My Hype Cycle

The hype cycle characterizes the over-excitement and subsequent disappointment with new technologies. I expanded this a bit to include research and social trends in science which seem prevalent nowadays. Any views represented in this hype cycle diagram are my own, and in no way represent the  views of my employers, family, friends, neighbors, greengrocer, auto […]