Deepak Singh › Comments

"Yep. Which is why on European trips, when possible I travel by train. More efficient, more comfortable and on the right routes, you get to enjoy some good scenery too. I miss trains in the US, both for local transit and long distance travel. I don't mind flying, and I fly crazy amounts, but it's become increasingly difficult to justify the headache, especially for some of the shorter fly-in, fly-out trips that I take" - Deepak Singh

have a great time Rajarshi - which city? - Jean-Claude Bradley

Have fun! Will miss your patch reviewing powers! - Egon Willighagen

Mum watching the Seattle Skyline and Mt. Rainier - Deepak Singh

Good, but very basic. Looks like they're just trying to bring standard OSS techniques to bioinformatics. - Donnie Berkholz

It is basic, but you'll be surprised how little of that happens. - Deepak Singh

I think publishing these very basic guides is "A Good Thing" - but I don't know that bioinformatics/computational biology journals is the right place. The readership of those journals tends to be those who find the information too basic. Might be better to publish such material in biological science journals - Nature Biotech, for example, runs a very good introductory maths/stats/computing series. - Neil Saunders

I would love to go there some day - Deepak Singh

I've never figured out why people do that - Deepak Singh

Table Tennis as the civilized folks call it :) - Deepak Singh

Are you driving? - Deepak Singh

Finished an 8 hr drive from DC to NYC. Should've flown - Rajarshi Guha

Egad .... yep that's likely to be one frightful experience - Deepak Singh from IM

"KINGSTON, Jamaica (AP) - An American Airlines flight carrying 154 people skidded across a Jamaican runway in heavy rain, bouncing across the tarmac and injuring more than 40 people before it stopped just short of the Caribbean Sea, officials and witnesses said. Panicked passengers screamed and baggage burst from overhead bins as Flight 331 from Miami careened down the runway in the capital, Kingston, on Tuesday night, one passenger said. The impact cracked open the fuselage, crushed the left landing gear and separated both engines from the Boeing 737-800, airline spokesman Tim Smith said." - bob from Bookmarklet

http://aviation-safety.net/photos... roadside bank looks brutal - Thomas Page

"I've wasted 2 months of distributed computing time on just bad assumptions made by mistakes I made, so as noted below, in the big picture, that's a relatively minor loss. Does it set back science. Of course, but is it catastrophic, no. As someone pointed out above, in fields where you collection and analysis times are measured in years if not decades you could run into trouble, but for chemistry and biology where you are at significantly shorter collection timescales, it isn't that big of an issie" - Deepak Singh

"I have an Ableton driven studio with oodles of softsynths. I'd say the difference is a factor of 10 at the least even with higher end software. What you do end up spending on is some of the hardware you can't avoid (quality audio interfaces, reverb units, controllers)." - Deepak Singh

The BWA/SAMtools separation is great. Other aligners like Bowtie are now producing SAM as well, so you can swap aligners in and out of analysis pipelines a little more freely. Absolutely the right direction to go. - Brad Chapman

Brad, that's great. I was a little concerned about the "use this aligner for this pipeline" model - Deepak Singh

automated tamil --> english translation. Might even be humorous - Deepak Singh

he following set of guidelines distill several key principals of effective bioinformatics programming, which the authors learned through insights gained across many years of combined experience developing popular bioinformatics software applications and database systems in both academic and commercial settings - Deepak Singh

This blog post is rather rough and ready - a work in progress - but I wanted to push it out before the holidays. Find out which items from this group in 2009 were most discussed (comments/likes)! - Neil Saunders

I like the idea of automated monthly analysis as a web app! Tricky bit will be fetching only new entries and not missing any, but once a db structure is in place, shouldn't be too hard. I'll give that some serious thought. - Neil Saunders

"Exactly. And that's often how fraud gets found. You are trying to build on someones research and some of the assumptions aren't working or you can't baseline the work. That usually leads to trying to reproduce the original work and voila ... fraud at the worst (I'd say most of the time it's just sloppy work)" - Deepak Singh

Lucky devil - Deepak Singh

Wowso... - Graham Steel

I've read a Kindle2 for hours (albeit mostly all books) and it was always stolen ;) - Deepak Singh from IM

Mother keyboard and virtual synths. Would LOVE to hear some new stuff from you and/or stuff you ain't released yet. - Graham Steel

I need to do that. Have one project currently underway - Deepak Singh

"Aron Pilhofer at DocumentCloud also comes from the NY Times and their CloudCrowd project is also great for this purpose http://wiki.github.com/documen..." - Deepak Singh

Avro is a data serialization system. Avro provides: * Rich data structures. * A compact, fast, binary data format. * A container file, to store persistent data. * Remote procedure call (RPC). * Simple integration with dynamic languages. Code generation is not required to read or write data files nor to use or implement RPC protocols. Code generation as an optional optimization, only worth implementing for statically typed languages. - Deepak Singh

Neil analyzes The Life Scientists - Deepak Singh

Love the diversity :) - Deepak Singh

"When I joined my group pretty much everyone was either using a blackberry (the majority) or Windows Mobile phones. Today the majority are iPhones. Thats for a group that has grown a lot since then too, so one could easily argue that the other manufacturers (at least Apple) are making inroads into the business phone market without the need to make dedicated devices." - Deepak Singh

"That's one reason I decided to stick with (a) and participate in (2) indirectly (software/infrastructure)" - Deepak Singh

A workshop in Lugano? sign me up - Deepak Singh

I guess I was into science, until I left my job. Now, I'm into food and clothing. - Mark A Jensen

I feel science communication is not taken seriously enough! - Jan Wessnitzer from iPod

Joshua Schacter on blogging tools - Deepak Singh

Publish - no. Read - Yes - Deepak Singh

Indeed Neil. I think that there is no doubt that the NAR database issue fulfills a need. However, the problem is in my opinion that this need exists in the first place. If you have made a good database or web resource, you should get credit for that without necessarily publishing a paper about it. - Lars Juhl Jensen

It's amazing how some US citizens can be so blind to not see where market economy fails... free market requires buyers to be able to decide, "no, perhaps when you lower your price..." But it just does not work like that for health care... or housing... there does not exist something like a free market when basic needs are involved... - Egon Willighagen

@Benjamin -- we're working on it. I should have said "temporarily" or similar. Can't explain in detail -- public company disclosure blah blah blah. Suffice to say I'm not being exploited, and didn't want to give that impression! - Bill Hooker

They shut down the firehose although they say they are going to bring it back - Deepak Singh