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This page shows you the most recent publications within this specialty of the MedWorm directory.

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Jealous of Geo (no not gene expression)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Image via Wikipedia In my day job, I get to see a lot of innovative geo-related software and services, and the O’Reilly Radar does a great job of tracking innovations in this space. SimpleGeo, WeoGeo, ESRI, Loki, Cloudmade, Quantum GIS, GeoCommons, etc are just some examples of companies/organizations/open source projects doing very interesting things around geospatial data of all kinds. There are a number of good open source efforts around geo-data and visualization, and I am almost certain I am missing a ton. These toolkits allow people to do interesting things. So where am I going with this? Somehow there seem...
Source: business|bytes|genes|molecules - March 21, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Big Data Bytes Genes Informatics Innovation Life Science Programming Software & Internet Source Type: blogs

How the hell do I model this thing?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A couple of months ago, I had a great email exchange with Andrey Voronkov from Moscow State University about simulation methods. Andrey provided a lot of great stuff (and handy references) and was happy enough to make it public. Now that I have a little time in my job-hunting hell, I’ve put it up for your reading pleasure. Bosco: Hi Andrey, just to start off, what’s your system? Andrey: Hi Bosco, well, I have a number of molecular models derived by homology based modeling from X-ray template with 1.36 A resoulution. These models are extracellular dimeric domains of GPCR. No natural or synthetic ligands for ...
Source: Trapped in the USA - March 21, 2010 Category: Bioinformaticians Authors: bosco Source Type: blogs

Game TheoryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Image by Sklathill via Flickr The other day I tweeting a link to a GigaOm article on How everything is becoming a game. In the tweet I jokingly referred to Matthew Sobol, the creator of the Daemon (if you haven’t read the book, do it now), but in reality this trend towards the gaming experience might just a very real one. In the sciences we have various screensaver products like folding@home that try and engage the user and even more directly we’ve seen foldit, an attempt to make protein structure a true game (foldit could be a great starting point for high school teaching), but when Matthew Ingram writes ab...
Source: business|bytes|genes|molecules - March 20, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Education Innovation Source Type: blogs

The disappearing postEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I recently deleted a post featuring a clip from Downfall, part of a meme, and specifically about peer review. Well something happened. I had people write to me asking me to delete it. They weren’t raving and ranting, but it obviously strikes a particular chord among people with German origins. Normally I would never do this, but I think I understand why they were upset, so the post is gone. I don’t shy away from controversy or being politically incorrect, but in this particular case, I was being neither and it didn’t add to the dialog on the subject of peer review really. You know where to leave your comp...
Source: business|bytes|genes|molecules - March 20, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Blog Source Type: blogs

Teaching scientific thinkingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Image via Wikipedia In CACM there is an interesting article on assessing computational thinking. As you know, I am a fan, but have always wondered about how it might be taught from an early age. In this article Judy Robertson talks about a test piloted with 11-12 year olds that uses visual systems to assess computational thinking, e.g. simple Boolean operators and identifying conditions. In her own words, the goal of these tests is to see if the “viewer can identify rules that govern the behavior of members of different classes and then extrapolate from these rules”. Fascinating stuff and it got me thinking....
Source: business|bytes|genes|molecules - March 19, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Education Source Type: blogs

Working around scaleEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
For those curious about what gets my juices flowing these days and why I am fascinated by scale and my current job, just watch this talk (you will need Silverlight to view this, so apologize in advance). Warning: If servers and power utilization aren’t your thing, you might be in trouble. (Source: business|bytes|genes|molecules)
Source: business|bytes|genes|molecules - March 18, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Bytes Computing Source Type: blogs

Second Generation Sequencing Sample Prep EcosystemsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A characteristic of each of the existing second generation sequencing instruments is that each manufacturer provides its own collection of sample preparation reagents and kits.Some of this variation is inherent to a particular platform. For example, the use of terminal transferase tailing is part of the supposed charm of the Helicos sample prep. Polonator needs to use a series of tag generation steps to overcome its extremely short read length. Illumina's flowcells need to be doped with specific oligos. So, some of this is natural.On the other hand, it does complicate matters -- especially for various third parties which a...
Source: Omics! Omics! - March 18, 2010 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs

Data democratizedEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In a brilliant piece entitled Big Data Is Less About Size, And More About Freedom, Bradford Cross talks about about the democratization of analyzing data at scale. As he so correctly points out, the data age has a lot to do with the cool things we can do with data today. Yes data sizes are getting large, but large is relative. I heard numbers today that make the output from many genomics centers sound like a walk in the park, but for the average lab, the average startup, increasing amounts of data are still only in the range of terabytes, not petabytes as some of us (like yours truly) like to talk about. Brad talks about t...
Source: business|bytes|genes|molecules - March 17, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Big Data Business Bytes Computing Software & Internet Source Type: blogs

Keeping your software operationalEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Jesse Robbins gave what looks like a great presentation at a cloud event recently about the value of being prepared for disaster. In a world of warehouse-scale computing an operational mindset is critical to success. What does it really mean? One way of looking at it is thinking about operational software, i.e. about software that understands that failure happens unexpectedly. Yes, this is something you can’t avoid at scale, but even at smaller scales having software that can be reliable deployed in a world where things break is essential. For more, just check out Jesse’s presentation Cloud Operations Bootcamp...
Source: business|bytes|genes|molecules - March 17, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Bytes Computing Software & Internet Source Type: blogs

Don’t move that dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Times change. Last week I was at a local science event and the speaker talked about their data being in Seattle and their compute literally being diagonally across the country in Florida (something that sort of happened for various reasons). That is quite the distance for data to travel. It’s even more for a lot of data to travel. As I commented when asked about solutions to that problem, my answer was “don’t move the data”. Well it’s true. Even with companies out there that help you move large quantities if data, the only good solution for data at this scale is to keep the data in one place a...
Source: business|bytes|genes|molecules - March 16, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Big Data Bytes Computing Software & Internet Source Type: blogs

Getting more out of scientific contentEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
For the past few months I have spent some time thinking about what those of us who are science literate and write blogs, columns, have online shows, etc should be called (because typing all of that is a mouthful). These days I tend to call those of us outside mainstream publishing scientific content producers. Nothing too original, but the role of scientific content producers seems to be becoming clearer to me. Some of us (yours truly) write for other scientists, and even more so for science and technology literate folks with crossover interests. Others write for the broader populace. Yet a third group write for their peer...
Source: business|bytes|genes|molecules - March 15, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Multimedia Publishing Source Type: blogs

Throwing down the hammerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I haven’t written about Personal Genomics in a long time. Quite honestly with all the time spent tracking the technology side of things, the consumer facing bit has been deprioritized. Of course, when you have folks like Daniel MacArthur around, you don’t really need to do that much. In a great, acerbic, post, Daniel throws down the hammer on an Op-Ed piece on personal genomics. It astonishes me that we live in a world where a top line publication can write something like this. If someone opposes personal genomics with rational, well grounded arguments it’s one thing. When someone bases an op-ed on person...
Source: business|bytes|genes|molecules - March 14, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Genes Your personal health Source Type: blogs

The sequencing market is beginning to shape outEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Dan Koboldt has a great post on the state of sequencing in 2010 (can we drop “next-gen” now?), and beyond I guess. It’s certainly getting crowded out there, and it did look like that the major players were essentially fighting for the same space and share of the market, but based on what Dan says, that seems to be changing. I should add that I am not in the trenches, and my interests lie on the data management, analysis and infrastructure side of things, so can’t comment on individual technologies per se. It’s interesting to see how various players seem to be positioning themselves, although ...
Source: business|bytes|genes|molecules - March 13, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Big Data BioIT Biopharma innovation Business Bytes Genes Industry Watching Source Type: blogs

Jon Udell’s anti-geek manifestoEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Image via Wikipedia Jon Udell, perhaps the geek I admire more than any other, doesn’t like being labeled a geek anymore. In A Geek Anti-Manifesto he asks Why is it geeky to marshal the best available data? Why is it geeky to use that data to improve your interaction with people and processes? To recast those questions, Jon is essentially talking about the labels and the types of people who do things like that. Jon wonders why “fluency with digital tools and techniques” labels you as this other kind of “geeky” person. Shouldn’t these traits, computational thinking, be a more general tr...
Source: business|bytes|genes|molecules - March 13, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Education Source Type: blogs

TWiV: podcasts about viruses... the kind that make you sickEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
TWiV (This Week in Virology) is a netcast about viruses hosted by two Columbia University Professors and a variety of expert guests. It's a great way to hear fascinating facts about viruses, and you don't need a PhD. It's all explained in a very casual conversation with extra info placed on the web site. http://www.twiv.tv/ You can also pick them up via iTunes podcasts!!! If you're a microbiology student, this is what you should be listening to on the bus to class!!! read more (Source: VBRC Blog)
Source: VBRC Blog - March 12, 2010 Category: Bioinformaticians Authors: cupton Source Type: blogs

The story that livesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Rich Apodaca points to Google’s Living Stories concept. He specifically calls out the web native aspects of the concept and points out how they allow you to do things in very unique ways and wonders what would happen if scientific publishers would push the characteristics of the Web to their limits. I’ve often written about web-centric systems, especially as pertains to publishing and information sharing. All too often we don’t seem to break out of legacy limitations, like essentially using a print paradigm to web publishing. When I first saw Living Stories, I was struck by both its simplicity and the pre...
Source: business|bytes|genes|molecules - March 12, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Innovation Publishing Software & Internet Source Type: blogs

Playing DirectorEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Last weekend was the Academy Award presentations. Fittingly, just before I had my first theatrical success -- with Actors.Actors are a Scala abstraction for multiprocessing. I've only really played with multiprocessing once, back in my waning days at Harvard. I tried writing some multithreaded Java code, and the results were pretty ugly. The code soon became cluttered with locks and unlocks and synchronized keywords, but my programs still locked up consistently. Multiple processes can be a real headache. But, there's also the benefit -- especially since I have a brand new smoking fast oligoprocessor box (I keep some myster...
Source: Omics! Omics! - March 11, 2010 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs

The hypocrisy of academiaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Warning: Rant ahead!!! Over the past decade, I have interacted with academia in various forms, as a collaborator, as a vendor, as a partner, and a few other ways not as easy to label. I’ve also been an observer and ardent supporter of open science, especially open data and open source software. It often appears that, as an open science community, we are often dismayed, or wonder how we can contribute. I won’t defend open science here, that is not the goal, and quite honestly, I am a pragmatist. While not all situations can work in an open world, I am convinced that under most circumstances science benefits from...
Source: business|bytes|genes|molecules - March 7, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Admin Source Type: blogs

BioStar – A bioinformatics stackexchangeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Image via CrunchBase I’ve always been intrigued by the concept of a reddit or Digg style system for scientific queries. When StackOverflow came along, it was clear (to me at least) that a StackOverflow-like system was the future of technical Q*A sites. Enter StackExchange, which provides exactly that, and StackExchange sites have been sprouting up around the web. Egon started one for Blue Obelisk, and Rich Apodaca started one on experimental chemistry. The latest entrant is one I’ve already spent some time on, BioStar. The site was started, or so it seems, by Istvan Albert (the bot resolves to his email addr...
Source: business|bytes|genes|molecules - March 6, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Informatics Search Social Networking Software & Internet Source Type: blogs

Asking questions on the webEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I am not sure where this post is going to go, but let’s start typing and see where the words lead. The germ of the post came while listening to an episode of This Week in Google. The episode featured Anil Dash who talked about Expert Labs, the initiative he talked about at Science Online 2010. In our conversation after his talk, he mentioned that Gina Tripani was going to come on board. What I didn’t catch at the time was the exact piece of software she was going to work on, ThinkTank. The idea is to develop a platform that will allow government and policy makers to be able to crowdsource ideas to various socia...
Source: business|bytes|genes|molecules - March 6, 2010 Category: Bioinformaticians Authors: Deepak Singh Tags: Search Social Networking Software & Internet Source Type: blogs

Programming Fossil Stumble, but Scala School ProgressesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
If you watch this space by RSS, make sure you catch the additions and corrections by BioIT World's Kevin Davies and my fellow Codon Devices alum Jack Leonard on the Ion Torrent technology (as well as Daniel MacArthur's piece on the last day of AGBT). All were on site & actually saw the machine -- it's a bit scary to see my piece on the PARE technology tweeted (and retweeted) as a substitute for a missed session.I'll take a break for at least a few days from AGBT & try to regain some calm -- a sequencing instrument that you can buy with a home equity loan is a dangerous temptation. I've been having trouble carving out time ...
Source: Omics! Omics! - February 28, 2010 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs

Posts that never made itEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Three blog posts have been sitting in my drafts folder for a year. Inspired by Andrew’s post on posts that never made it, I’d like to describe them briefly, before I hit “delete” and move on. “Doing it right with DataMapper” As an old-school SQL guy, it took me a while to get my head around object-relational mapping but when I finally understood the concept, I was pretty excited. My first productive script was written using Ruby’s DataMapper. I planned a brief post outlining some of its features and how they could be applied to biological data. I still like DataMapper a lot, but I...
Source: What You're Doing Is Rather Desperate - February 27, 2010 Category: Bioinformaticians Authors: nsaunders Source Type: blogs

Last Day of Eavesdropping on Marco IslandEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Today was the last day of the Marco Island conference, so I won't be hammering Twitter again for quite a while. The afternoon session focused on emerging technologies.Complete Genomics appears to have dispelled the skepticism they had been met with last year. It certainly helped that two customers presented data (Anthony Fejes' notes on CG workshop). Apparently they hinted at some additional technological improvements coming down the pike to get even more data out. Life Technologies presented on their single molecule system, which they hope to get to early access customers by the end of the year. It's a single molecule sys...
Source: Omics! Omics! - February 27, 2010 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs

PacBio's big splashEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Pacific Biosciences instrument is officially unveiled now, with those lucky/smart (or SMRT?) enough to go to Marco Island filling in all of us not in that position. Sounds like a great lot of hoopla, though they didn't drag the Hornet for the splashdown. First of all, it's a beast. "In this corner, weighing in a nearly an imperial ton...". Too bad their marketing picture has nothing good for judging the scale -- it's apparently 6.5 feet wide.Kevin Davies at Bio-IT World has a wonderfully detailed article and there is a lot of nuggets in the Twitter feed. Anthony Fejes has two different sets of notes out -- one from a w...
Source: Omics! Omics! - February 26, 2010 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs

Personalized Annoyance of Research Enthusiast (PARE)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Last night I finally got my paws on a paper which started out on a frustrating tack. Last week, a flurry of news items heralded a new approach from Vogelstein's group at Johns Hopkins that involved second generation sequencing of patient tumor samples. But, the early reports claimed it had been published in Science Translational Medicine, whereas it most certainly wasn't there except a suggestive teaser about the next week's issue. I thought perhaps someone had really blown it and ignored an embargo, but then it turned out the AAAS meeting is going on and the work was presented there. Few things more irritating than a pape...
Source: Omics! Omics! - February 25, 2010 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs

Marco Island is HOT!Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Marco Island Advances in Genome Biology and Technology, or AGBT (or just Marco Island) conference started up today. Whatever weather they're having is better than the cold rain that soaked my commute.A sure sign a conference is hot is that there are lots of announcements prior to the conference that could be at the conference. So, we've been treated to lots of announcements from established players (such as Illumina and ABI) and new entrants -- Pacific Biosciences has announced that they will launch their system there and has already been lining up sample prep & informatics partners and announcing their early access si...
Source: Omics! Omics! - February 24, 2010 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs

A Mysql user defined function (UDF) for Gene Ontology (GO)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this post I'll create a Mysql Defined function (UDF) answering if a defined GO term is a descendant of another term. This post is not much different from two previous posts I wrote here:MYSQL UDF, trees of data, hierarchy Mysql user defined function (UDF) for Bioinformatics. Here I built a binary file containing an array of pairs(term,parent_term) of GO identifiers from the XML/RDF file (Source: YOKOFAKUN)
Source: YOKOFAKUN - February 23, 2010 Category: Bioinformaticians Authors: Pierre Lindenbaum Source Type: blogs

Preview of Python Testing Beginner’s GuideEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I have been invited by Packt Publishing to review Python Testing Beginner’s Guide. You can take a look at the preview here and even download one chapter of the book. (Source: Blind.Scientist)
Source: Blind.Scientist - February 22, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion book python review Source Type: blogs

The streamEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
http://www.flickr.com/photos/hamed/ CC BY 2.0 Google unveiled recently Yet Another Try at social networking in the form of Google Buzz. It is a social network borrowing heavily from Friendfeed, a website build by ex-googlers. If you are not familiar with Friendfeed here is a post that goes through some of its features. One interesting thing about all this proliferation of social networks and feed aggregators is seeing their evolution over time. Over the past couple of years some of their features became somewhat standard. You could say that this is just because some websites keep stealing ideas from others...
Source: Public Rambling - February 21, 2010 Category: Bioinformaticians Tags: tech Source Type: blogs

Conference survival guide in downtown San FranciscoEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I would love to have hung out with some of you guys in San Francisco at the 2010 BPS at the Moscone center. But alas, my postdoc contract has ended (send job tips for a computational structural biologist/scientific programmer my way!) and I am now kicking back with family and old friends in Australia. The downtown of San Francisco is tricky to navigate if you want the good stuff (I am skipping the obvious stuff like 3D-Imax Avatar at the Metreon), so here’s a list of my favorites within striking distance of the Moscone center: Blue Bottle Cafe for some of the best coffee in the city, and my favorite interior. ItR...
Source: Trapped in the USA - February 20, 2010 Category: Bioinformaticians Authors: bosco Source Type: blogs

If we tell you to Buzz …Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
… you will Buzz! (Source: Blind.Scientist)
Source: Blind.Scientist - February 20, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Misc longer than one line one liners buzz comedy google humour wave Source Type: blogs

I don’t understand the USEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
It seems to be a great country, a nice society, but sometimes it gets too nutty and idiotic. I don’t think a person who has more than 1 billion dollars in the bank, makes any sacrifice by doing what this idiot did. And while I’m at it, golf is not a sport. (Source: Blind.Scientist)
Source: Blind.Scientist - February 19, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Misc longer than one line Source Type: blogs

Do you deny Climate Change (nee Global Warming)?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The read this Phil Jones holds himself defensively, his arms crossed tightly in front of his chest as if shielding himself from attack. Little wonder: Jones has spent the past three months being vilified for his central role in what is now called ‘climategate’ (sic, arch). and “I don’t think we should be taking much notice of what’s on blogs because they seem to be hijacking the peer-review process.” and concluding It is now essential for climate researchers to stand up for their science, he says. “[I'd] like to see the climate science community supporting the climate science more. Lots of...
Source: Blind.Scientist - February 19, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Science global warming villains Source Type: blogs

Intelligent design?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
If God created everything “as is” 6000 years ago, why He/She didn’t give use enough knowledge to understand His/Her design right away? Every time I look at a gene network, I feel dumb (maybe that’s just me), and if the design was more intelligent (and made sense) everything would be easier. (Source: Blind.Scientist)
Source: Blind.Scientist - February 19, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Science longer than one line intelligent design Source Type: blogs

Please stop …Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
… using ‘gate’ for every crisis, problem, scandal. ‘Throttlegate‘ for the Toyota recall? Really, are you sure? Sometimes I wish that the Watergate hotel was called Watercrap or something similar. But that’s only a wish. (Source: Blind.Scientist)
Source: Blind.Scientist - February 19, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Misc longer than one line gate Source Type: blogs

To Stockholm via Ph.D. ThesisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Scientist has a profile of Aaron Ciechanover, who shared the Nobel Prize for work on the proteasome. His Nobel-cited work began in his Ph.D. thesis.In one of the physics books I was recently reading (I forget which one now, might have been How to Teach Physics to Your Dog, but I think it was Six Easy Pieces) it was mentioned that Louis de Broglie's committee wasn't sure what to do with his crazy proposal that everything has both particle and wave natures, but after consulting with Einstein awarded him his degree. Of course, this proposal withstood experimental test and led to a Nobel.Anyone know other examples of Nobel...
Source: Omics! Omics! - February 19, 2010 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs

London 2012, Vancouver 2010Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Image via Wikipedia I’m buying a front row seat to every event in the London’s 2012 Olympics, even at the simultaneous ones (I will figure out cloning by then), and I will report every small glitch th happens there. Still on the topic, how come a country/city/whatever that designed that logo can criticize anyone, ever, in any subject of modern and past life? Related articles by Zemanta Gold for whining goes to… British reporters (calgaryherald.com) UK/Canada Spat Uncharacteristically Crude, Penis-Related [Media Meltdowns] (deadspin.com) (Source: Blind.Scientist)
Source: Blind.Scientist - February 18, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs

Non-benign genetic carrier statusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Earlier this week the Wall Street Journal carried an article addressing the growing interest in finding health issues related to being a carrier of a recessive genetic disease.Three diseases were discussed in some detail. Sickle-cell anemia is generally thought of as being very harmful when homozygous but essentially benign when heterozygous. But, it has been known for a while that heterozygotes (called sickle trait) can experience red blood cell sickling (and the accompanying pain and tissue damage) under low oxygen tension. The WSJ journal article points out that such sickling can also occur during strenuous physical exe...
Source: Omics! Omics! - February 18, 2010 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs

eXist: The Open Source Native XML Database : My notebookEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In a previous post, I've played with Oracle's BerkeleyDB-XML. Here, I used with eXist-db, an open source database management system built using XML technology. It stores XML data according to the XML data model and features efficient, index-based XQuery processing.Download & Installwget http://downloads.sourceforge.net/project/exist/Stable/1.4/eXist-setup-1.4.0-rev10440.jarjava -jar eXist-setup- (Source: YOKOFAKUN)
Source: YOKOFAKUN - February 18, 2010 Category: Bioinformaticians Authors: Pierre Lindenbaum Source Type: blogs

Google Wave and BuzzEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
is a bust. So much hype, for nothing, useless piece of software (or website). Then came Buzz and the amount of crap increase ten-fold. And then the privacy problems came, something they apologized for, but will forget next time they release some new forever-beta product. Sometimes, I wish I was able to remove Google from my life, but then what I would use: Bing, Hotmail? (Source: Blind.Scientist)
Source: Blind.Scientist - February 17, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Misc longer than one line Source Type: blogs

Books 2010Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
1 – The New New Thing: A Silicon Valley Story 2 – What Do You Care What Other People Think?: Further Adventures of a Curious Character 3 – Days Between Stations: A Novel 4 – A Bridge Too Far: The Classic History of the Greatest Battle of World War II (Source: Blind.Scientist)
Source: Blind.Scientist - February 17, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Bioinformatics - opinion Source Type: blogs

Anybody know some good bioinformatic programming problems?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I recently found out that I've received a summer undergraduate intern slot. I have a soft spot for summer internships -- my own was a great experience -- and the company runs a very nice program, with specific social and learning experiences for the cadre. Anyone interested in applying should do so through the company website (and not here!). I do promise not to fill this space with "can you believe what the intern did today?!?!?", though executing "sudo rm -r /" might earn a slot!I'm still trying to sketch out a grand scheme for the internship. But, it will certainly combine a certain amount of data analysis with a certai...
Source: Omics! Omics! - February 17, 2010 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs

The path from EgonWillighagen to Jandot : Neo4j , a graph API for java: my notebook.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
neo4j "Neo4j is a graph database. It is an embedded, disk-based, fully transactional Java persistence engine that stores data structured in graphs rather than in tables. A graph (mathematical lingo for a network) is a flexible data structure that allows a more agile and rapid style of development.".In the current post, I'll use the neo4j API to load a set of pubmed entries and find the shortest (Source: YOKOFAKUN)
Source: YOKOFAKUN - February 17, 2010 Category: Bioinformaticians Authors: Pierre Lindenbaum Source Type: blogs

More Than One Way to Skin a KumquatEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
My recent piece on citrus seems to have struck a chord, based on the multiple comments and the fact that GenomeWeb's blog picked up on it as well. That's all very gratifying, tbut also stirred me to notice what I had missed on the subject. No, not the obvious point that getting some genome sequences is just a tiny first step to my grand bioengineering dream. And not what the TIGS review pointed out, that American markets in particular have tended to favor uniformity over quality or novelty (though perhaps that is changing, at least in high-end markets). Nope, what bugs me now is missing the obvious about kumquats.Now, as I...
Source: Omics! Omics! - February 16, 2010 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs

That’s basically itEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Feynman summarizes everything I think about awards, prizes and societies in science. No, I never won anything, and if I do someday (remote probability) I will decline it. This only reminds me more and more about some scientists websites that first mention their awards, prizes and interviews before any scientific content. You know who you are. (Source: Blind.Scientist)
Source: Blind.Scientist - February 15, 2010 Category: Bioinformaticians Authors: Paulo Nuin Tags: Science awards feynman nobel Source Type: blogs

Another Tiny tool : RDF-to-DotEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
RDFToDot Transforms an XML/RDF input to Graphviz-dot ( http://www.graphviz.org )Usage -h help; This screen. -p {prefix} {uri} add this prefix mapping (rdf stdin | rdf files | rdf urls )ExampleThe following example my linkedin profile as a graph using a HTML Canvas: xsltproc --html linkedin2foaf.xsl http://www.linkedin.com/in/lindenbaum |\ java -jar rdf2dot.jar |\ dot -Tsvg |\ (Source: YOKOFAKUN)
Source: YOKOFAKUN - February 15, 2010 Category: Bioinformaticians Authors: Pierre Lindenbaum Source Type: blogs

Semantic Web Services with the SADI Framework: my notebook.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective of SADI is to make it easy for data and analytical (Source: YOKOFAKUN)
Source: YOKOFAKUN - February 15, 2010 Category: Bioinformaticians Authors: Pierre Lindenbaum Source Type: blogs

Dear GoogleEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I think you’re a pretty good company. I like many of your products and use them daily, for work and at home. I admire many of your innovations and technical solutions. But this Buzz thing. You’ve really messed up. Two points: Social networks should always be opt-in. Never, never opt-out. I choose whether to join in the first place. If I do join, I choose who to connect with, what to share and who can see it. And I expect complete control over the entire process, from the outset. My list of email contacts is not a social network. It’s a list of people with whom I’ve corresponded by email at least on...
Source: What You're Doing Is Rather Desperate - February 12, 2010 Category: Bioinformaticians Authors: nsaunders Tags: google networking buzz Source Type: blogs

Celebrating CitrusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I've been on a citrus kick at work lately, trying out different varieties I picked up at one of the adjacent grocery stores (curiously, we're sandwiched between 2). When I was growing up I think I knew only seeded oranges, navel oranges, tangerines, tangelos, grapefruit, lemons and limes. Through some combination of better awareness and better availability, there's a lot more I can find. I gained some notoriety this week by bringing a pummelo to a breakfast meeting; if you haven't seen one, they make grapefruit look small. Tastewise, it's a bit milder and a bit sweeter than a grapefruit.A lot of this is seasonal, as I've b...
Source: Omics! Omics! - February 12, 2010 Category: Bioinformaticians Authors: Keith Robison Source Type: blogs

Processing large XML documents with XSLTEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
I've resurrected an old java program called xsltstream which might be useful for biohackathon2010. This program applies a XSLT stylesheet only for the given node from a large xml document. The DOM is read from a SAX stream, built in memory for each target element , processed with XSLT and then disposed. Now, say you want to transform a XML file from dbSNP with XSLT to make a RDF document. You (Source: YOKOFAKUN)
Source: YOKOFAKUN - February 12, 2010 Category: Bioinformaticians Authors: Pierre Lindenbaum Source Type: blogs