MedWorm: Bioinformaticians

The disappearing post

business|bytes|genes|molecules — Sat, 20 Mar 2010 15:17:29 +0100

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 complaints. (Source: business|bytes|genes|molecules)

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Teaching scientific thinking

business|bytes|genes|molecules — Fri, 19 Mar 2010 04:12:36 +0100

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. How could we teach scientific thinking to 11-12 year olds and what would that mean? In my opinion scientific thinking essentially should follow a path that teaches child...

Working around scale

business|bytes|genes|molecules — Thu, 18 Mar 2010 02:10:21 +0100

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)

Second Generation Sequencing Sample Prep Ecosystems

Omics! Omics! — Thu, 18 Mar 2010 00:00:00 +0100

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 are producing sample preparation options. For example, targeted resequencing using hybridization really needs to have the sequencing adapters blocked with competing oligos...

Data democratized

business|bytes|genes|molecules — Wed, 17 Mar 2010 12:00:40 +0100

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 trends in computing and software that have allowed data-driven companies like Flightcaster to get to market faster. He breaks down these trends into three chunks Storing ...

Keeping your software operational

business|bytes|genes|molecules — Wed, 17 Mar 2010 04:17:05 +0100

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: Culture View more presentations from Jesse Robbins. On a related note, check out this talk by Paul Borrill on Rethinking time in distributed systems (slides and abstra...

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Don’t move that data

business|bytes|genes|molecules — Tue, 16 Mar 2010 12:00:35 +0100

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 and move the compute around. Cheaper, more efficient, and a better use of the network. IMO, the days of moving data sets over the wire are long gone. You can move slices a...

Getting more out of scientific content

business|bytes|genes|molecules — Mon, 15 Mar 2010 12:00:32 +0100

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 peers. The value of all this content and commentary is the bit that is of critical importance. Being able to provide objective commentary on the state of the art of science, ...

Throwing down the hammer

business|bytes|genes|molecules — Sun, 14 Mar 2010 20:34:38 +0100

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 personal opinion, a lack of understanding, and uses inaccurate statements, they deserve to be called out. (Source: business|bytes|genes|molecules)

The sequencing market is beginning to shape out

business|bytes|genes|molecules — Sat, 13 Mar 2010 21:19:29 +0100

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 where folks end up and who survives will depend on all kinds of factors. The scientific market is fickle and quite honestly, the factors that define success are not alway...

Jon Udell’s anti-geek manifesto

business|bytes|genes|molecules — Sat, 13 Mar 2010 20:25:40 +0100

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 trait. I might even extend his thinking a little, by adding scientific thinking to the list (i.e. the ability to formulate and test hypotheses), although that is a little l...

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TWiV: podcasts about viruses... the kind that make you sick

VBRC Blog — Fri, 12 Mar 2010 07:54:01 +0100

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)

The story that lives

business|bytes|genes|molecules — Fri, 12 Mar 2010 04:06:54 +0100

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 presentation. Why can’t we have scientific stories, e.g. publications, stories, blog posts, all presented together with a timeline to see how the story evolves. Wouldn...

Playing Director

Omics! Omics! — Thu, 11 Mar 2010 00:00:00 +0100

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 mystery in the precise number). Tools such as bowtie and BWA are multithreaded, but it would be useful to have some of the downstream data crunching tools enabled as well.Actor...

The hypocrisy of academia

business|bytes|genes|molecules — Sun, 07 Mar 2010 21:20:06 +0100

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 open sharing of data and protocols. Much of the challenges faced today are a function of an axis of publishing model, recognition model and funding model that needs to e...

BioStar – A bioinformatics stackexchange

business|bytes|genes|molecules — Sat, 06 Mar 2010 04:25:52 +0100

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 address) and is focussed on bioinformatics and computational biology. It’s still a small site and in bootstrap mode. Hopefully it will get a good audience and progress ...

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Asking questions on the web

business|bytes|genes|molecules — Sat, 06 Mar 2010 03:27:38 +0100

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 social networks. ThinkTank is open source, uses existing technologies and applications, and while it began life targeting Twitter, will be extended to other platforms. This is...

Programming Fossil Stumble, but Scala School Progresses

Omics! Omics! — Sun, 28 Feb 2010 00:00:00 +0100

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 -- and enthusiasm -- for my Scala retraining exercise. A week or so ago I did make one try and hit an annoying roadblock. I had previously worked through online examples ...

Posts that never made it

What You're Doing Is Rather Desperate — Sat, 27 Feb 2010 02:10:08 +0100

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 realised that (1) I didn’t have anything especially insightful to say and (2) I was more excited about ORMs in general, as opposed to one in particular. So my advi...

Last Day of Eavesdropping on Marco Island

Omics! Omics! — Sat, 27 Feb 2010 00:00:00 +0100

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 system with many similarities to Pacific Biosciences. One interesting twist is that they can add new polymerase when the old ones die, so in theory they can keep sequencing ...

PacBio's big splash

Omics! Omics! — Fri, 26 Feb 2010 00:00:00 +0100

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 workshop and one from another speaker; Dan Koboldt has some good notes too (and if I haven't shouted out your notes, it's probably because I'm oblivious -- leave me a comm...

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Personalized Annoyance of Research Enthusiast (PARE)

Omics! Omics! — Thu, 25 Feb 2010 00:00:00 +0100

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 paper being bandied about that I can't get my eyes on! Plus, I have a manuscript due next week that this might be relevant to, so the desire to get a copy was intense!Yesterd...

Marco Island is HOT!

Omics! Omics! — Wed, 24 Feb 2010 00:00:00 +0100

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 sites. PacBio has also started making noise about a follow-on instrument that will be for clinical apps -- launched in 2014!! Puh-leeze, that is the inconceivable future!AB...

A Mysql user defined function (UDF) for Gene Ontology (GO)

YOKOFAKUN — Tue, 23 Feb 2010 00:00:00 +0100

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)

Preview of Python Testing Beginner’s Guide

Blind.Scientist — Mon, 22 Feb 2010 18:22:14 +0100

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)

The stream

Public Rambling — Sun, 21 Feb 2010 08:29:00 +0100

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 but it also says which features seam to be useful and which implementations are intuitive to theirs users. One idea that is central and common to all of these social we...

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Conference survival guide in downtown San Francisco

Trapped in the USA — Sat, 20 Feb 2010 21:44:00 +0100

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. It’s also a very nice place to hang-out the Matador, the best hipster bar downtown right next door is Tu Lan, a formidably cheap greasy-spoon Vietnamese tha...

If we tell you to Buzz …

Blind.Scientist — Sat, 20 Feb 2010 15:58:19 +0100

… you will Buzz! (Source: Blind.Scientist)

I don’t understand the US

Blind.Scientist — Fri, 19 Feb 2010 22:14:43 +0100

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)

Do you deny Climate Change (nee Global Warming)?

Blind.Scientist — Fri, 19 Feb 2010 20:18:29 +0100

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 them are trying but they’re being drowned out.” Some points: 1- He was and still is vilified, not because we (the public) think he is a villain, but his acti...

Intelligent design?

Blind.Scientist — Fri, 19 Feb 2010 16:33:09 +0100

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)

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Please stop …

Blind.Scientist — Fri, 19 Feb 2010 15:17:49 +0100

… 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)

To Stockholm via Ph.D. Thesis

Omics! Omics! — Fri, 19 Feb 2010 00:00:00 +0100

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 Nobels which cite the laureate's thesis work? (Source: Omics! Omics!)

London 2012, Vancouver 2010

Blind.Scientist — Thu, 18 Feb 2010 14:47:39 +0100

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)

Non-benign genetic carrier status

Omics! Omics! — Thu, 18 Feb 2010 00:00:00 +0100

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 exercise; the NCAA even has specific guidelines for extra rest for sickle cell heterozygotes.An emerging story mentioned in the article is the risks of being a carrier for f...

eXist: The Open Source Native XML Database : My notebook

YOKOFAKUN — Thu, 18 Feb 2010 00:00:00 +0100

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)

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Google Wave and Buzz

Blind.Scientist — Wed, 17 Feb 2010 17:05:26 +0100

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)

Books 2010

Blind.Scientist — Wed, 17 Feb 2010 14:48:29 +0100

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)

Anybody know some good bioinformatic programming problems?

Omics! Omics! — Wed, 17 Feb 2010 00:00:00 +0100

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 certain amount of programming. One person I've phone-screened has already asked about suggestions for programming problems to practice on. It's a great show of initiative, whic...

The path from EgonWillighagen to Jandot : Neo4j , a graph API for java: my notebook.

YOKOFAKUN — Wed, 17 Feb 2010 00:00:00 +0100

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)

More Than One Way to Skin a Kumquat

Omics! Omics! — Tue, 16 Feb 2010 00:00:00 +0100

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 mentioned, they're hard to find. I checked some mail order places and the seasons apparently vary depending on where they are grown. But at Christmas time I could find o...

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That’s basically it

Blind.Scientist — Mon, 15 Feb 2010 16:45:16 +0100

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)

Another Tiny tool : RDF-to-Dot

YOKOFAKUN — Mon, 15 Feb 2010 00:00:00 +0100

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)

Semantic Web Services with the SADI Framework: my notebook.

YOKOFAKUN — Mon, 15 Feb 2010 00:00:00 +0100

The objective of SADI is to make it easy for data and analytical (Source: YOKOFAKUN)

Dear Google

What You're Doing Is Rather Desperate — Fri, 12 Feb 2010 15:17:04 +0100

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 once. That’s all they have in common. Furthermore, there’s a big difference between them exposing their public profiles and me exposing their presence in my add...

Celebrating Citrus

Omics! Omics! — Fri, 12 Feb 2010 00:00:00 +0100

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 been finding. Kumquats are a nearly perfect desk snack -- completely neat except for the need to spit the pips -- but seem to be available only around the New Year -- and ...

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Processing large XML documents with XSLT

YOKOFAKUN — Fri, 12 Feb 2010 00:00:00 +0100

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)

Freebase and Biohackathon 2010

YOKOFAKUN — Thu, 11 Feb 2010 00:00:00 +0100

This post is a quick overview of Freebase for the participants of biohackathon2010 who attended François Belleau's lecture this morning. It was suggested here that Freebase could be used to store and share some predicates for the semantic web. In the current post, I'm going to use CURL to programmatically add a new Namespace in freebase .OK. First, let's send a MQL query to Freebase and get the (Source: YOKOFAKUN)

Mapping RDBMS to RDF with D2RQ (yet another geeky title)

YOKOFAKUN — Thu, 11 Feb 2010 00:00:00 +0100

One of the coolest thing have seen here at Biohackathon 2010 is D2RQ (thank you Jan !):D2RQ is a declarative language to describe mappings between relational database schemata and OWL/RDFS ontologies. The D2RQ Platform uses these mapping to enables applications to access a RDF-view on a non-RDF database.In this post, I'll describe how I've installed a D2RQ server.First, Download D2RQ:wget http:// (Source: YOKOFAKUN)

The 80-80 principle

business|bytes|genes|molecules — Wed, 10 Feb 2010 04:51:04 +0100

I was reading yet another great post by Paul Buchheit, this one entitled If your product is Great, it doesn’t need to be Good. He talks about the right approach to new products, suggesting that we “Pick three key attributes or features, get those things very, very right, and then forget about everything else”. This reminded me of my own guideline to new products, a guideline I call the 80-80 principle. The tendency for the first version of a product is to pack it full of features, to try and make everyone happy, to go through that list of requested features and try and put in everything that your top customers asked for, often focusing on the features and not the goals. More often than not you end up with bloatware or a product that’s too complicated or just not fun...

Palin

Blind.Scientist — Sun, 07 Feb 2010 21:42:18 +0100

Sarah Palin is the closest you can get to a populist Latin American president, such as Lula, the Kirchners, Chavez, etc. If you live in US, raise your hands to heaven and thank whoever that you don’t live in Latin American. You can get the taste. (Source: Blind.Scientist)

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I Really need to sleep: inserting the SNPs into MongoDB with C++

YOKOFAKUN — Sun, 07 Feb 2010 00:00:00 +0100

In the previous post I showed how to parse dbSNP/XML with libxml. In the current post I'll insert the results into MongoDB using the native Mongo C++ API. Some others have already posted about MongoDB: for example see Jan's, Brad's or Neil's posts The Boost-C++library is required: my code failed to compile with boost 4.* but it compiled fine with boost 3.9.Starting mongoDB> mkdir ~/tmp/MONGODB/ (Source: YOKOFAKUN)

Id rather bee sleeping: fast parsing of dbsnp/XML with libxml

YOKOFAKUN — Sun, 07 Feb 2010 00:00:00 +0100

Hello world ! I'm now in Japan for Biohackathon 2010 it's 00H30 here and, of course, I cannot sleep. I should be tired : I spent 11H00 in a plane, 1H30 in a train and three hours skating in Tokyo with my kick scooter :-)I'm killing the time with libxml, the C library for parsing XML. In the current post I'll write a simple SAX parser extracting the flanking sequences from the SNPs of dbSNP/ (Source: YOKOFAKUN)

The distributed web of data – messaging included

business|bytes|genes|molecules — Sat, 06 Feb 2010 23:05:03 +0100

I’ve written about the distributed self and science data platforms. A lot of the former was around the notion of pubsub, and pushing data to various places. Now imagine a scenario where you are using data from a variety of scientific repositories and you’ve built applications that use APIs to collect data. What if your data sources would update you everytime there was a change, so that your systems could automatically fetch any updates and rebuild anything that needed to be rebuilt, do any pre-computing that needed to be done. The model that Anil Dash talked about in his classic Push-Button Web post is relevant here as well. We have the tools to do this today. Real time, asynchronous messaging is part of distributed computing, and the variety of data repositories out there sho...

Laboratory Walkover: a pitch for a TV show

Blind.Scientist — Sat, 06 Feb 2010 20:55:28 +0100

I can count in one hand how many times I’ve ever been in a ultra organized scientific lab. In some of them I don’t know how people work and are able to publish results obtained in the lab. Because of that and inspired by the countless reality TV shows, I decided to start pitching the idea of the Laboratory Walkover. We will come to your lab with a TV crew, a interior designer and a high level authority in your field of research and we are going to stop to nothing to make your lab the best research space on earth. You won’t need to pay a dime for the makeover/walkover/takeover, on the contrary we will give you $5000 for consumables and a new PCR machine (if applicable). I’m already looking for sponsors and channels, and if you want your lab o qualify for the walkover...

Science Commons Symposium Pacific Northwest – Discount Codes

business|bytes|genes|molecules — Fri, 05 Feb 2010 15:54:12 +0100

There is a stellar lineup of speakers at the forthcoming Science Commons Symposium here in the Seattle area (actually in Redmond). The announcement is below. bbgm readers in Seattle can use the code bbgmto get a discount on the tickets In the spirit of Creative Commons Salons — global, informal events focused on bringing together the community around a central topic or focus — Science Commons will be holding a day-long event this February in Seattle. The event will aim to bring a broader understanding on the term “open” and all of its flavors when applied to science. From Open Access publishing and data sharing efforts, to more transparent ways to conduct bench science and the various “open”s (data, science, access) – the benefits of implementing �...

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Review - You are not a gadget

Public Rambling — Fri, 05 Feb 2010 04:07:00 +0100

I just finished reading "You are not a gadget" by Jaron Lanier. The book is very much in the same tone as an article he recently wrote the Edge called "DIGITAL MAOISM: The Hazards of the New Online Collectivism". Very few other books made me want to say "No!" out loud so many times while reading it. I enjoy reading opinions that run contrary to my own because I think it is important to challenge our ideas. This is why I like reading Rough Type. This book, however, was extremely confusing too me. It reads mostly as a collection of essays and often deviates from the path. I still think it was an interesting book to read because of the importance of the topic. If you read the essay linked above you will get the general feeling conveyed in the book. As Lanier writes in the end of t...

Predicting and explaining drug-drug interactions

Public Rambling — Fri, 05 Feb 2010 02:40:00 +0100

I am generally interested in chemogenomic studies and drug interaction studies as a complement to what we work on in the Krogan lab (genetic interactions). Much like in genetic interaction screening, where the fitness of double mutant strains is compared with that of the individual single mutants, chemogenomics tries to identify drug-gene interactions while drug-drug interaction screening attempts to find cases where the combined effect of two compounds on fitness is different from the expected from the combination of the single independent effects. I read two recent papers that I found interesting regarding drug-drug interactions. One was by Bollenbach and colleagues from the Kishony lab (published in Cell) and the other was by Jansen and colleagues (published in MSB). In ...

The new javascript Map/Reduce in Riak

business|bytes|genes|molecules — Thu, 04 Feb 2010 04:09:22 +0100

An Introduction to JavaScript Map/Reduce in Riak from Basho Technologies on Vimeo. Riak is a non-relational datastore with a cool API and nifty Map/Reduce features. The new features in version 0.8 are described here (Source: business|bytes|genes|molecules)

Disagreeing to Disagree

Omics! Omics! — Thu, 04 Feb 2010 00:00:00 +0100

A year ago (almost exactly) I wrote an entry taking to task a paper analyzing protein kinases in the draft chimpanzee genome. After writing that entry, I felt it proper to leave a comment at the journal (BMC Genomics). Instead of publishing the comment, the editor invited me to formalize my criticisms and perhaps give positive suggestions of how to do such an analysis. Between Codon dissolving, my interlude of consulting and starting Infinity this got pushed to late May, it went out for review & a round of revision & then the original authors were invited to write a rebuttal. By the time their rebuttal came back (late fall), I decided I was getting a bit worn on the whole thing and just tweaked my submission to underline a few things rather than go hammer-and-tongs for a counter-rebuttal.A...

LinkedIn+XSLT = FOAF / People from Biohackathon 2010

YOKOFAKUN — Wed, 03 Feb 2010 00:00:00 +0100

I've created a XSLT stylesheet transforming the public HTML pages on LinkedIn about the people going to Biohackathon 2010 to FOAF. The stylesheet worked fine (of course it won't work anymore if LinkedIn change the layout of the HTML pages) and it is available here:http://code.google.com/p/lindenb/source/browse/trunk/src/xsl/linkedin2foaf.xslNote: if possible, the XSLT stylesheet uses geonames.org (Source: YOKOFAKUN)

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Using a FASTA file as a source of RDF statements for SPARQL.

YOKOFAKUN — Wed, 03 Feb 2010 00:00:00 +0100

In this post, I'll show how a Fasta file can be used as a source of RDF statements for the Jena API.The DNA sequences in the Fasta file will be used by Jena without any prior transformation: the file will be used as a Graph by Jena by implementing com.hp.hpl.jena.graph.Graph.Here, my example uses a Fasta file but it could have been any kind of input: a SQL database, a XML file, a GFF file, etc... (Source: YOKOFAKUN)

Searching for Genotypes with SPARQL.

YOKOFAKUN — Mon, 01 Feb 2010 00:00:00 +0100

This week-end, I've noticed that the NCBI has an interface called Genotype Query Form used to query some genotypes the generating the following kind of XML output: (Source: YOKOFAKUN)

ISMB/ECCB 2009 reports

What You're Doing Is Rather Desperate — Sat, 30 Jan 2010 04:22:12 +0100

Great to see more reports describing the use of online tools to cover scientific meetings. Here are the publications, from PLoS Computational Biology: Live Coverage of Scientific Conferences Using Web Technologies. doi:10.1371/journal.pcbi.1000563 Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009. doi:10.1371/journal.pcbi.1000640 And here’s Ally a.k.a the robo-blogger on Social Networking and Guidelines for Life Science Conferences. Looks like we’ve started a trend, long may it continue at future meetings. Filed under: bioinformatics, meetings, publications Tagged: 2009, eccb, friendfeed, ismb, report (Source: What You're Doing Is Rather Desperate)

PhosphoGRID

What You're Doing Is Rather Desperate — Sat, 30 Jan 2010 04:10:45 +0100

I no longer work on protein kinases but when I did, PhosphoGRID is the kind of database that I would have wanted to see. It features: A nice clean interface, with good use of Javascript Useful information returned from a simple search form Data for download in plain text format with no restrictions or requirements for registration All it lacks is a RESTful API, but nothing is perfect :-) Published in the little-known but often-useful journal Database: PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. doi:10.1093/database/bap026. Filed under: bioinformatics, publications, web resources Tagged: database, phosphory, protein kinases (Source: What You're Doing Is Rather Desperate)

PubChem, CouchDB and data pipelines

business|bytes|genes|molecules — Sat, 30 Jan 2010 03:56:30 +0100

Rich Apodaca has a great set of blog posts on using PubCouch, the CouchDB interface for PubChem. The series is great in itself, but I was especially intrigued by the title of the third installment, PubCouch: Streams Aren’t Just for Pipeline Pilot. In the post Rich describes how PubCouch makes it possible to work with the PubChem FTP archive like it was a single large SD file. Recently, I’ve started believing that modern programming paradigm and increasing awareness of RESTful architectures, distributed data processing, messaging etc makes systems like Pipeline Pilot look somewhat dated. They aren’t going to go anywhere soon, but I believe that the power of being able to deliver services to the end user is becoming the norm and developing those services is getting easier ...

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Podcasting in Science

business|bytes|genes|molecules — Sat, 30 Jan 2010 03:02:55 +0100

At ScienceOnline 2010 I had the pleasure of organizing a fun an intimate session on podcasting along with Dr. Kiki. The video for the session is now up in six parts. The entire set is embedded below (Source: business|bytes|genes|molecules)

Publishing scientific code

business|bytes|genes|molecules — Fri, 29 Jan 2010 03:22:49 +0100

Software engineers on the team must equally understand that the code is just part of the science, and not usually a goal in its own right. That’s from an article titled Are we taking supercomputing code seriously? by Andrew Jones from the Numerical Algorithms Group Does that mean that code doesn’t have to be published after all? (Source: business|bytes|genes|molecules)

It’s really strange or why the iPad?

Blind.Scientist — Fri, 29 Jan 2010 01:37:34 +0100

It’s really strange to read so many negative stories about the iPad, why it will fail, why it sucks, etc, etc. So many bytes wasted (including these here) to cover something that nobody used yet, no one has ever seen, nor was actually released. So many bytes wasted on stories about something that, if you don’t like and think Apple and Steve Jobs are trying to control their users/customers, you have full control of: like it, buy it, don’t, don’t buy it. So many stories about how closed source computer, software is being forced upon fearful customers. While we worry about that, in the US, companies, corporations are now persons. (Source: Blind.Scientist)

Whither science museums?

Omics! Omics! — Fri, 29 Jan 2010 00:00:00 +0100

Last week at this time I was surviving a terrible electrical storm -- tremendous cracks and crackles all around me. Luckily, it was just the lightning show at the Boston Museum of Science, featuring the world's largest Van de Graaf generator and a pair of huge Tesla coils and other sparking whatnots. TNG was part of a huge overnight group.I love the MoS and always enjoy a trip there. But it isn't hard to go there and wonder what the future of such museums are and how the current management is taking them. Exhibit #1: The big event at the MoS right now is the traveling Harry Potter show. We of course got tickets and lumped on audio tour. It's great fun, especially if you enjoyed the movies (it is mostly movie props & costumes), but makes absolutely no pretensions of having even a veneer of ...

Whiter science museums

Omics! Omics! — Fri, 29 Jan 2010 00:00:00 +0100

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Something is not open at PLoS, maybe …

Blind.Scientist — Thu, 28 Jan 2010 17:44:04 +0100

I really like reading some articles posted on Hacker News. Usually they focus on the entrepreneur side of the software/web business, but sometimes there are some nice pointers to scientific stuff. And most of the comments are also really nice, a lot of clever people around there. But this is what you expect of these virtual communities. Anyway, I’m here to talk about PLoS. Yesterday somebody posted at HN, an article about open access to publications: Open Access to Scientific Publications The good, the bad, and the ugly. It’s a so-so read, but gives some information on the current scenario of open and closed access publishers. But what really caught my eye (thanks initially to a comment on HN) is this passage: But how much are authors ready to pay to publish an article? A few h...

Science and libraries: Letting the crowd talk

business|bytes|genes|molecules — Thu, 28 Jan 2010 16:24:37 +0100

I will write about this more in a later post, but thought it would be interested to throw out the discussion that started when I stated out aloud that librarians need to evolve their role. The genesis comes from the assumption that as experts librarians are required to connect people to information, which to me sounds a lot like the argument that print/traditional media kept making as they failed to evolve. Maybe the analogy is not a viable one, but in the search era, the role must evolve. My thoughts on this are still in the works, so for now, the Friendfeed discussion (Source: business|bytes|genes|molecules)

iPad is excellent!!!

Blind.Scientist — Thu, 28 Jan 2010 15:08:17 +0100

Just sayin’. With all the negative reviews, ponderations, blog posts, newspaper reports, I just wanted to give so kudos to Steve and the Apple family. Is it the best product ever? No. Is it the next coming of Jesus Christ? No. So what is it? It’s just another product, and you, only you (maybe with your wife/husband/partner/household) will decide if it fits your budget, if it is useful for you and if you actually need to buy it. Apart from that, rants are always good for the people that writes them (I know it firsthand). The icing on the cake is when I overheard two homeless guys discussing if you could multitask on an iPad. When they discovered you couldn’t, they decided not to buy it. Last time I saw them they were in the public library computers. (Source: Blind.Scientis...

Microsoft is more detrimental to Science, than the lack of Open Science, …

Blind.Scientist — Thu, 28 Jan 2010 14:56:54 +0100

than the lack of funding, than the publishing companies, than old-fashioned scientists, than PZ Meyers, more than Linux, more than Apple, more than anything I know. Ok, let me explain then. But before that, a disclaimer: I own Windows 95, 98, XP and Vista, and this represents only my opinion, not the opinion of my employers, co-workers and family. And why is MSFT more detrimental to Science than anything else? It’s simple: the openness of their system. Maybe open is not the right word, transparency might better to explain it. As MSFT has the leadership on the OS market, vendors tend to attach their products (in this case laboratory equipments, analysis software, etc) to the OS. And how that is bad? Because when it works, it works fine, but when it doesn’t work, it’s a ni...

From the “blogosphere”? Hardly.

What You're Doing Is Rather Desperate — Thu, 28 Jan 2010 02:40:23 +0100

I generally skip over “From the Blogosphere”, a (mostly) weekly-summary of one or two blog posts in Nature’s “Authors” section (here is the latest). Why? Well, I’ve always suspected that the title is rather misleading. Now, I have the hard numbers to prove it. My feed reader contains an archive of 128 articles, dating back to May 10 2007. I used them to create this CSV file with 3 fields: Date, Blog and Source. The “Blog” field contains the name of the primary blog mentioned in “From the Blogosphere”. On rare occasions where 2 blogs are mentioned, 2 entries were added to the CSV file. I skimmed each article rather quickly, so I may have missed blogs that were mentioned in passing. Next, a short R script: library(ggplot2) # read ...

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Feynman and me

Blind.Scientist — Thu, 28 Jan 2010 01:40:01 +0100

I’m reading the second book on Feynman, What Do You Care What Other People Think?: Further Adventures of a Curious Character and the only thing I can he was an incredible person, one that any one can admire. I have no idols, I don’t worship anyone, but Feynman gets the closest possible to being one for me. (Source: Blind.Scientist)

A little more Scala

Omics! Omics! — Thu, 28 Jan 2010 00:00:00 +0100

I can't believe how thrilled I was to get a run-time error today! Because that was the first sign I had gotten past the Scala roadblock I mentioned in my previous post. It would have been nicer for the case to just work, but apparently my SAM file was incomplete or corrupt. But, moments later it ran correctly on a BAM file. For better or worse, I deserve nearly no credit for this step forward -- Mr. Google found me a key code example.The problem I faced is that I have a Java class (from the Picard library for reading alignment data in SAM/BAM format). To get each record, an iterator is provided. But my first few attempts to guess the syntax just didn't work, so it was off to Google.My first working version is package helloimport java.io.Fileimport org.biojava.bio.Annotationimport org.bioja...

Elementary school for Bioinformatics: Suffix Arrays

YOKOFAKUN — Thu, 28 Jan 2010 00:00:00 +0100

I was recently asked to map the flanking ends of a large set of SNPs on the human genome. As a perfect match algorithm was sufficient I've implemented a suffix array algorithm to map each flanking sequence. Via Wikipedia:A suffix array is an array of integers giving the starting positions of suffixes of a string in lexicographical order. It can be used as an index to quickly locate every (Source: YOKOFAKUN)

All-in-one usually does not work

business|bytes|genes|molecules — Wed, 27 Jan 2010 06:42:50 +0100

Weren’t all-in-one services like Launchpad supposed to save us from this insanity? Stuart Sierra poses that question in a blog post where he bemoans the fact that the Clojure community is spread out across a number of places. As a result, being an active member of the community, he needs to pay attention to half a dozen, perhaps more, to keep on top of things. He answers his own question But they never can, because everyone has different tastes when it comes to bug tracking, version control, and mailing lists That is not a phenomenon just for programming languages, but for various other groups, including scientists, who tend to have very different tastes across a number of areas. Which is why I don’t think a single destination site is going to work for research and collaboration. Y...

Clustering GEO samples by title (briefly) revisited

What You're Doing Is Rather Desperate — Wed, 27 Jan 2010 01:29:56 +0100

So, we had a brief discussion regarding my previous post and clearly the statement: The longest key for which values exist classifies your titles does not hold true for all cases. Not that I ever said that it did! I remind you that this blog is a place for the half-formed ideas that spill out of my head, not an instruction manual. Let’s look, for example, at GSE19318. This GEO series comprises 2 platforms: one for dog (10 samples) and one for humans (1 sample), with these sample titles: ['Dog-tumor-81705', 'Dog-tumor-78709', 'Dog-tumor-88012', 'Dog-tumor-8888302', 'Dog-tumor-209439', 'Dog-tumor-212227', 'Dog-tumor-48', 'Dog-tumor-125', 'Dog-tumor-394', 'Dog-tumor-896', 'Human-tumor'] Run that through the Ruby code in my last post and we get: {"Dog-tumor-48"=>["...

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The Scala Experiment

Omics! Omics! — Wed, 27 Jan 2010 00:00:00 +0100

Well, I've taken the plunge -- yet another programming language.I've written before about this. It's also a common question on various professional bioinformatics discussion boards: what programming language.It is a decent time to ponder some sort of shift. I've written a bit of code, but not a lot -- partly because I've been more disciplined about using libraries as much as possible (versus rolling my own) but mostly because coding is a small -- but critical -- slice of my regular workflow. At Codon I had become quite enamored with C#. Especially with the Visual Studio Integrated Development Environment (IDE), I found it very productive and a good fit for my brain & tastes. But, as a bioinformatics language it hasn't found much favor. That means no good libraries out there, so I must buil...

QuoteEditor

YOKOFAKUN — Tue, 26 Jan 2010 00:00:00 +0100

It's 00H25 here, and while one of my programs is aligning some SNPs on the human genome, I'm going to describe the tiny tool I wrote this Week-end. QuoteEditor is a java editor used to store some famous quotes in a RDF/XML file. The java 'jar' and the documentation are available at :http://code.google.com/p/lindenb/wiki/RDFQuotes.Usagejava -jar lindenb/build/quotes.jar [-f ]the (Source: YOKOFAKUN)

Never understood

Blind.Scientist — Mon, 25 Jan 2010 14:38:13 +0100

I never understood why people with good functioning limbs (all four of them) press the button that automatically opens doors in public buildings. I guess they are the ones that have a disabled parking permit and drive a pickup truck. (Source: Blind.Scientist)

“Thinking algorithmically”: clustering GEO samples by title

What You're Doing Is Rather Desperate — Sun, 24 Jan 2010 05:03:00 +0100

Today’s challenge. Take a look at this array, which contains the “title” field for the 6 samples from GSE1323, a series in the GEO microarray database: ['SW-480-1','SW-480-2','SW-480-3','SW-620-1','SW-620-2','SW-620-3'] Humans are very good at classification. Almost instantly, you’ll see that there are 2 classes, “SW-480″ and “SW-620″, each with 3 samples. How can we write a program to do the same job? I’m sure that for those with formal training in computer science and algorithms, this is pretty trivial. The rest of us have to figure it out from first principles. Here’s what I did, in words: # Imagine that you have 2 titles: "abc1" and "abc2" # Take the first character - call it the key, call the remaining...

Books 2010

Blind.Scientist — Sat, 23 Jan 2010 14:54:54 +0100

1 – The New New Thing: A Silicon Valley Story 2 – What Do You Care What Other People Think?: Further Adventures of a Curious Character (Source: Blind.Scientist)

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Thanks Conan!

Blind.Scientist — Sat, 23 Jan 2010 13:47:10 +0100

Seven months of fun, barely missed one episode. (Source: Blind.Scientist)

Hosting Applets in Google Docs

eric.jain.name — Fri, 22 Jan 2010 23:44:46 +0100

Google Docs recently added support for uploading arbitrary files (up to 250MB large). Can this be used to host Java applets? I uploaded a jar file containing a simple test applet to Google Docs and referenced it like so: <applet width="440" height="60" code="JavaVersionDisplayApplet.class" codebase="http://docs.google.com/" archive="uc?id=0B9ANnqvnRtroOTM5YWE3YmMtMGZkMy00ZGE5LWE2NWUtOGZhNzk5MzA2NzBk"> </applet> The result: (Source: eric.jain.name)

Recently read - Jan 2010

Public Rambling — Fri, 22 Jan 2010 22:13:00 +0100

In this study HeLa cells were synchronized in different stages of the cell cycle and their proteins and phosphorylation sites were quantified relative to asynchronous cells using a SILAC mass-spec approach. Changes in protein abundance and phosphorylation were combined with transcriptional changes and these were used to identify previously known and potentially novel complexes and kinase-substrate interactions important for cell-cycle progression. In addition, I thought it was pretty cool that the authors found a way to directly quantify the phosphorylation site occupancy from the mass-spec results. I was only slightly disappointed that the authors did not attempt to do a cross-species analysis given the available data from Liam Holt et al. on Cdk1 phosphorylation in S. cerevisiae. (Bonus-...

Stay away

Blind.Scientist — Fri, 22 Jan 2010 19:22:10 +0100

from Toronto’s (GTA’s) streets for sometime. Twelve people died crossing the streets this year in the region. Stay away. (Source: Blind.Scientist)

The Great Australian Internet Blackout Wordpress Plugin

Your bones got a little machine. — Fri, 22 Jan 2010 00:28:49 +0100

Normally I stick to posts about science and technology on this blog. Like most Australians, I vote in elections, try to remain informed, but otherwise stay away from getting involved in politics. However, occasionally certain things become important enough issues that they need to be advertised more widely. As you may know, the Australian Federal Government is attempting to censor the Internet within Australia by forcing ISPs to block a list of websites. This proposed internet filter will not be optional; it will effect all Australians, and the blocklist will compiled by a small group of people. The list of blocked sites will remain secret, so the Australian public will find it difficult to determine if this power is being abused. It will not prevent the spread of illegal material, which i...

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Science Online 2010 – Where are the geeks?

business|bytes|genes|molecules — Thu, 21 Jan 2010 05:05:03 +0100

My obvious biases are going to come out in this post, but it needs to be written. Bora and Anton organize this great conference every January that allows many people to get together to discuss science on the web. As always, I quite enjoyed the event, mostly cause of the social interactions, and some excellent sessions. This year I got to finally meet in person Pawel Szczesny, Steve Koch, Dr. Kiki, and Michael Habib (I am sure I’ve missed someone). Jonathan Eisen has a great post (and this funny one) about the event. Having said that, I find something troubling. There are far too many sessions on journalism and policy, and far too little on doing science and even less on the “developer” side of things. So consider this post a call to action. Next year, we should get better...

Premium

Blind.Scientist — Thu, 21 Jan 2010 01:32:52 +0100

Brazilian president is receiving a prize for global leadership in Davos. If you are not Brazilian, leave a comment if you know what his/her name is. Don’t google it or check Wikipedia. Replies on Twitter (@nuin) or Friendfeed are also valid. (Source: Blind.Scientist)

A plethora of MRSA sequences

Omics! Omics! — Thu, 21 Jan 2010 00:00:00 +0100

The Sanger Institute's paper in Science describing the sequencing of multiple MRSA (methicillin-resistant Staphylococcus aureus) genomes is very nifty and demonstrates a whole new potential market for next-generation sequencing: the tracking of infections in support of better control measures.MRSA is a serious health issue; a friend of mine's relative is battling it right now. MRSA is commonly acquired in health care facilities. Further spread can be combated by rigorous attention to disinfection and sanitation measures. A key question is when MRSA shows up, where did it come from? How does it spread across a hospital, a city, a country or the world?The gist of the methodology is to grow isolates overnight in the appropriate medium and extract the DNA. Each isolate is then converted into a...

I'm definitely not volunteering for sample collection on this project

Omics! Omics! — Wed, 20 Jan 2010 00:00:00 +0100

My post yesterday was successful at narrowing down the identity of the mystery creature to a spider of the genus Araneus. Another victory for crowd sourcing! It also points out the value of questioning your assumptions & conclusions. My initial thought on looking at the photos was that the body plan looked spider-like and details of the head and abdomen sometimes pointed me that way -- but then the lack of eight legs convinced me it must be an insect (I thought I could count six in some photos).One of the commenters addressed my mystery vine with a suggestion that underscored a key detail I inadvertantly left out. The vine raised welts on my legs when it grabbed me -- not in some exaggerated sense, but it definitely had some sort of fine projections (trichomes?) which were not what I'd cal...

Why I won’t watch Avatar (or at least pay for)

Blind.Scientist — Tue, 19 Jan 2010 17:51:05 +0100

That works for me, maybe not for you. And that is where the mask of Canadian-style humility and niceness came off James Cameron, the engineer’s son from Kapuskasing, and the scarily arrogant, tactless King of the World (as he called himself at the 1998 Oscar show) slipped out. (Source: Blind.Scientist)

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Green Krittah

Omics! Omics! — Tue, 19 Jan 2010 00:00:00 +0100

As a youth, I was fortunate enough to spend four summers working as a camp counselor. Three of those were spent in the Nature Department, performing all sorts of environmental education functions (one year I taught archery). One of my enjoyable duties was to wander the wilds of the camp looking for interesting living organisms to put in our terraria and aquaria, a job I relished -- though the campers could often top me for interesting (I never could find a stick insect, but we rarely lacked for one). During one of those forays, most likely in my favorite sport of hand-catching of frogs, I stumbled onto a patch of a plant I did not recognize. I still remember it rather well -- perhaps because of the small itchy welts it raised on my unprotected legs. No, not nettles (we had plenty of those,...

What I learned this week about: productivity, MongoDB and nginx

What You're Doing Is Rather Desperate — Fri, 15 Jan 2010 08:45:46 +0100

Productivity It was an excellent week. It was also a week in which I payed much less attention than usual to Twitter and FriendFeed. Something to think about… MongoDB I’m now using MongoDB so frequently that I’d like the database server to start up on boot and stay running. There are 2 init scripts for Debian/Ubuntu in this Google Groups thread. I followed the instructions in the second post, with minor modifications to the script: # I like to keep mongodb in /opt PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/mongodb/bin DAEMON=/opt/mongodb/bin/mongod # you don't need 'run' in these options DAEMON_OPTS='--dbpath /data/db' # I prefer lower-case name for the PID file NAME=mongodb # I think /data/db should be owned by the mongodb user sudo chown -R ...

I’m with Coco

Blind.Scientist — Thu, 14 Jan 2010 23:45:28 +0100

(Source: Blind.Scientist)

The joys of print

Public Rambling — Thu, 14 Jan 2010 22:14:00 +0100

For the past two months I have been enjoying my first ever print subscription to a scientific journal. The good folks over at Nature Reviews Genetics offered my a small discount that nudged me to it (thank you!). I thought that if I ever tried a print subscription it would be for sure a review journal. I can't say I regret the decision. Having the print issue to read on my commute makes me read articles that I would not normally print out and the front section (research highlights) is a good way to catch up to science news. Maybe this explosion of e-readers will make it easier to emulate the browsing experience of a bound print copy. As Nicholas Carr (and others) have pointed out, changes in internet technology shape the way we think and use information. In a recent post, Carr giv...

A new twist on the identifier mapping problem

What You're Doing Is Rather Desperate — Tue, 12 Jan 2010 03:57:02 +0100

Yesterday, Deepak wrote about BridgeDB, a software package to deal with the “identifier mapping problem”. Put simply, biologists can name a biological entity in any way that they like, leading to multiple names for the same object. Easily solved, you might think, by choosing one identifier and sticking to it, but that’s apparently way too much of a challenge. However, there are times when this situation is forced upon us. Consider this code snippet, which uses the Bioconductor package GEOquery via the RSRuby library to retrieve a sample from the GEO database: require "rubygems" require "rsruby" if ENV['R_HOME'].nil? ENV['R_HOME'] = "/usr/lib/R" end r = RSRuby.instance r.library("GEOquery") sample = r.getGEO("GSM434143"...

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Video: Building a data intensive application with Hadoop and Hive

business|bytes|genes|molecules — Tue, 12 Jan 2010 02:52:56 +0100

I have written about TrendingTopics before. Pete Skomoroch gave a talk on how to build a data intensive web app using Hadoop, Hive and Amazon EC2 at Hadoopworld and the video is now available Building Data Intensive Apps with Hadoop and EC2 from Cloudera on Vimeo. Please see this disclaimer (Source: business|bytes|genes|molecules)

The Array Killers?

Omics! Omics! — Tue, 12 Jan 2010 00:00:00 +0100

Illumina announced their new HiSeq 2000 instrument today. There are some great summaries at Genetic Future and PolitGenomics; read both for the whole scoop. Perhaps just as jaw dropping as some of the operating statistics on the new beast is the fact that Beijing Genome Institute has already ordered 128 of them. Yow! That's (back-of-envelope) around $100M in instruments which will consume >$30M/year in reagents. I wish I had that budget!Illumina's own website touts not only the cost (reagents only) of $10K per human genome, but also that this works out to 200 gene expression profiles per run at $200/profile. That implies multiplexing, as there are 32 lanes on the machine (16 lanes x 2 flow cells -- or is it 32 lanes per flowcell? I'm still trying to figure this out based on the note that i...

In science, data without purpose is sometimes required

Public Rambling — Mon, 11 Jan 2010 03:00:00 +0100

The title is probably flamebait but it might get you to read my little rant about data production in science. Its something I have been meaning to write about for a while but Deepak's post provided the extra incentive. I think Deepak's post was a reminder that science is nothing without hypothesis and I certainly agree with that. To put this into context maybe it worth pointing again to the wired article about "The End of Theory" where Chris Anderson painfully tries to make the point that with the deluge of data that we are seeing we don't need models or hypothesis we just need to crunch the data to look for correlations. I strongly disagree with this viewpoint. What would we learn about reality this way ? At most we would see correlations and could have some predictive power about fut...

BridgeDB: Middleware for ID mapping

business|bytes|genes|molecules — Mon, 11 Jan 2010 02:19:09 +0100

Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. This is the background behind a paper on BridgeDB by Iersel, et al. BridgeDB is an ID mapping framework that provides a standardized interface which can be used to connect bioinformatics tools to different identifier mapping services. Without pushing it myself, I can only comment on intent, and this is exactly the kind of idea that some of us have been encouraging bioinformatics types to develop and use. One of the most important aspects of buildi...

Memories

Blind.Scientist — Sun, 10 Jan 2010 17:50:34 +0100

Image via Wikipedia (I’m really behind on my promise to post 365 in 365, four to keep the average on 1, three to go after this one) In mid-October I went to Brazil, first to attend the 2009 X-Meeting in Angra dos Reis and for a first vacation period since 2005. When I moved to Canada, I wasn’t able to bring all the scientific literature I had amassed over the years, mostly stuff about frogs, evolution and phylogenetics. Nowadays printed or copied papers and out-of-date, PDF is the new in, so I decided to throw away most of the things I would be able to recover online later, but still keep some copies of rare stuff and original copies of papers. Some of the original copies I saved where from the 50’s, 60’s and 70’s, and some of these contained the stamp tha...

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Movies 2010

Blind.Scientist — Sun, 10 Jan 2010 15:43:48 +0100

The Box – 5/5 (Source: Blind.Scientist)

Books 2010

Blind.Scientist — Sun, 10 Jan 2010 15:42:59 +0100

1 – The New New Thing: A Silicon Valley Story (Source: Blind.Scientist)

What is the CSS style of that HTML element ?: CSSPopup, an extension for firefox

YOKOFAKUN — Sun, 10 Jan 2010 00:00:00 +0100

Trying to find the CSS style of a HTML element is a common task for me and I often look in the of the pages to try to find what can be "this inspiring CSS". So, I've created CSSPopup, a small extension for firefox. This extension appends a new button in the contextual menu that will print all the CSS selectors of the element that was clicked. For example when I clicked on "Welcome to (Source: YOKOFAKUN)

There's Plenty of Room at the Bottom

Omics! Omics! — Sun, 10 Jan 2010 00:00:00 +0100

Friday's Wall Street Journal had a piece in the back opinion section (which has items about culture & religion and similar stuff) discussing Richard Feynman's famous 1959 talk "There's Plenty of Room at the Bottom". This talk is frequently cited as a seminal moment -- perhaps the first proposition -- of nanotechnology. But, it turns out that when surveyed many practitioners in the field claim not to have been influenced by it and often to have never read it. The article pretty much concludes that Feynman's role in the field is mostly promoted by those who promote the field and extreme visions of it.Now, by coincidence I'm in the middle of a Feynman kick. I first encountered him in the summer of 1985 when his "as told to" book "Surely You're Joking Mr. Feynman" was my hammock reading. The n...

To handle lots of data, we need to think differently

business|bytes|genes|molecules — Sat, 09 Jan 2010 17:09:35 +0100

In a recent editorial (sub might be required) talking about next-gen sequencing and cloud computing, Nature Biotech makes an all to familiar error. It remains unclear, however, whether the cost of routinely renting time on the cloud would be cost effective in the long term, particularly if a user intends to analyze billions of base pairs of genome sequence on a regular basis. What’s more, if the wide uptake of sequence analysis on clouds depends on the availability of user-friendly, debugged software, bioinformaticians might not be willing to spend the time to familiarize themselves with hadoop, the open source program needed to process large data sets on a cloud—especially when their jobs focus on developing algorithms for their own local computer clusters. The context for that...

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In science, data is nothing without purpose

business|bytes|genes|molecules — Sat, 09 Jan 2010 04:16:39 +0100

In an article on TechFlash, a VC, talking about trends in 2010, had this to say while talking about increased IT needs in cleantech and biotech Both areas are generating terabytes of data and it is no longer just about science — it is about digesting mountains of data. For some reason that statement scared me. Digesting mountains of data is all about the science. If we forget that, we are in big trouble. Yes, from a pure technology perspective it is about digesting mountains of data, but (a) that has to be looked at in the context of science (sense-making?), and (b) the digesting is a necessary pre-requisite to getting to the science. You really don’t have much of a choice, but if you forget about the science, you will end up with noise, a whole lot of it. My advice to all ...

Samples per series/dataset in the NCBI GEO database

What You're Doing Is Rather Desperate — Fri, 08 Jan 2010 01:01:09 +0100

Andrew asks: I want to get an NCBI GEO report showing the number of samples per series or data set. Short of downloading all of GEO, anyone know how to do this? Is there a table of just metadata hidden somewhere? At work, we joke that GEO is the only database where data goes in, but it won’t come out. However, there is an alternative: the GEOmetadb package, available from Bioconductor. The R code first, then some explanation: # install GEOmetadb source("http://bioconductor.org/biocLite.R") biocLite("GEOmetadb") library(GEOmetadb) # connect to database getSQLiteFile() con <- dbConnect(SQLite(), "GEOmetadb.sqlite") # count samples per GDS gds.count <- dbGetQuery(con, "select gds,sample_count from gds") gds.count[1:5,] # first 5 results...

How to: archive data via an API using Ruby and MongoDB

What You're Doing Is Rather Desperate — Thu, 07 Jan 2010 00:17:46 +0100

I was going to title this post “How to: archive a FriendFeed feed in MongoDB”. The example code does just that but (a) I fear that this blog suggests a near-obsession with FriendFeed (see tag cloud, right sidebar) and (b) the principles apply to any API that returns JSON. There are rare examples of biological data with JSON output in the wild, e.g. the ArrayExpress Gene Expression Atlas. So I’m still writing a bioinformatics blog ;-) Let’s go straight to the code: #!/usr/bin/ruby require "rubygems" require "mongo" require "json/pure" require "open-uri" # db config db = Mongo::Connection.new.db('friendfeed') col = db.collection('lifesci') # fetch json 0.step(9900, 100) {|n| f = open("http://friendfeed-api.com/v2/feed/...

Transforming Pubmed to Simile/Exhibit with XSLT

YOKOFAKUN — Wed, 06 Jan 2010 00:00:00 +0100

Cameron Neylon recently asked on friendfeed:"Advice request: What is the best approach to exposing a publications list online. Any good tools for generating html/xml/rdfa?".In the comments, it was suggested to use Simile/Exhibit. This gave me the idea to write a XSLT stylesheet to transform a pubmed xml result to an Exhibit file. This XSLT stylesheet is available at:http://code.google.com/p/ (Source: YOKOFAKUN)

On Being a Scientific Zebra

Omics! Omics! — Wed, 06 Jan 2010 00:00:00 +0100

I got a phone call today from someone asking permission to suggest me as a reviewer of a manuscript this person was about to submit. For future reference, if it's similar to anything I've blogged about, I'd be happy to be a referee. I generally get my reviews in on time (though near deadline), a practice I have gotten much better about since getting a "your review is late" note from a Nobelist -- not the sort of person you want to get on the wrong side of.I end up reviewing a half dozen or so papers a year, from a handful of journals. NAR has used me a few times & I have some former colleagues who are editors are a few of the PLoS journals. There's also one journal of which I'm on the Editorial Board, Briefings in Bioinformatics (anyone who wishes to write a review is welcome to leave cont...

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A Decade in Computational Structural Biology

Trapped in the USA — Tue, 05 Jan 2010 08:53:30 +0100

I shake my head and suddenly realize a decade has almost passed since I first became a computational structural biologist. Feeling that I’ve earnt some kind of perspective, I hereby present to you my list of highlights in computational structural biology of the naughties: 1. Rosetta. There is no doubt in my mind that the greatest contribution to computational structural biology this decade is the suite of programs known as Rosetta, written by David Baker and his lab. Look at the accomplishments. Rosetta has consistently won CASP (see next item) in the new fold category. Nothing else comes close in deducing the structure of a protein from an arbitrary protein sequence. Rosetta was used to create a protein with the first artificial fold. Rosetta was also used to design the first ar...

Phrase of the day

Blind.Scientist — Tue, 05 Jan 2010 00:33:23 +0100

Post of the day is the phrase of the day, overheard online in an interview on the Brazilian TV channel, Globo News: “(…) Brazil’s urban planning is prehistorical (…)”. I can say that not only urban planning is prehistorical. (Source: Blind.Scientist)

My Python notebook: displaying the state of the Genome Projects

YOKOFAKUN — Tue, 05 Jan 2010 00:00:00 +0100

This post if about my first Python program. I'm still a newbie so please, don't flame ! :-)The NCBI hosts a XML file describing the state of the Genome Projects at ftp://ftp.ncbi.nih.gov/genomes/genomeprj/gp.xml. The very first lines of the file look like this: (Source: YOKOFAKUN)

HPC over the past decade

business|bytes|genes|molecules — Mon, 04 Jan 2010 15:42:00 +0100

Joe Landman has a series of posts providing a great perspective on HPC over the past decade. I suggest anyone interested in computing read them Part 1 Part 2 Part 3 – This one is a must read Part 4 Part 5 – Another great read and a subject that I used to blog about a lot (mostly channeling Joe) Part 6 – Close to home Part 7 – Storage technology, something I care about more and more (Source: business|bytes|genes|molecules)

Stitching different web tools to organize a project

Public Rambling — Sun, 03 Jan 2010 18:12:00 +0100

A little over a year ago I mentioned a project I was working on about prediction and evolution of E3 ligase targets (aka P1). As I said back then, I am free to risk as much as I want in sharing ongoing results and Nir London just asked me how the project is going via the comments of that blog post so I decided to give a bit of an update. Essentially, the project quickly deviated from course since I realized that predicting E3 specificity and experimentally determining ubiquitylation sites in fungal species (without having to resort to strain manipulation) were not going to be an easy tasks. So, since the goal was to use these data to study the co-evolution of phosphorylation switches (phosphorylation regulating ubiquitylation) it makes little sense to restrain the analysis speci...

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APIs are powerful platforms

business|bytes|genes|molecules — Sun, 03 Jan 2010 04:32:11 +0100

APIs; an area that we life science folks are not very good at. I once heard Mark Shuttleworth talk about building stuff that people can use to build more stuff (paraphrasing heavily). In other words we need to think about application and data platforms and for modern bioinformatics that is pretty much what we should strive to be doing. If one looks at the type of programming that needs to be done in the life sciences, you have applications that solve specific problems; alignments, assembly, etc, and ideally these should be applications that can be brought together without the developer having to worry about data formats, or at least handle those with minimal fuss. There are those who specialize in information retrieval, digging deep into data, slicing and dicing data sets. In a perfect wor...

Lies, lies and even more lies

Blind.Scientist — Sun, 03 Jan 2010 02:59:28 +0100

At the time of the Copenhagen meeting about climate change, Brazilian representatives were major protagonists, specially when criticizing all developed countries about their carbon emissions. The crook, also known as the Brazilian president, kept reminding everyone how advance Brazil is on “green” policies, how much native forests are still there, and saying the the developed countries have to do something to erase their polluted heritage. Well, I don’t think many of my 3 readers (yes, I got an extra one this last week!) have ever been to Brazil, so I would like to list some of the lies about Brazilian “green” policies and actions: - São Paulo is the largest city of the Southern Hemisphere, and there’s no effective recycling service. Now, imagine, 10+ ...

2009 – the posts that never made it

Your bones got a little machine. — Sat, 02 Jan 2010 11:57:23 +0100

So, people tell me 2009 ended recently. Apparently there were fireworks and stuff. This blog as seen very little action during 2009, despite my various good intentions for a blog ‘reboot’ (ala Pawel). Like many of my online friends, I blame FriendFeed. I find commenting on a FriendFeed post a much more productive way of having a conversation around some new development sweeping the web than writing a dedicated blog post. Still, despite this being my “year of FriendFeed”, I started writing a few blog posts / articles / essays this year which never made it out of the Drafts folder. There is a positive side to unpublished drafts – they serve to nicely organize some thoughts, even if they are ultimately never shared. Anyhow, it’s time to clean them out and m...

365 in 365

Blind.Scientist — Fri, 01 Jan 2010 15:37:04 +0100

I plan to post 365 entries either here, here or here in 2010. I might not post everyday, but I will try to keep the mark, even if it’s only a one-liner or some link to interesting news/software/paper. Happy New Year everyone! (Source: Blind.Scientist)

Yet another year is in the can

business|bytes|genes|molecules — Fri, 01 Jan 2010 00:35:33 +0100

It is now four years to the day that this incarnation of bbgm was born. And it’s come a long way since then as have I. No longer do I feel the need to push out a blog post or more per day and it’s only partly due to a lack of time. The way I look at it, there is a time in the life of a blog where writing often is almost necessary if you want to build an audience, but you ultimately reach a place where unless blogging is your core output, there are other avenues (Twitter, Posterous, FriendFeed, etc) that are more appropriate for certain forms of discussion. Over those years, I’ve covered a number of topics and been involved in many communities, and it’s rather pleasing to see all the new blogs and new names in the online world that so many of us live in. I am more pa...

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Best of the decade

Blind.Scientist — Thu, 31 Dec 2009 03:37:38 +0100

Friends, as the year draws to a close, I felt compelled to compile the best of the decade of 00s. The list is: will be posted here as soon as the decade ends on Dec 31st, 2010. (Source: Blind.Scientist)

More musings on MapReduce and bioinformatics

business|bytes|genes|molecules — Tue, 29 Dec 2009 06:15:08 +0100

Jeff Dean and Sanjay Ghemawat have an updated MapReduce paper (doi) in the Communications of the ACM. The paper is a pretty strong rebuttal to some claims by Mike Stonebraker and others on the value of the MapReduce model. I am going to let you read the paper (as well as the original papers). What I wanted to talk about were some of the key aspects of the MapReduce model and how this way of thinking is relevant to the life sciences. The first point that Dean and Ghemawat talk about is heterogenous systems. The way I see it, the entire field of bioinformatics is full of heterogenous systems. Even data we generate in internal systems needs to be combined with data from other systems. In fact, I am pretty sure that as we improve delivery models and APIs for life science data resources, we wil...

Length matters!

Omics! Omics! — Mon, 28 Dec 2009 00:00:00 +0100

I was looking through part of my collection of papers using Illumina sequencing and discovered an unpleasant surprise: more than one does not seem to state the read length used in the experiment. While to some this may seem trivial, I had a couple of interests. First, it's useful for estimating what can be done with the technology, and second since read lengths have been increasing it is an interesting guesstimate of when an experiment was done. Of course, there are lots of reasons to carefully pick read length -- the shorter the length, the sooner the instrument can be turned over to another experiment. Indeed, a recent paper estimates that for RNA-Seq IF you know all the transcript isoforms then 20-25 nucleotides is quite sufficient and you are interested in measuring transcript levels (...

Loosely coupled tools: BWA

business|bytes|genes|molecules — Thu, 24 Dec 2009 08:12:12 +0100

I am hardly a practitioner anymore, so take the following with that caveat firmly in your mind. I first heard about the Burrows-Wheeler transform from slides presented by Mike Schatz. That particular method underlies BWA, which from the looks of it is one top notch aligner. What I found interesting about BWA was not the quality or breadth of alignment capabilities, but that it did one thing well. The other day I wrote about loosely coupled tools. It’s not always ideal to have a tool that does one thing well, but in many cases it makes a lot of sense. In this particular case, being able to combing BWA with an existing set of tools (SAMTools) does not take away any power, but makes the core functionality more effective, or so it seems. I wonder how the world of APIs and loosely coupled...

Developing effective bioinformatics programming skills

business|bytes|genes|molecules — Thu, 24 Dec 2009 07:32:04 +0100

Back on Coast to Coast Bio #13 we talked about Joel Dudley’s seminar on programming effectively for bioinformatics (slides). Joel has converted that into a article in PLoS Computational Biology. For many Biogangers, the article might be obvious, but for many getting their start, or getting into the programming side of things, this paper is a great read. It also is very contemporary and talks about a lot of current best practices. Some of the key areas which are often forgotten by scientific programmers Documenting and managing projects Maintaining source code Parallel computing, including shoutouts to the kinds of distributed computing paradigms that I find particularly interesting Structured data If you are expecting a deep dive into each topic this is not the article you are look...

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The Life Scientists at FriendFeed: 2009 summary

What You're Doing Is Rather Desperate — Wed, 23 Dec 2009 08:15:40 +0100

The Life Scientists 2009 It’s Christmas Eve tomorrow and so I declare the year over. My Christmas gift to you is a summary of activity in 2009 at the FriendFeed Life Scientists group. It’s crafted using R + Ruby, with raw data and some code snippets available. If you want to see the most popular items from the group this year, head down to the bottom of this post. (Note: this post is a work in progress) The contributors First of all, take a look at yourselves. There are, allegedly, 1250 subscribers to the group, but I can only retrieve profiles for 1053 of them. 248 of you are rather shy, opting for the default avatar and one or two of you look rather like porn stars. If nothing else, this illustrates the difficulty of compiling reliable user statistics. Here’s how this ...

Loosely coupled tools

business|bytes|genes|molecules — Tue, 22 Dec 2009 07:29:18 +0100

Joshua Shachter has a pretty interesting blog post about blogging tools, one that makes a lot of sense and appeals to a bunch of instincts. In the post, Joshua talks about the separate pieces that make up a blogging system and how they can be served up. In other words, you don’t have to create one complete piece of software, but use existing components to create a blog authoring and serving package. He writes I wonder if there is a way to define loose interfaces between these systems so that they could both work together but also not set APIs in concrete solid enough to stop innovation. Because the various pieces of the systems currently are all tightly bound together, it is very hard for the parts to move forward separately. For example, I’ve wanted to be able to specifically ...

You're Just Not that into Science

Trapped in the USA — Tue, 22 Dec 2009 05:08:11 +0100

It’s sad to say this but most people I work with are just not that into science. It’s not that they’re not good at it – they clearly are – it’s just that they’re interested only in their little niche, and are thoroughly satisfied with all that it entails. Case in point: recently, I was at work looking up a biology textbook on basic paleontology, spurred on by the intriguing hypothesis that the Cambrian explosion was induced by the evolution of eyes. My buddy S wanders by and notices that I am reading a first-year biology textbook. Being a curious guy, he asks me why. That’s when, whilst explaining to S the whole theory about eyes and the Cambrian explosion, we were interreputed by a third guy J, who burst out with “Ha ha, that’s...

2009 in review

Blind.Scientist — Sun, 20 Dec 2009 00:55:53 +0100

Here’s the best and worst of 2009: - Movie: Rockrolla, not the best one, but highly entertaining, worst: Funny People - Book: Born Standing Up: A Comic’s Life by Steve Martin, highly entertaining too - Website: The Secret Diary of Steve Jobs, worst: of the ones I usually read is the Daring Fireball - Software: Textmate, worst Mendeley, by 1000 miles - TV: Stephen Colbert and Jon Stewart, the best hour of TV, worst: Dexter’s finale - Purchase: MacBook 13”, the best computer I ever had - Money-grabbing-scheme: Global Warming or Climate Change - Politician: no best in the category, but the worst is the Brazilian President. - Music: I didn’t have a favourite this year. but Matthew Good’s Vancouver is growing on me. No worst, or too many to care about - Best ...

Nano Anglerfish or Feejee Mermaids?

Omics! Omics! — Fri, 18 Dec 2009 00:00:00 +0100

A few months ago I blogged enthusiastically about a paper in Science describing an approach to deorphan enzymes in parallel. Two anonymous commenters were quite derisive, claiming the chemistry for generating labeled metabolites in the paper impossible. Now Science's editor Bruce Alberts has published an expression of concern, which cites worries over the chemistry as well as the failure of the authors to post promised supporting data to their website and changing stories as to how the work was done.The missing supporting data hits a raw nerve. I've been frustrated on more than one occasion whilst reviewing a paper that I couldn't access their supplementary data, and have certainly encountered this as a reader as well. I've sometimes meekly protested as a reviewer; in the future I resolve ...

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Name that lab ...

Public Rambling — Thu, 17 Dec 2009 17:24:00 +0100

In the last editorial in Nature, the need for an author ID is introduced with the simple notion that each one of us has specific sets of skills: In his classic book Management Teams, UK psychologist Meredith Belbin used extensive empirical evidence to argue that effective teams require members who can cover nine key roles. These roles range from the creative 'plants' who generate novel ideas, to the disciplined 'implementers' who turn plans into action and the big-picture 'coordinators' who keep everyone working together.From this perspective the author ID is a tool that might help us get appropriate credit for skill sets that are currently undervalued. This sort of argument reminds me of a discussion I had several times in the past about the management structure of academic labs. Why...

Intelligence in Chaos

business|bytes|genes|molecules — Thu, 17 Dec 2009 07:51:18 +0100

Greg Linden has a great article in Communications of the ACM on The Rise of the External Brain. As Greg notes, we have spent a lot of time trying to develop an Artificial Intelligence, a task at which we have not been successful. But he notes that we have had some success from in the form of chaos from the internet. The web, especially search engines supplement our own brain, filling in incomplete bits of knowledge when required. This viewpoint is in direct contradiction to the kinds expressed by Nick Carr, who believes that search engines are not a positive influences on our intelligence. I find myself aligning with Greg. He writes And so it is fitting that the biggest progress on building an external brain also comes from chaos. Search engines pick out the gems in a democratic sea of c...

Playing with Erlang (3): concurrency

YOKOFAKUN — Thu, 17 Dec 2009 00:00:00 +0100

In this post I'll show how to write a multithreaded erlang program where each child process will calculate if a given number is a Prime Number (not rocket science, a brute force algorithm will be used).First this erlang module is called 'prime':-module(prime).The method named 'test' with no argument is public -export([test/0]).The method named 'start' creates a new thread for the function 'loop'. (Source: YOKOFAKUN)

A Doublet of Solid Tumor Genomes

Omics! Omics! — Thu, 17 Dec 2009 00:00:00 +0100

Nature this week published two papers describing the complete sequencing of a cancer cell line (small cell lung cancer (SCLC) NCI-H209 and melanoma COLO-829) each along with a "normal" cell line from the same individual. I'll confess a certain degree of disappointment at first as these papers are not rich in the information of greatest interest to me, but they have grown on me. Plus, it's rather churlish to complain when I have nothing comparable to offer myself.Both papers have a good deal of similar structure, perhaps because their author lists share a lot of overlap, including the same first author. However, technically they are quite different. The melanoma sequencing used the Illumina GAII, generating 2x75 paired end reads supplemented with 50x2 paired end reads from 3-4Kb inserts, wh...

Funding biological data resources revisited

business|bytes|genes|molecules — Tue, 15 Dec 2009 05:48:09 +0100

It is time for a whole new approach. Front-line biology cannot function without these resources, so solutions must be found at both national and international levels. That’s from an editorial in Nature talking about the need to change the way data resources are funded, a topic I have visited before. In this particular case, the resource under question is The Arabidopsis Information Resource (TAIR), which had been funded by the NSF for a decade but is seeing that sole source of funding phased out. As the editorial points out, such challenges are not unique to TAIR, but a problem facing biological databases and repositories, i.e. part of the core infrastructure for the life sciences. I say that because to sustain any data resource you need to sustain infrastructure as well as the devel...

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"The Sound and the Fury": Incomprehensible Gothic

Trapped in the USA — Mon, 14 Dec 2009 02:46:18 +0100

William Faulkner’s “The Sound and the Fury” is one of most reader-unfriendly book I’ve ever read. Written in 1929, it’s clear that Faulkner was enamoured with the new innovations in prose flowing out of Europe such as that diarrhea of words known as stream of consciousness. But there’s good stream of consciousnessness and there’s bad stream of consciousness. Good stream of consciousness conjures up a heightened state of mind. By writing from the inner psyche of the protaganist, we get a better sense of the character through free associations and displacements of languge. Still, stream of consciousness should flow, ratcheting tension through a logic of comprehensible symbolism. Bad stream of consciousness grates on the nerves like an open-mike ...

Parsing a genetic code using flex and bison. Part 1/2

YOKOFAKUN — Mon, 14 Dec 2009 00:00:00 +0100

In this post I'll show how to write a lexer and a parser using Flex and Bison for parsing the genetic codes at NCBI. I'll write a non-reentrant parser that is to say that the generated code contains some global variables and cannot be safely executed concurrently. The input file is an ASN1 file that looks like this:--*************************************************************************-- (Source: YOKOFAKUN)

Parsing a genetic code using flex and bison. Part 2/2

YOKOFAKUN — Mon, 14 Dec 2009 00:00:00 +0100

(this post was inspired from this tutorial: "Writing a Reentrant Parser with Flex and Bison").In the previous post I've shown how to parse a NCBI genetic code in ASN.1 using flex and bison. However the generated code is non reentrant that is to say that some globals variables prevent it to be used in a concurrent environment.If we want to use this code in a multithread environment, some changes (Source: YOKOFAKUN)

Panda Genome Published!

Omics! Omics! — Mon, 14 Dec 2009 00:00:00 +0100

Today's big genomics news is the advance publication in Nature of the giant panda (aka panda bear) genome sequence. For I'll be fighting someone (TNG) for my copy of Nature!Pandas are the first bear (and alas, there is already someone making the mistaken claim otherwise in the Nature online comments) and only second member of Carnivora (after dog) with a draft sequence. Little in the genome sequence suggests that they have abandoned meat for a nearly all-plant diet, other than an apparent knockout of the taste receptor for glutamate, a key component of the taste of meat. So if you prepare bamboo for the pandas, don't bother with any MSG! But pandas do not appear to have acquired enzymes for attacking their bamboo, suggesting that their gut microflora do a lot of the work. So a panda ...

APIs: I wish the life sciences would learn from social networks

What You're Doing Is Rather Desperate — Fri, 11 Dec 2009 02:50:49 +0100

I was prompted by a thread on the apparent decline of FriendFeed to look for evidence of declining participation in my networks. First, a quick and dirty Ruby script, tls.rb to grab the Life Scientists feed and count the likes and comments: #!/usr/bin/ruby require 'rubygems' require 'json/pure' require 'net/http' require 'open-uri' def format_date(d) if d =~ /(\d{4}-\d{2}-\d{2})T(\d{2}:\d{2}:\d{2})Z/ return "#{$1},#{$2}" else return d end end def count_items(i) if i.nil? return 0 else return i.count end end n = ARGV[0] u = "http://friendfeed-api.com/v2/feed/the-life-scientists?start=#{n}" f = open(u).read j = JSON.parse(f) j.each_pair do |k,v| if k == "entries" v.each do |entry| date = format_date(entry['date']) likes = count_it...

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Bioinformatics and mythology. You still need to manage the data

business|bytes|genes|molecules — Thu, 10 Dec 2009 03:43:17 +0100

Image by dullhunk via Flickr In a great blog post at Code for Life, Grant Jacobs writes By contrast, early bioinformatics work was almost invariably founded on biological concepts from the onset. A biological issue was raised and then a technique to address that issue was presented. That is, theoretical biology was the foundation on which [early] bioinformatics was built. I fear this is being lost in the mass-data and technology-hype driven bioinformatics. It seems to me that unless companies and research groups are careful many will waste time and money “stamp collecting and cataloging”. Certainly the organized data is useful, but only if it is applied with biological principles Grant writes this in the context of the early days of bioinformatics, a time when there was a lot of the...

Questions and information streams

business|bytes|genes|molecules — Tue, 08 Dec 2009 04:02:13 +0100

So Google announced a whole bunch of new features today. There are also rumors about Google making a play for Aardvark, a just-in-time social Q&A service that I like and use. This post is not about Google, nor about Aardvark per se, but rather about networks in science, and real time information flow. We ask questions in forums, in mailing lists, on Friendfeed; we search on Google, at NCBI; we track hashtags on Twitter. All of these questions and streams are flying by the web all the time, even in the sciences, but we have to go to various places to get access to them. What if I could sit at an interface and ask questions which land up in the right place, or allow me to track questions of interest being asked around the web and have those questions and their answers delivered to me? I ...

Playing with SOAP. Implementing a WebService for the LocusTree Server

YOKOFAKUN — Mon, 07 Dec 2009 00:00:00 +0100

In a previous post I've described the LocusTree server and showed how the wsimport command can be used to generate the java code that will query a Web-Service. Today, I've implemented a few web services in the LocusTree server but I wrote the entire code generating the SOAP messages rather than using the Java API for Web Services (JAXWS-API) because 1) I wanted to learn about the SOAP internals 2 (Source: YOKOFAKUN)

Scaling out for analytics

business|bytes|genes|molecules — Fri, 04 Dec 2009 16:57:19 +0100

Image via Wikipedia In a post announcing the open sourcing of Crane (more on Crane later), Bradford Cross writes A big concern with the modern JVM languages like Scala and Clojure is the ability to scale out from the single JVM address space into distributed environments. Different approaches include a distributed JVM (terracotta), distributed actors (akka), message queues (AMQP/rabbitmq), or solutions for specific computational models, like hadoop He also writes For those of us who are researchers, all our jobs are ad hoc transient clusters, and the problem is even more pronounced unless we have a dedicated research cluster, for the cluster must be brought up and torn down for every job. Researchers become “babysitters” to clusters and jobs; the master serves the servant. I...