MedWorm: Bioinformaticians

Warren Delano passes away

business|bytes|genes|molecules — Fri, 06 Nov 2009 06:18:15 +0100

Earlier today, I got an email from Hari pointing me to a note from Axel Brunger on the CCP4 mailing list with the sad news that Warren Delano had passed away. I got to know Warren during my time at Accelrys, and was lucky enough to discuss science and visualization with him on more than one occasion (we didn’t exactly agree on everything, but it was always a healthy debate), so I am still trying to absorb the news. To say it is shocking would be an understatement For those who don’t know, Warren was the author of PyMol, the best pure viewer I have ever used, and a revolution in it’s day. An open source viewer better than anything you paid for. It was certainly a key reason why companies like Accelrys ended up releasing free molecular viewers. Seeing slide after slide at c...

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R has a JSON package

What You're Doing Is Rather Desperate — Thu, 05 Nov 2009 23:44:44 +0100

Named rjson, appropriately. It’s quite basic just now, but contains methods for interconversion between R objects and JSON. Something like this: > library(rjson) > data <- list(a=1,b=2,c=3) > json <- toJSON(data) > json [1] "{\"a\":1,\"b\":2,\"c\":3}" > cat(json, file="data.json") Use cases? I wonder if RApache could be used to build an API that serves R data in JSON format? Posted in computing, R, statistics Tagged: cran, json, r-project, statistics (Source: What You're Doing Is Rather Desperate)

Brief notes on Ubuntu 9.04 (jaunty) -> 9.10 (karmic)

What You're Doing Is Rather Desperate — Mon, 02 Nov 2009 08:18:12 +0100

Recording my Ubuntu upgrade experience has become something of a tradition, so here goes. Machine 1 (laptop, LG T1 Express Duo). Largely trouble-free. On-board soundcard not seen on reboot. Fixed (temporarily, lost on reboot) using “sudo alsa force-reload”. Machine 2 (various generic hardware, cobbled together over many years). Upgrade smooth until final restart, when machine froze. Rebooted to a blank screen. Fixed by swapping out ATI video card for old NVidia FX5200. Discovered that rsyslog is running riot due to a hot CPU and is trying to fill up /var/log. Machine 3 (Dell Optiplex GX550). Install froze at “stopping winbind server”. Rebooted with rescue CD, mounted and chroot-ed into Linux partition, tried “dpkg –force-all –configure -a”, ...

Data driven science revisited

business|bytes|genes|molecules — Sat, 31 Oct 2009 17:50:35 +0100

Chris Anderson once infamously wrote The data deluge makes the scientific method obsolete, an opinion that I do not share. Eric Drexler on the other hand comes at this new age of data driven science with the right mindset. In a post on data explosion and the scientific method, Eric writes Tradition demands that science always be hypothesis-driven: First, try to guess the truth, and only afterward collect experimental data to test whether the guess predicts the results. Indeed, this has been termed “The Scientific Method”. The new data-driven approach suggests that we collect data first, then see what it tells us. This becomes practical when experimental methods can amass enormous amounts of data, enough data to test more hypotheses than any mortal scientist could conceivably imagine. T...

Matt’s manifesto for a science data platform

business|bytes|genes|molecules — Thu, 29 Oct 2009 03:37:13 +0100

There are a select few people whose every word I try and absorb and chew on because I have great respect for their thinking and intelligence. Matt Wood is one of those people, and today he decided to tweet a manifesto. The whole series started with I’m starting a manifesto. There are no technical, political or funding reasons why an open data platform for science couldn’t excel He then followed that up with five tweets (Matt’s Twitter stream). I don’t know if that’s the entire manifesto, but I reproduce those tweets below, a series entitled Towards a science data platform Easy, flexible retrieval and reuse above all else A laser sharp focus on scientific productivity and progress Scalability and speed are not mutually exclusive Well designed, high quality pro...

My Most Expensive Paper

Omics! Omics! — Thu, 29 Oct 2009 00:00:00 +0100

Genome Research has a paper detailing the Mammalian Gene Collection (MGC), and if you look way down on the long author list (which includes Francis Collins!) you'll see mine there along with two Codon Devices colleagues. This paper cost me a lot -- nothing in legal tender, but a heck of a lot of blood, sweat & tears.The MGC is an attempt to have every human & mouse protein coding sequence (plus more than a few rat)available as an expression clone, with native sequence. Most of the genes were cloned from cDNA libraries, but coding sequences which couldn't be found that way were farmed out to a number of synthetic biology companies. Codon decided to take on a particularly challenging tranche of mostly really long ORFs, hoping to demonstrate our proficiency in this difficult task.At the start...

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HPC and software … again

business|bytes|genes|molecules — Tue, 27 Oct 2009 02:30:43 +0100

Software is really becoming the broader language of science. Even broader than mathematics, but we don’t really know how to fund it. Those are words from Ed Seidel, Director of the NSF’s Office of Cyberinfrastructure. They are included in an article at Inside HPC, where Ed tries to clear up the air on some controversial positions on the status of supercomputing software. Whether you agree with Ed Seidel on whether Fortran is antiquated or not, it’s pretty clear, and not just in HPC that science does not know how to fund sustainable software development, and if we do want to get a generation of programmers into scientific computing, we have to embrace more “modern” programming languages, or develop our own, because whether you like it or not, getting good Fortran p...

DTC CNVs?

Omics! Omics! — Mon, 26 Oct 2009 00:00:00 +0100

Curiosity question: do the current DTC genomics companies report out copy number variations (CNVs) to their customers? Are any of their technologies unable to read these? Clearly Knome (or Illumina, which isn't DTC but sort of competing with them) should be able to get this info from the shotgun sequencing. But what about the array-based companies such as Navigenics & 23andMe? My impression is that any high density SNP array data can be mined for copy number info, but perhaps there are caveats or restrictions on that. It would seem that with CNVs so hot in the literature and a number of complex diseases being associated to them, this would be something the DTC companies would jump at. But have they? (Source: Omics! Omics!)

The bioinformatic-journal/software hydrid

Trapped in the USA — Sun, 25 Oct 2009 15:46:48 +0100

The real bioinformatics journal has not been created yet. Wait, let me explain. What we currently have are traditional journals that deal with articles on bioinformatics. The journal themselves, though they may provide digital PDF files, are still stuck in the paper paradigm. The journal itself is not bioinformatic. What crack am I smoking? In a recent article on the future of science publishing, Michaell Nielsen speculates that the crunch in scientific publishing will not simply lead to an age of open-access science publishing, but in all likelihood, will lead to new forms of publishing centered around services. Well there’s one service that I wish bioinformatics journals provide. How about actually providing what you promise? Here’s the situation. You find an 6 year old ...

Now where did I misplace that genome segment of mine?

Omics! Omics! — Sat, 24 Oct 2009 00:00:00 +0100

One of the many interesting ASHG tidbits from the Twitter feed is a comment from "suganthibala" which I'll quote in fullOn average we each are missing 123 kb. homozygously. An incomplete genome is the norm. What a goofy species we are..I'm horribly remiss in tracking the CNV literature, but this comment makes me wonder whether this is atypical at all. How extensively has this been profiled in other vertebrate species and how do other species look in terms of the typical amount of genome missing? I found two papers for dogs, one of which features a former lab mate as senior author and the other one has Evan Eichler in the author list. Some work has clearly been done in mouse as well. Presumably there is some data for Drosophila, but how extensive? Are folks going through their collections o...

ASHG Tweets: Minor Fix or Slow Torture?

Omics! Omics! — Fri, 23 Oct 2009 23:00:00 +0100

Okay, I'll admit it: I've been ignoring Twitter. It doesn't help that I never really learned to text (I might have sent one in my life). Maybe if I ever get a phone with a real keyboard, but even then I'm not sure. Live blogging from meetings seemed a bit interesting -- but in those tiny packets? I even came up with a great post on Twitter -- alas a few days after the first of April, when it would have been appropriate.But now I've gotten myself hooked on the Twitter feed coming from attendees at the American Society for Human Genetics. It's an interesting mix -- some well established bloggers, lots of folks I don't know plus various vendors hawking their booths or off-conference tours and such. Plus, you don't even need a Twitter account!The only real problem is its really making me wish ...

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Physical Maps IV: Twilight of the Clones?

Omics! Omics! — Wed, 21 Oct 2009 23:00:00 +0100

I've been completely slacking on completing my self-imposed series on how second generation sequencing (I'm finally trying to kick the "next gen" term) might reshape the physical mapping of genomes. It hasn't been that my brain has been ignoring the topic, but somehow I've not extracted the thoughts through my fingertips. And I've figured out part of the reason for my reticence -- my next installment was supposed to cover BACs and other clone-based maps, and I'm increasingly thinking these aren't going to be around much longer.Amongst the many ideas I turned over was how to adapt BACs to the second generation world. BACs are very large segments -- often a few hundred kilobases -- cloned into low copy (generally single copy) vectors in E.coli. One approach would be to simple sequence the BA...

Dealing With Big Data In Bioinformatics

Bioinformatics Zen — Wed, 21 Oct 2009 23:00:00 +0100

Bioinformatics usually involves shuffling data into the right format for plotting or statistical tests. I prefer to use a database to store and format data as I think this make projects easier to maintain compared with using just scripts. I find a dynamic language like Ruby and libraries for database manipulation like ActiveRecord makes using a database relatively simple. Using a database however stops being simple when you have to deal with very large amounts of data. Here I’m outlining my experience of analysing gigabytes of data with millions of data points and how tried to improve my software’s performance when manipulating this data. I’ve ordered each approaches with I think is the most pragmatic first. The simple things Obvious but sometimes overlooked. 1. Use a...

Local Perturbations in Explicit Solvent

Trapped in the USA — Tue, 20 Oct 2009 03:42:13 +0100

Finally ported my Molecular Dynamics perturbation method RIP from AMBER to GROMACS. I find it kind of eerie watching the tyrosine sweep out a hole in the water: (Source: Trapped in the USA)

The disconnect in funding data resources

business|bytes|genes|molecules — Sun, 18 Oct 2009 18:25:53 +0100

Scientists spend years collecting and generating increasing amounts data. The data ranges from raw instrument data, “finished” data (e.g. a genome sequence which is constructed after aligning all the short reads from a next-gen sequencer), and annotated data, which has been marked up to add additional information. We have repositories where a lot of this data goes, RCSB, NCBI, etc. In many cases there is clarity in these destinations and for the better part, resources like RCSB and NCBI are well funded and long lived (although I am always nervous about RCSB). However, many data repositories are dependent on funding, with no guarantees that the funding will be renewed. Given the size of some of these data resources, shouldn’t we be thinking of a more sustainable model for ...

Biotech and NMEs

business|bytes|genes|molecules — Sat, 17 Oct 2009 18:21:10 +0100

In a post called Banning Biotech Paul Kedrosky points to a slide from a presentation he gave last week. The slide compares the number of approved New Molecular Entities (NME’s) to pharma spending over a period of time. As you can see, the chart shows that all that spending has not necessarily resulted in new drugs. I don’t know the gist of the entire presentation, but he writes In short, the mapping of the genome, and other such inflection points in this failure-prone industry, has done nothing to accelerate news drugs, while causing costs to escalate dramatically. That’s success? I would have expected better from Paul. I’ve seen that argument made a lot and you can’t really deny that we haven’t had a lot of success to show for the progress we’ve mad...

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Molecular Dynamics and things like that

Trapped in the USA — Fri, 16 Oct 2009 21:30:42 +0100

Anyone who does simulations of proteins should post this quote up on their wall: … if you really want to understand the detailed molecular interactions that make it go in a particular direction, make certain contacts, break other contacts, hydrolyze GTP, you know, form bonds, etcetera, and do it all amazingly accurately, then you do need a high resolution picture of those states. But, that’s not going to be enough. It’s going to take a lot of work by biochemists, by computational people who do molecular dynamics and things like that to really, eventually, understand it in the sense that we would understand, say, a more typical reaction. ~ Venkatraman Ramakrishnan, in his Nobel prize phone interview (Source: Trapped in the USA)

Awesomeness

business|bytes|genes|molecules — Thu, 15 Oct 2009 04:42:29 +0100

There is no magic, there is only awesome That is the title of a three part series (well three thus far. There will be more) by Jamis Buck. The articles are about programming and development, but the tenets apply equally well to the sciences. In Part 1, Jamis sets forth his argument convincingly. As he writes, “It’s not magic that separates the exceptional from the mundane: it’s awesomeness.” “Awesomeness” in this context is excellence, an excellence borne out of a willingness to dig into one’s domain. As scientists, we are used to doing so, sometimes to an extreme. To some extent it is part of our psyche, but it’s a lesson that we need to make sure young scientists learn well. Jamis proposes four rules as well Know your tools Know your languages Kno...

Experiments in bbgm land

business|bytes|genes|molecules — Thu, 15 Oct 2009 02:59:29 +0100

One of the legacies of a blog that is now almost 4 years old is a lot of stuff that is difficult to change. For one, I experimented with a move to Squarespace, an experiment that didn’t work. I am really busy these days and figured that I didn’t want to deal with blog administration. Unfortunately, thanks to the legacy, the move would have required a lot of work to get things properly moved over, and that required time I didn’t have, so wordpress lives to see another day. The other change is in the category section of the blog. For one, the theme I am using is a magazine style theme and expects thumbnails. Secondly, I got this bright idea, one I should have had 4 years ago, but my brain is a little slow. The idea that the categories for bbgm should be business, bytes, gen...

Loose coupling and biopharma

business|bytes|genes|molecules — Wed, 14 Oct 2009 06:29:04 +0100

A few days ago, via the typical following of links that is typical of a good search and browse section on the interwebs, I chanced upon a discussion about a presentation given by Justin Gehtland at RailsConf. The talk was entitled Small Things, Loosely Joined, Written Fast and that title has been stuck in my head ever since. Funnily enough, what was in my head was not software, and web architectures, cause today, I consider that particular approach almost essential to building good applications and scalable infrastructures, and most people in the community seem to understand that (not sure about scientific programmers though). What I started thinking about was if that particular philosophy could be extended to the biopharma industry. Without making direct analogies, but without suspending...

Why I'm Not Crazy About The Term "Exome Sequencing"

Omics! Omics! — Tue, 13 Oct 2009 23:00:00 +0100

I find myself worrying sometimes that I worry too much about the words I use -- and worry some of the rest of the time that I don't worry enough. What can seem like the right words at one time might seem wrong some other time. The terms "killer app" are thrown around a lot in the tech space, but would you really want to hear it used about sequencing a genome if you were the patient whose DNA was under scrutiny?One term that sees a lot of traction these days is "exome sequencing". I listened in on a free Science magazine webinar today on the topic, and the presentations were all worthwhile. The focus was on the Nimblegen capture technology (Roche/Nimblegen/454 sponsored the webinar), though other technologies were touched on.By "exome sequencing" what is generally meant is to capture & sequ...

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My contribution to Wikipedia

YOKOFAKUN — Mon, 12 Oct 2009 23:00:00 +0100

In reply to Duncan Hull, here are the articles I've created on l&ucuser=plindenbaum&uclimit=500">wikipedia since 2006. At the beginning, I copied the abstracts in pubmed which led to some copyright problems.(See also this older post : Leonard Colebrook: Creating a Biography in Wikipedia). 230);border: 1px solid black;width:100%;height:300px;overflow:auto;font-size:10pt;">Abel-Dominique BoyéAbu (Source: YOKOFAKUN)

Bad blog! Bad, bad, bad blog!

Omics! Omics! — Thu, 08 Oct 2009 23:00:00 +0100

Thanks to Dan Koboldt from Mass Genomics, I've discovered that another blog (the Oregon Personal Injury Law Blog had copied my breast cancer genome piece. Actually, it appears that since it started this summer it may have copied every one of my posts here at Omics! Omics! without any attribution or apparent linking back. I've left a comment (which is moderated) protesting this.curiously, the author of this blog (I assume it has one) doesn't seem to have left any identifying information or contact info, so for the moment the comments section is my only way of communicating. Perhaps this is some sort of wierd RSS-driven bug; that's the only charitable explanation I can contemplate. But it is strange -- most of these have no possible link to personal injury -- or can PNAS sue me for complaini...

Nano Anglerfish Snag Orphan Enzymes

Omics! Omics! — Thu, 08 Oct 2009 23:00:00 +0100

The new Science has an extremely impressive paper tackling the problem of orphan enzymes. Due primarily to Watson-Crick basepairing, our ability to sequence nucleic acids has shot far past our ability to characterize the proteins they may encode. If I want to measure an RNA's expression, I can generate an assay almost overnight by designing specific real-time PCR (aka RT-PCR aka TaqMan) probes. If I want to analyze any specific protein's expression, it generally involves a lot of teeth gnashing & frustration. If you're lucky, there is a good antibody for it -- but most times there is either no antibody or one of unknown (and probably poor) character. Mass spec based methods continue to improve, but still don't have an "analyze any protein in any biological sample anytime" character (yet?)....

The genomic history of a breast cancer revealed

Omics! Omics! — Tue, 06 Oct 2009 23:00:00 +0100

Today's Nature contains a great paper which is one more step forward for cancer genomics. Using Illumina sequencing a group in British Columbia sequenced both the genome and transcriptome of a metastatic lobular (estrogen receptor positive) breast cancer. Furthermore, they searched a sample of the original tumor for mutations found in the genome+transcriptome screen in order to identify those that may have been present early vs. those which were acquired later.From the combined genome sequence and RNA-Seq data they found 1456 non-synonymous changes which was then trimmed to 1178 after removing pseudogenes and HLA sequences. 1120 of these could be re-assayed by Sanger sequencing of PCR amplicons from both normal DNA and the metastatic samples -- 437 of these were confirmed. Most of these (4...

Diagramming the Atari Pathway

Omics! Omics! — Mon, 05 Oct 2009 23:00:00 +0100

Okay, it was an outside speaker at work who planted this seed in my brain, and now I can't shake the image -- but perhaps by writing this I will (but also perhaps I will infect my loyal readers with it).The stated observation was that some biological pathway diagrams "look like Space Invaders". Now, I hold such games dear to my heart -- they were quite the rage in our neighborhood growing up, though we didn't own one & I was never very good. Nowadays one can buy replicas which play many of the old games -- except the entire system fits inside the replica of the old joysticks. My hardware-oriented brother loves to point out all the interesting workarounds which are now fossilized in these players -- such as limits on the number of moving graphics ("sprites") which could occupy a scan line.B...

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Why does PNAS clip their RSS feeds?

Omics! Omics! — Mon, 05 Oct 2009 23:00:00 +0100

Okay, minor pet peeve. I've pretty much switched over to using Outlook as an RSS reader to keep up with journals of interest. I still get a few ToC by email, but the RSS mechanism has lots of advantages. First, I'm in Outlook all the time, so it's a natural place. Second, I can leave behind copies of the papers of interest, with all the tools in Outlook for moving them or tagging them & such. One minor annoyance is you can't (as least as far as I can tell) force a scan of the RSS feeds. Sure, mostly this is obsessive or time-killing, but when you have intermittent net access it's really handy.But one big difference in the feeds. Most ToC feeds send out one entry per article and that entry contains the title, authors & abstract. But PNAS sends out only the authors, title & a very short head...

Post Hadoop World thoughts

business|bytes|genes|molecules — Sun, 04 Oct 2009 06:54:24 +0100

I just returned from a hectic trip to New York City. The highlight of that trip, and the primary purpose, was Hadoop World. I had always planned to be there, and had registered a long time ago, but ended up giving a talk on Hadoop for Bioinformatics (slides below). Hadoop for Bioinformatics View more presentations from Deepak Singh. Much of the discussions I had were work related, so I won’t talk about them. What I would like to talk about were some general trends that are of relevance to the life science informatics community. It’s pretty clear to me that Hadoop is here to stay. It’s not just the number of people using Hadoop, or the size of the data sets, but rather the variety of data-intensive computing that people are doing, and the thriving ecosystem. Those two te...

Next-Generation Ruby Deployment with Heroku

business|bytes|genes|molecules — Sat, 03 Oct 2009 23:11:06 +0100

via slideshare.net Posted via web from Flashing Neurons!!! (Source: business|bytes|genes|molecules)

Do you know what is a RSS feed ?

YOKOFAKUN — Fri, 02 Oct 2009 23:00:00 +0100

Friday , October 2nd 2009.University of Rouen, BIOtechno ForumA lecture hall with about 100 PhD students.Image via wikipedia"Do you know what is a RSS feed ?"...No... Nobody knows... (Source: YOKOFAKUN)

Data Analysis Using R Functions As Objects

Bioinformatics Zen — Thu, 01 Oct 2009 23:00:00 +0100

The R language is useful because of the available statistical and plotting functions in the base and addon packages. Before using any function though it’s usually necessary to get your input data into the format that the function expects. Performing complicated data manipulations with R’s standard methods for accessing and subsetting data can however quickly lead to complex and confusing R scripts. Processing a complex dataset in someway, for example to find the mean for a range of subsets, generally means creating variables to keep track of a series of levels to subset the data by, then creating a new variable for each subset. Creating many new variables can lead to complex R scripts that are difficult to understand. I’m going to try an outline here an interesting featu...

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Google Wave invite: who wants one?

Blind.Scientist — Thu, 01 Oct 2009 14:12:26 +0100

I have two Google Wave invites to go. If you want one send me an email (paulo.nuin on Gmail) or leave a comment here. The best “offer” takes it. Offer means anything: a poem, a sticker, another invite to another service, a scientific collaboration, anything. Be creative and you will have it. Update: I will send both invites later tonight, Canada’s ET. Google says it might take a while for the invite to reach the recipient. Some people are selling invites on Ebay, some for 100 dollars. Again the best “offer” wins. And remember, I’m not checking Twitter or Friendfeed. (Source: Blind.Scientist)

Pondering Polonators

Omics! Omics! — Wed, 30 Sep 2009 23:00:00 +0100

Standing next to the Polonator like a proud relative is Kevin McCarthy, who leads the Polonator effort at Dover Systems. I had remembered him giving permission to photograph it at the first day of the Providence meeting & brought my camera along the second day. When I mentioned it was for my blog, Kevin leaped into the frame. All in good fun!The Polonator is an intriguing gadget. No other next-gen sequencer can be had for under $200K -- or about 1/2 to 1/4 the price of any of the other instruments. But it's no tinfoil-and-paperclip contraption -- not only does it look very solid & professional, with everything laid out neatly in the cabinet, but in one small test it was quite robust. Kevin had it running mock sequencing cycles and he said "if you put your hand on the stage". I thought he w...

Mendeley’s PR machine and more

Blind.Scientist — Wed, 30 Sep 2009 20:00:55 +0100

There has been a somewhat heated debate in Roderic Page’s blog about Mendeley’s hype in the current reference management scenario. Also, I was forwarded to this blog post, which praises the right horse in the ref-management race, Zotero. The comments in that post are pure gold, showing how PR in science is pernicious to science itself. I will give two examples. For those who don’t know, I’m one of the poster-boys of the anti-Mendeley movement. Not because I want to be a poster-boy, but because I’m not afraid to confront their PR machine, even more after the censorship attempt. One of the worst aspects of this efficient PR machine is to use scientists to inflate the hype on the so-called social media websites, and answer everyone that might be criticizing the ...

There can be only one

YOKOFAKUN — Mon, 28 Sep 2009 23:00:00 +0100

Image via wikipediaFrench Scientists executed by decapitation:Antoine Lavoisier (1743-1794)Chrétien Guillaume de Lamoignon de Malesherbes (1721–1794- )Jean Baptiste Gaspard Bochart de Saron (1730-1794)Jean Sylvain Bailly (1736-1793)Louis-Guillaume Le Veillard(1734-1794) Philippe-Frédéric_de_Dietrich (1748-1793)computed with wpsubcat (Source: YOKOFAKUN)

This is when I say farewell …

Blind.Scientist — Mon, 28 Sep 2009 20:46:34 +0100

to “social websites”. Yes, this is a farewell to my two readers and the handful of people that read my tweets/friendfeed posts. I’m not going away, everything is still going to be channeled through FriendFeed, and posted on Twitter, but I won’t comment anymore or actually write them. It will be automatic, and personal to the level where it’s generated by my selections, not meaning they are good or bad, right or wrong, just that whatever caught my eye. I will still write here, have my Facebook account and the other “social” things, but myself, I’ll be gone. There’s a feeling of deja vu writing this, I feel that I’ve written this before, but this time it’s true and definitive. I need to focus on my work, and got tired of the ...

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Locking in new functions

Omics! Omics! — Sun, 27 Sep 2009 23:00:00 +0100

The September 24th Nature came in the mail today and as always with this journal (otherwise I wouldn't pay for it!) is full of interesting stuff. One paper of particular interest is a cool merger of evolution, computational biology, structural biology and protein engineering.An interesting question in evolution is to what degree are changes reversible. In the simplest case, of purely neutral characteristics, the answer would seem to be largely that they are. However, even a purely neutral change will have a certain probability of reverting. For example, since transversions (mutation of a pyrimidine to a purine or vice versa) are less common than transitions (purine->purine or pyrimidine->pyrimidine), a C->G mutation (transversion) is less likely to return to C than a C->T (transition). Si...

When HPC will not be the HPC you remember

business|bytes|genes|molecules — Sun, 27 Sep 2009 03:24:36 +0100

Image via Wikipedia Just read the transcript of what sounded like an excellent talk by Greg Pfister about the next 20 years of HPC. Here are some of the key points of his talk Computing will become cheaper, but not necessarily much faster per processor There will be democratization of at least some HPC. In other words with faster processors and accelerators, we might all have access to some sort of TeraFLOPS device Computing will be done all over the place, with a lot being done in the cloud. I am not quite sure I get what Greg was aiming at with his section on garbage computing, but my guess is that the cycles we’ll consume might not be the highest quality cycles but they’ll get the job done You will be billed by how much power and bandwidth your computation consumes, not ...

Extracting Scientists &SF writers from Wikipedia.

YOKOFAKUN — Sat, 26 Sep 2009 23:00:00 +0100

Images via wikipediaIn a recent post on FriendFeed, Christopher Harris asked: do you know of any science fiction writer who is/was also a scientist?. My first approach to automatically retrieve those names, was to use Freebase. For example, the following MQL query retrieves the Scientists and the SF Writers.[{ "id":null, "name":null, "type" : "/people/person", "a:profession":[{"name":" (Source: YOKOFAKUN)

How many genomes did I just squash?

Omics! Omics! — Thu, 24 Sep 2009 23:00:00 +0100

Yesterday was a good day for catching up on the literature; not only did I finally get around to the IL28B papers I blogged about yesterday, but I also took a run through the genome fusion paper which is being seen as the fitting marker of the end of the "Communicated by" mechanism of PNAS (sample coverage by In The Pipeline and Science, though the latter requires a subscription).The paper, by Donald Williamson and communicated by Lynn Margulis, takes the position that " in animals that metamorphose, the basic types of larvae originated as adults of different lineages, i.e., larvae were transferred when, through hybridization, their genomes were acquired by distantly related animals". This is a whopper of a proposal and definitely interesting.Margulis is famous for proposing the endosymbio...

Notable

business|bytes|genes|molecules — Thu, 24 Sep 2009 02:55:50 +0100

Image by Joi via Flickr Earlier today, I noticed a tweet from Lisa Green saying that a Wikipedia article on Timo Hannay had been marked for deletion. Other science folks have since jumped into the discussion. The whole debate got me thinking. What does “notability” mean? I suppose that this is a constant philosophical discussion on Wikipedia, despite the guidelines, but from where I sit, notability is purely contextual. In the sciences, Timo is certainly more notable than Robert Scoble, who has a pretty lengthy one. In general, his work has probably added more to the world than Robert’s who is much better known due to the nature of his role. We talk a lot about context and field when we talk about scientific publishing. We talk about how it’s not just a numbers g...

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Unwarranted pessimism on IL28A/B & HCV?

Omics! Omics! — Wed, 23 Sep 2009 23:00:00 +0100

I finally got around to reading the Nature News & Views article by Iadonato and Katze summarizing and opining on the recent quartet of papers linking genetic variation around IL26B and the response to standard therapy for Hepatitis C Virus. The N&V has at least one glaring flaw and also (IMHO) goes down the cliched route of concluding that the result will be clinically useless.The four GWAS studies found the same cluster of SNPs around IL28B, nicely cross-validating the studies. One curious statement in the N&V isAlthough all of the identified variants in the three studies lie in or near the IL28B gene, none of them has an obvious effect on the function of this gene, which encodes interferon-3, a growth factor with similarities to the interferon- preparations used as treatment.Two of the p...

XSLT+Pubchem Reloaded : XSLT+Pubchem = Processing

YOKOFAKUN — Wed, 23 Sep 2009 23:00:00 +0100

In a Previous post I've show how XSLT can be used to transform a NCBI/Pubchem entry into a SVG figure. Here, I've sightly modified the original stylesheet to produce a script for Processing generating a 3D model.From processing.org: Processing is an open source programming language and environment for people who want to program images, animation, and interactions. (...) It is created to teach (Source: YOKOFAKUN)

Invite codes for Infochimps.org

business|bytes|genes|molecules — Wed, 23 Sep 2009 02:27:38 +0100

Today I got a chance to see a short pitch by Dhruv Bansal from Infochimps announcing the launch of “the world’s largest open platform for data”. I have talked about the Infochimps here before, but this announcement launches them as a marketplace for data, and they have kindly given me 50 invite codes. So if you use the code “bigbiodata” you can sign up for a beta account as well. Let’s get our data out there. Related articles by Zemanta Infochimps: Share and Sell Your Raw Data (readwriteweb.com) Infochimps Wants Folks to Monkey Around With Its Data (gigaom.com) DEMO: Infochimps lets users share and sell data (venturebeat.com) Since some of the data seta on AWS Public Data Sets come from the good folk at the Infochimps, please read this disclaimer (Sou...

CHI Next-Gen Conference, Day 3 (final)

Omics! Omics! — Tue, 22 Sep 2009 23:00:00 +0100

Final day of conference, with some serious fatigue setting in (my hotel room was too close to, and faced, a highway. Doh!)Discovered that I was indeed getting a reputation. Two people I met today asked about my recurrent interest in FFPE (Formalin Fixed, Paraffin Embedded) -- which is how most of the nucleic acids I want to work with are stored. FFPE is notoriously difficult for molecular studeis, with the informational macromolecules having been chemically and physically abused in the fixation process, but it is also famously stable, preserving histological features for years.Rain Dance sponsored the breakfast & announced that their maximum primer library size has gone up to 20K. To back up, Rain Dance uses microfluidics to create libraries of very tiny (single digit picoliter) droplets i...

db_sql: the new utility for BerkeleyDB. My Notebook.

YOKOFAKUN — Tue, 22 Sep 2009 23:00:00 +0100

The new version of BerkeleyDB 4.8 has been released. This new version of the key/value storage engine comes with a new utility called db_sqlFrom Oracle: Db_sql is a utility program that translates a schema description written in a SQL Data Definition Language dialect into C code that implements the schema using Berkeley DB. It is intended to provide a quick and easy means of getting started with (Source: YOKOFAKUN)

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SGI brings back the Octane

business|bytes|genes|molecules — Tue, 22 Sep 2009 01:51:32 +0100

John West puts it best Iris. Indigo. Indy. Octane. O2. Crimson. All SGI machines that I had on (or under) my desk back when I used to do real work. They were the best graphics machines money could buy in the day and they are still strong brands today, decades after their introduction. Makes me all nostalgic. The machine can be configured with 80 Nehalem cores and is being positioned along similar lines as the Nvidia Tesla-based machines, i.e. as a "personal supercomputer" John has a lot more on the announcement, not all sweet and nostalgic Posted via email from Flashing Neurons!!! (Source: business|bytes|genes|molecules)

CHI Next-Gen Conference, Day 2

Omics! Omics! — Mon, 21 Sep 2009 23:00:00 +0100

I'll confess that in the morning I took notes on only one talk, but the afternoon got back into gear.The morning talk was by John Quackenbush over at Dana Farber Cancer Institute and covered a wide range of topics. Some was focused on various database approaches to tracking clinical samples but a lot of the talk was on microarrays. He described a new database his group has curated from the cancer microarray literature called GeneSigDb. He also described some work on inferring networks from such data & how it is very difficult to do with no prior knowledge, but with a little bit of network information entered in a lot of other interactions fall out which are known to be real. He also noted that if you look at the signatures collected in GeneSigDb, most human genes are in at least one -- sug...

CHI Next-Gen Conference, Day 1

Omics! Omics! — Sun, 20 Sep 2009 23:00:00 +0100

Interesting set of talks today. I never did explicitly check on the blogging policy, but given that the session chair kidded a speaker that I would be blogging her live, it wouldn't seem to be a problem. I would honor a ban (particularly since blogging is a bit hard to hide after the fact!), but quite a few folks were photographing slides despite an admonition not to (one person was clearly worried neither about being caught nor being courteous nor being clever; he had his flash on, which is clearly useless for projected images!).The morning talks ended up as just a trio. The best of the three was Robert Cook-Deegan's talk "So my genome costs less than my bike, what's the big deal?". He obviously has more expensive tastes in bicycles than I do -- or knows a really cheap genome shop! He cov...

Industry watching: The future of pharma is small?

business|bytes|genes|molecules — Sun, 20 Sep 2009 05:07:45 +0100

Anyone who reads bbgm knows that I am not a fan of bureaucratic big companies and the current pharma model. So this bit from a talk by Stefan Loren and reported by In the Pipeline piqued my interest Break up large pharma into therapeutic areas and build shared networks between distinct entities. Small organizations can operate far more efficiently in decision making about research directions – use the network to maintain manufacturing efficiencies. Small focused companies will revitalize the industry and offer opportunities for scientists coming out of academia. This is not dissimilar to the model I have thought about, although I do like the idea of an entity that orchestrates the network, since you do need direction. While there is some innovation going on in the biotech industry to...

Xalan part 3: BerkeleyDB+XSLT+pubmed

YOKOFAKUN — Sat, 19 Sep 2009 23:00:00 +0100

In my previous post I showed how to call mysql from the XALAN XSLT engine. In the current post, I'll show how a custom function for XALAN can return a new DOM/XML document that will be later used by the XSLT stylesheet: To get a source of data, i'm going to create a key-value database with berkeleyDB (Java Edition) storing strings (as the key) and XML document (as the value).The Database (Source: YOKOFAKUN)

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From FriendFeed to Nucleic Acids Research.

YOKOFAKUN — Sat, 19 Sep 2009 23:00:00 +0100

Deepak Singh and Andrew Su have both already posted on their blog about it: I'm proud to be the second author of a paper published in the "Database Issue" of Nucleic Acids Research.The Gene Wiki: community intelligence applied to human gene annotationJon W. Huss III, Pierre Lindenbaum, Michael Martone, Donabel Roberts, Angel Pizarro, Faramarz Valafar, John B. Hogenesch and Andrew I. Su Nucleic (Source: YOKOFAKUN)

Next-Generation Sequencing Conference, Providence RI, Day 0

Omics! Omics! — Sat, 19 Sep 2009 23:00:00 +0100

I'm going to be at Cambridge HealthTech's Next-Gen Sequencing Conference in exotic Providence RI for the next few days. I need to check on their blogging policy, though I guessing it is lenient. I probably won't try to write from within sessions but may try to skim some highlights at the end of the day (Source: Omics! Omics!)

Modern computing paradigms and the life sciences

business|bytes|genes|molecules — Sat, 19 Sep 2009 03:33:17 +0100

Over the next few months, I’ll be giving a bunch of talks about large scale data. I will be talking at Hadoop World about “Hadoop for Bioinformatics“, at a Cloud Computing for Hedge Funds and at Supercomputing. Thinking through what I want to cover at all these talks has my brain in overdrive these days. At the same time discussions with various people facing data-related challenged provides a reality check and reminds me that there is still a long way to go. The one concept that people need to start putting their head around is the relative location of compute and data. Many people still think along the “move data to the compute” paradigm. When our data sets were small, this was not a problem. As instruments provide more and more data, ever faster, that tends...

XSLT+MySQL=Append GeneOntology terms to TinySeq

YOKOFAKUN — Fri, 18 Sep 2009 23:00:00 +0100

In my previous post I showed how to add a new functions to the Xalan XSLT engine. In this post I'll show how to connect to a mysql server via Xalan. A TinySeq XML will be transformed with XALAN and a XSLT stylesheet querying the GeneOntology public mysql server. This stylesheet will search the GO terms for each sequence.The TinySeq SequencesThe sequences were downloaded from the NCBI. (Source: YOKOFAKUN)

Translating DNA with XALAN: A custom extension for XSLT

YOKOFAKUN — Thu, 17 Sep 2009 23:00:00 +0100

In this post, I'll show how I've create a custom extension for XALAN , a java-based XSLT engine. My favorite XSLT processor has always been xsltproc but I was missing the capacity to create a custom function to process the XML document: Here I show how a java class can be plugged to XALAN to translate a DNA sequence to a peptide.The Java classThe following class test.Translate translate a DNA to (Source: YOKOFAKUN)

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A genome too far?

Omics! Omics! — Wed, 16 Sep 2009 23:00:00 +0100

I've crossed fruit flies, tomatoes and yeast, but I would clearly draw the line before taking on this project.A genetic linkage map for the saltwater crocodile (Crocodylus porosus). BMC Genomics. 2009 Jul 29;10:339Actually, the Wikipedia entry for the species is a bit reassuring. Don't believe those ridiculous stories of 21 footers -- the largest measured individual was only 20 feet. And only one or two fatal attacks occur each year, and they make headlines in the papers. I'll sleep like a rock tonight! (Source: Omics! Omics!)

From Friendfeed to Nucleic Acids Research

business|bytes|genes|molecules — Wed, 16 Sep 2009 02:17:17 +0100

About 11 months ago, Andrew Su asked for some help on Friendfeed. He needed programming help related to the MediaWiki API and the Gene Wiki project. As you can see, one of the responses was from Pierre Lindenbaum, indicating he had sent Andrew an email. Today we see the results. Andrew has a nice blog post highlighting a paper published in Nucleic Acids Research. The paper, which will also be published in the 2010 Database issue, presents an update describing recent systematic improvements in the Gene Wiki. The paper, and blog post, are interesting in their own right, but my favorite bit is the end of the blog post I’d also be remiss if I didn’t also note the critical role online collaboration played in this effort. Of the seven coauthors on this paper, two I’ve met only...

Flickr slideshow in WordPress.com using Vodpod

What You're Doing Is Rather Desperate — Tue, 15 Sep 2009 01:33:12 +0100

Not work-related but fun: How to embed a flickr slideshow in WordPress.com using Vodpod. Vodpod is new to me and quite amazing; I imagine this method will allow you to post any Flash with embed code as a video. As an example, a slideshow of Lane Cove images from my Flickr account. posted with vodpod Posted in this blog, web resources Tagged: flickr, gallery, photography, slideshow, vodpod (Source: What You're Doing Is Rather Desperate)

Industrial Protein Production: Further Thoughts

Omics! Omics! — Mon, 14 Sep 2009 23:00:00 +0100

A question raised by a commenter on yesterday's piece about codon optimization is how critical is this for the typical molecular biologist? I think for the typical bench biologist who is expressing small numbers of distinct proteins each year, perhaps the answer is "more critical than you think, but not project threatening". That is, if you are expressing few proteins only rarely will you encounter show-stopping expression problems. That said, with enough molecular biologists expressing enough proteins, some of them will have awful problems expressing some protein of critical import.But, consider another situation: the high-throughput protein production lab. These can be found in many contexts. Perhaps the proteins are in a structural proteomics pipeline or similar large scale structure de...

Codon Optimization is Not Bunk?

Omics! Omics! — Sun, 13 Sep 2009 23:00:00 +0100

In a previous post I asked "Is Codon Optimization Bunk?", reflecting on a paper which showed that the typical rules for codon optimization appeared not to be highly predictive of the expression of GFP constructs. A paper released in PLoS One sheds new light on this question.A quick review. To the first approximation, the genetic code consists of 3 nucleotide units called codon; there are 64 possible codons. Twenty amino acids plus stop are specified by these codons (again, 1st approximation). So, either a lot of codons are never used or at least some codons mean the same thing. In the coding system used by the vast majority of organisms, two amino acids are encoded with a single codon whereas all the others have 2, 3, 4 or 6 codons apiece (and stop gets 3). For amino acids with 2, 3 or 4 c...

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The web as platform: Search as UI

business|bytes|genes|molecules — Sun, 13 Sep 2009 22:05:37 +0100

In a recent episode of the Stack Overflow Podcast (I believe #66) Jeff and Joel talked about how in the early stages of designing Stack Overflow they made the decision that their UI would be Google. In other words, the majority of their traffic would come from search and they designed the site accordingly, and today, 90% or so of their traffic, which is quite substantial, comes from Google. Most of us probably view Stack Overflow as a resource. In other words, we are passive consumers of the body of knowledge that is accumulating there. In the sciences, there are a number of resources that many of us use, some almost daily. I wonder, if anyone has made that design decision. I am not an active practitioner, but most still seem to work under the assumption that the entry point to the site w...

The purpose behind research

business|bytes|genes|molecules — Sat, 12 Sep 2009 15:49:46 +0100

And no, I’m not trying to make that case that academic labs should make drugs. If they want to try, then come on down. If they don’t, that’s fine, too – there’s a lot of important research to be done in the world that has no immediate practical application. But this sort of paper that I’ve written about today seems to miss both of these boats simultaneously: it isn’t likely to produce a drug, and it doesn’t seem to be addressing any other pressing needs that I can see, either That’s from a blog post by Derek Lowe where he discusses a paper in J. Med. Chem.. His beef with the paper, which is scientifically sound, is that it doesn’t really do anything useful. One of the points made by others is that academic work doesn’t have ...

When “good enough” just doesn’t cut it

business|bytes|genes|molecules — Sat, 12 Sep 2009 05:06:57 +0100

My father’s younger brother once was a decently ranked squash player back in India. As the story goes, someone once asked him why he didn’t continue with squash and try to get to #1. His response was, and I paraphrase from my memory, “It’s not that hard to get from #100 to #10, but to get to #1 from #10 is very hard”. In other words, he was happy being good enough. That’s true across the board in many fields for many people. On the flip side you have people like Michael Jordan, who was never satisfied with being anything other than the best. We all have to make our choices in life, whether to be good enough, or be the best, or at least make the effort to be the best. There is nothing wrong with being good enough in mos...

Iterative software development

business|bytes|genes|molecules — Fri, 11 Sep 2009 03:37:12 +0100

Image via Wikipedia Most of my professional life, I’ve worked in organizations with formal, long, software development processes, although in some there have been attempts at adopting agile practices, but not necessarily iterative, frequent software releases. It was pretty clear to me back then that the marketing/tech requirements driven development cycle with projects that lasted years at time didn’t cut it. My experiences, mostly indirectly, of the modern web development process has only confirmed that opinion Greg Linden has an article in Communications of the ACM where he talks about how frequent releases change software engineering. He points out Frequent releases are desirable because of the changes it forces in software engineering. It discourages risky, expensive, la...

RESTful architectures and chemical tracking

business|bytes|genes|molecules — Wed, 09 Sep 2009 04:35:15 +0100

I am a great fan of Rich Apodaca’s work for various reasons. At the top of the list is his affinity for RESTful architectures and services. He is currently on Part 4 of a series on building a RESTful chemical tracking system. This series is interesting at multiple levels. A tracking system is something any scientific organization requires, but struggles with given the fluidity inherent in any scientific discovery process. One of the core principles that I first started appreciating when we built our first simple data munging pipelines, grokked when I first played with pipeline pilot and really understood (or so I think) after I moved to AWS, is the principle of loose coupling. The REST architectural style is ideally suited to build systems from loosely coupled components and services...

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A Blight's Genome

Omics! Omics! — Tue, 08 Sep 2009 23:00:00 +0100

Normally this time of year I would be watching the weather forecasts checking for the dreaded early frost which slays tomato plants, often followed by weeks of mild weather that could have permitted further growth. Alas, this year that will clearly not be the case. A wet growing season and commercial stock contaminated with spores has led to an epidemic of late blight, and my tomato plants (as shown, with the night photography accentuating the horror) are being slaughtered. This weekend I'll clear the whole mess out & for the next few years plant somewhere else. Late blight is particularly horrid as it attacks both foliage and fruits -- many tomato diseases simply kill the foliage. What looked like promising green tomatoes a week ago are now disgusting brown blobs. Late blight is caused by...

Keyboard, Command Line, And Text Files

Bioinformatics Zen — Tue, 08 Sep 2009 23:00:00 +0100

Here I’m outlining an approach to bioinformatics focusing on using three tools: the keyboard to enter commands, the wide range of functions available at the command line, and storing data in easily searched and manipulated text files. The combination of these three can make bioinformatics analysis faster than using graphical user interfaces (GUIs) because typing into the command line is faster than clicking buttons and selecting menus with a mouse. A series text commands is also easier to reproduce and automate than remembering a sequence of GUI commands. The Keyboard The best reason for using the keyboard is that it’s faster to type a command compared with doing the same thing with a mouse and GUI. If you’re using the keyboard to write code the more you can also use th...

Next-generation Physical Maps III: HAPPy Maps

Omics! Omics! — Mon, 07 Sep 2009 23:00:00 +0100

In conclusion, HAPPy mapping comes close to my personal ideal of a purely in vitro mapping system which looks like a clever means of preparing next-gen libraries. The minimum and maximum distances resolvable are about 10-fold apart, so more than one set of HAPPy libraries is likely to be desirable for an organism. Typically this is two sizes, since the maximum fragment size is around 1Mb (and may be smaller from organisms with difficult to extract DNA). A key problem to resolve is that HAPPy pools contain single digit picograms of DNA. Amplification is a potential solution but may introduce bias; clever library preparation (or screening) may be another approach. An open problem is the best depth of coverage of the multiplexed HAPPy next-gen libraries. HAPPy can be used both for physical ma...

Intergalactic networking

business|bytes|genes|molecules — Mon, 07 Sep 2009 02:01:02 +0100

If all goes well Dr Cerf says that by September there should be three nodes on the interplanetary network—including Earth via economist.com Just reading that sounds cool Posted via web from Flashing Neurons!!! (Source: business|bytes|genes|molecules)

Farewell to Summer

Omics! Omics! — Sun, 06 Sep 2009 23:00:00 +0100

The autumnal equinox is still a few weeks away, but today marks the traditional end of the summer vacation season. How does a genomics geek dress for the beach? I present the KR's Career Collection, with sun protection from Infinity, a lovely Codon Devices beach bag and a towel from Millennium, with gorgeous Crane's Beach in Ipswich lending the background. This collection was more spontaneous than planned, so I didn't dig for one of my remaining Harvard T-shirts or the Centocor frisbee that's stashed somewhere.I haven't yet worked for an Iguana Pharmaceuticals, so perhaps that is a portent of my future. And while I am quite happy in my job, if someone were to start a bioinformatics shop on St. Thomas, I would have to listen to the pitch... (Source: Omics! Omics!)

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Tagging, context and … data

business|bytes|genes|molecules — Sat, 05 Sep 2009 03:55:53 +0100

Image via Wikipedia I subscribe to a mailing list of foo camp alumni, and there was a question around tagging. About systems where tags are added by the creator vs. systems where the tags are created by the consumer. Joshua Shachter pointed out that delicious’ core paradigm is to have someone else, not the content creator do the tagging. Got me thinking about intent and something a former colleague always talking about; “your point of view”. The creators intent and the consumers interpretation or context may not be the same. So the tags you might use might be different from those the content creator, or some other consumer, chooses. Not just because of a different tag convention, but because you have a different context from the creator or other consumer. You can exten...

Protein Society Symposium Report

Trapped in the USA — Fri, 04 Sep 2009 17:12:29 +0100

I went to my first large conference in several years, a few months ago. It was the Protein Society Symposium held in Boston. It’s very important that a conference is held in a decent city like Boston. That means you can escape from the conference hall, have some nice food, and merge with normal people between sessions. I went three times to this amazing French bistro several blocks from the conference center at the Mariott hotel. My tongue was every bit as stimulated as my brain. Just to state the bleeding obvious, conferences are places where you can learn about what’s happening in the field in a fun and efficient way. It points out the fact that publishing a paper is only the beginning of a piece of work. The long process of selling your work to other researchers has now be...

My Notes about Bowtie

YOKOFAKUN — Thu, 03 Sep 2009 23:00:00 +0100

Image via wikipediaBowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie is open source http://bowtie.cbcb.umd.edu (Langmead B, & al. "Ultrafast and memory-efficient (Source: YOKOFAKUN)

Building a naive Interactome Database with Hibernate.

YOKOFAKUN — Wed, 02 Sep 2009 23:00:00 +0100

This is my notebook for building a naive database of protein-protein interactions with Hibernate (a java object/relational persistence and query service).Files and Directories./project./project/lib./project/src./project/src/hibernate.cfg.xml./project/src/org./project/src/org/lindenb./project/src/org/lindenb/hbn01./project/src/org/lindenb/hbn01/Journal.java./project/src/org/lindenb/hbn01/ (Source: YOKOFAKUN)

Physical Maps II: Reading the signposts

Omics! Omics! — Wed, 02 Sep 2009 23:00:00 +0100

ConclusionsCould any of these next-gen approaches compete with direct hybridization of labeled pools to microarrays? Given the wide (10X) swing in costs I estimated above, it's hard to be sure but I am wondering if perhaps for many mapping approaches microarray hybridization may have some longevity as the landmark reading method. However, where either the economics become very different or next-gen can extract additional information, that is where sequencing may have an edge. This is a useful way to focus thoughts as we proceed through the different mapping approaches. (Source: Omics! Omics!)

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Generating a C Pull Parser for dbSNP with XSLT

YOKOFAKUN — Wed, 02 Sep 2009 23:00:00 +0100

I've used the XSD schema describing dbSNP to generate a C "Pull parser" reading the content of the dbSNP XML files. To transform the schema into a C code I wrote the following XSLT stylesheet:http://code.google.com/p/lindenb/(...)/xsd2libxml.xsl. This stylesheet was specifically developed for dbSNP so it might not handle a more complicated schema (for example a schema that would use (Source: YOKOFAKUN)

Speculative Execution in Hadoop

business|bytes|genes|molecules — Wed, 02 Sep 2009 22:34:49 +0100

Image via CrunchBase Disclaimer: Newbie post ahead One of the more fascinating aspects of Hadoop is speculative execution. In many bioinformatics setups, there is some logic written, which examines your available resources, especially if you are using Sun Grid Engine, LSF, etc, the size of your input and chunks up your data appropriately and makes that data available to various nodes for computing on that chunk. In most of the implementations that I am aware of, this is done using a shared filesystem, often an NFS server. More recently, cluster file systems have become more popular for their improved availability characteristics. But in most pipelines job completion is analyzed post-job and you re-run any failed job. When you have a few 100 GB’s of data and a few 100 jobs that don...

Komplete 6

business|bytes|genes|molecules — Wed, 02 Sep 2009 06:50:18 +0100

Posted via web from Flashing Neurons!!! (Source: business|bytes|genes|molecules)

Fix Kile for Ubuntu 9.04

What You're Doing Is Rather Desperate — Tue, 01 Sep 2009 08:36:48 +0100

Ubuntu/jaunty rocks, on the whole. However, to prove that newer does not always equal better, they threw in a couple of shockers. The first is the upgrade from the excellent Amarok 1.4 to the completely-broken 2.0. Head here to repair the damage. Kile is by far my favourite LaTeX editor and suffered, though not as badly, in the upgrade from 2.0 to 2.1. Reports of various problems litter the web; in my case I see broken toolbar buttons that do nothing when clicked. This fix is much simpler. Just “sudo apt-get remove kile”, scroll to the bottom of the intrepid package page, choose your architecture, download the deb file and “sudo dpkg -i kile_2.0.1-1ubuntu1_i386.deb”. I had no dependency problems and it works just fine. Finally – open up Synaptic, find kile and...

Using the BerkeleyDB Direct Persistence Layer: my notebook

YOKOFAKUN — Mon, 31 Aug 2009 23:00:00 +0100

In this post I show how I've used the Java BerkeleyDB API / Direct Persistence Layer to store a set of individuals in a BerkeleyDB database.In a prevous post, I've shown how to use the BerkeleyDB API, a key/value database, to store some RDF statements. In this example, a set of TupleBinding was created to read and write the java Objects from/to the BerkeleyDB database.Via Oracle: The Direct (Source: YOKOFAKUN)

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First steps with BerkeleyDB-XML. My notebook.

YOKOFAKUN — Mon, 31 Aug 2009 23:00:00 +0100

Berkeley DB XML is an embeddable XML database engine that provides support for XQuery access to documents stored in containers and indexed based on their content. Oracle Berkeley DB XML is built on top of Oracle Berkeley DB. Berkeley DB XML is available at : http://www.oracle.com/database/berkeley-db/xml/index.html. The distribution comes with a shell command.pierre@linux-zfgk:.../dbxml-2.4.16> (Source: YOKOFAKUN)

Physical Maps: Part I of a series

Omics! Omics! — Mon, 31 Aug 2009 23:00:00 +0100

A recent review/opinion paper I saw has led me to attempt to write something substantial about a topic I've generally given short shrift to: physical mapping. Given that fact, I won't be surprised if some of what I say will lead to corrections, which are always welcome, as with the recent bits on genome assembly which I posted here.A physical map is an ordering of markers along a stretch of DNA, often with some concept of distance between the markers. The most useful physical maps link these markers to unambiguous islands of sequence. Common examples of physical maps include restriction maps (where the landmarks are sites for one or more restriction enzymes) and cytogenetic maps (where the sequence landmarks are placed in relation to the pattern of bands visible in stained DNA).When I was ...

Industry watching: Is there an equivalent of a github for Biobanks?

business|bytes|genes|molecules — Sun, 30 Aug 2009 21:51:29 +0100

Image by Getty Images via Daylife When _why disappeared from the web, there was an effort to come up with a distributed _why, by hosting his works on github and similar repositories. There are other examples of open source projects continuing when the original developer moves on to other things. The whole idea of distributed content, with each person acting as their own hub came up when Facebook acquired Friendfeed. I couldn’t held draw an analogy when I read about DeCODE looking for someone to take over their biobank due to their financial troubles. From the link in Science Iceland’s deCODE Genetics announced earlier this month that it has enough cash to keep going for only a few more weeks. The genomics company’s troubles are raising questions abo...

Books 2009

Blind.Scientist — Sun, 30 Aug 2009 17:36:00 +0100

List of books read in 2009 – updated regularly 1 – The Max (Hard Case Crime) 2 – Gentlemen (33 1/3) 3 – Celine Dion’s Let’s Talk About Love: A Journey to the End of Taste (33 1/3) 4 – Musicophilia: Tales of Music and the Brain, Revised and Expanded Edition 5 – Born Standing Up: A Comic’s Life 6 – The Dogs of Riga 7 – Hold Tight 8 – Mystic River 9 – The White Lioness 10 – Long Lost 11 – Echo Burning (Jack Reacher) 12 – And Then There Were None 13 – Fake I.D. (Hard Case Crime) 14 – The Shock Doctrine 15 – Cocaine Nights 16 – Cocaine Nights 17 – The Man in the High Castle Related articles by Zemanta How To Make 2009 Your Best Blogging Year (Source: Blind.Scientist)

Will the commercial research lab ever make a comeback?

business|bytes|genes|molecules — Sat, 29 Aug 2009 06:28:46 +0100

Image via Wikipedia I have written about Bell Labs in the past, mostly wishing that something like Bell Labs still existed. A recent article in BusinessWeek wonders aloud how basic research can repair the American model as it wonders where Bell Labs disappeared to. From the article The U.S. scientific innovation infrastructure has historically consisted of a loose public-private partnership that included legendary institutions such as Bell Labs, RCA Labs, Xerox PARC, the research operations of IBM, DARPA, NASA, and others. In each of these organizations, programs with clear commercial potential were supported alongside efforts at “pure” research, with the two streams often feeding one another. With abundant corporate and venture-capital funding for eventual commercializatio...

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FriendFeed Life Scientists: 14-day summary

What You're Doing Is Rather Desperate — Fri, 28 Aug 2009 07:03:56 +0100

Since I haven’t posted for 14 days, what better (and lazier) way to post something than to surf over to a 14-day summary from the Life Scientists Group and link to the top ten items! Review process files in the EMBO Journal – but why only for “the majority of papers”? How XML threatens Big Data. Or not. How JSON might be an alternative – or not. Solve any computer problem – with this classic XKCD flowchart. Science reviews the revolution in ’strategic scientific reading’ – are they way behind the curve, or providing a useful summary for the uninitiated? Best practice in microbial genome annotation – spirited discussion on the nature of best bioinformatics practice. FriendFeed Life Scientists user survey – no further word on...

Creating opportunities for others

business|bytes|genes|molecules — Fri, 28 Aug 2009 04:39:32 +0100

Image via Wikipedia As mentioned in a prior blog post, Kevin Kelly is reissuing an older book in blog form. In that post I was fascinated by his thoughts around plentitude, networks and opportunities. In a more recent thoughts around plentitude he talks about maximizing opportunities for others. You want to entice others to create services centered around the customer attention you have won This reminds me of Mark Shuttleworth at Oscon 2008, where he talked about architecting for innovation, albeit in simpler terms. That simplicity resonated with me. As scientists, our goal is to understand the world around us and put that knowledge to use. Let’s say you are a well known scientist, or the developer of a well known scientific software package. It behooves you to try to make that...

Haven’t we been hearing this story for a while?

business|bytes|genes|molecules — Thu, 27 Aug 2009 14:33:33 +0100

At the Hot Chips conference there was a lot of discussion around the need for a killer app for multicore. First, I hate the phrase "killer app". Sounds like a marketing cliche in the world of engineering, but looking past that, I remember writing a blog post from a conference I attended in 2006 where Jack Dongarra talked about the problem being the software. Unfortunately more than three years later, we still seem to be talking about the same things. I am with Dan Reed. Where are the abstractions? Until this, this will remain a very niche space whether we like it or not. Posted via email from Flashing Neurons!!! (Source: business|bytes|genes|molecules)

What happened to the eighth dog hair style?

Omics! Omics! — Wed, 26 Aug 2009 23:00:00 +0100

For the second time this summer Science has another step forward in understanding the genetics of dog breeds. Previously it was the identification of a post-wolf event which led to short-legged dogs (which includes my faithful assistant); this time it is that a large (600+ dogs) genetic study has shown that vast majority of dog coat types can be explained by just three genes (you'll need a Science subscription to access these).Figure 3 of the paper makes the point quite graphically. The three genes found in the study are FGF5, RSPO2 and KRT71. FGF5 is a secreted growth factor previously implicated in hair development, RSPO2 is a regulator of the Wnt pathway known to be important in hair follicles and KRT71 is a keratin which causes a curly phenotype when mutated in mice. So even though the...

Switched the commenting over to Disqus

Trapped in the USA — Wed, 26 Aug 2009 18:40:30 +0100

I run this blog on Textpattern, a nice clean Content Management System. I like the way they do things, their aesthetic gives me joy, and I grok their programming model. However, their commenting system is sorely lacking. I have experienced constant pain with dealing with comments of Textpattern. I imagine this is because Textpattern is a small operation (at least compared to Wordpress or Movable Type) and they don’t devote a lot of resources to comments. For a while, I was just sucking up and taking the punches from the hordes of comment spam. Then my comp-sci life-line Mark Reid told me about Disqus, something that I had probably used but been oblivious to. After seeing it in glorious action, I’ve finally decided to switch the commenting on this blog to Disqus. (Source: Tr...

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The Lumpy Shape of Science Publishing in the not too Distant Future

Trapped in the USA — Wed, 26 Aug 2009 18:09:07 +0100

I recently attended my very first un-conference, Sci Bar Camp, held in the pleasant genteel buorgeoisie neighborhood of Palo Alto, home of Stanford and Google. The etymology of “Sci Bar Camp” is a tad obscure. “Sci Bar” is the cheapskate open-invite counterpart to the invite-only “Sci Foo”, which is funded by Google and O’Reily. The “Foo” in “Sci Foo” allegedly comes from Friends-Of-O’Reily. The “Bar” in “Sci Bar” is a pun from the traditional programming place-holder function name “def foo-bar()”. But I digress. I’d read about these web 2.0 unconferences in blogs, and the reality was as fun as those self-congratulory blog posts make it out to be, probably because the attende...

Coast to Coast Bio hits a quarter century

business|bytes|genes|molecules — Wed, 26 Aug 2009 07:02:34 +0100

When Hari and I started recording Coast to Coast Bio, we were not sure we'd make it to episode 10. While we've never been able to keep up the regular schedule we hoped to given our schedules, we've now reached Episode 25 and no end in sight. We even recorded one interview, have others in the works, and in general have managed to keep the balance of geekdom and science that we set out to keep. Thank you to all of you who listen and provide feedback. If we ever reach 50, we'll just have to figure out how to celebrate. Posted via email from Flashing Neurons!!! (Source: business|bytes|genes|molecules)

The quirks that make drug development so hard

business|bytes|genes|molecules — Tue, 25 Aug 2009 23:12:37 +0100

Image via Wikipedia People outside the pharma industry rarely realize how difficult a task the drug discovery process is. But perhaps, even among scientists, there is a significant lack of knowledge of the complexities of the drug development process. Part of the reason is that this process happens behind the closed walls of pharma and is rarely published, but it’s also not the sexy part of bringing a therapeutic to market. Derek Lowe’s post on a patent dispute between Novartis and the Government of India speaks to this complexity (in this case polymorphs). The comments are very interesting too as he asks for examples of drugs where getting a particular polymorph was essential to getting proper efficacy. The whole process of bringing a drug to life involves everything from b...

Putting the cart before the horse

business|bytes|genes|molecules — Mon, 24 Aug 2009 23:19:39 +0100

The industry expects processors with 64 cores or more will arrive by 2015, forcing the need for parallel software, said David Patterson of the Berkeley Parallel Lab. Although researchers have failed to create a useful parallel programming model in the past, he was upbeat that this time there is broad industry focus on solving the problem. – Source: EE Times That lack of a programming model is already a major issue. Where is the equivalent of a Hadoop for multicore? I’m not the only one who’s wondered that. Or is it just a problem that’s too hard to solve Posted via email from Flashing Neurons!!! (Source: business|bytes|genes|molecules)

Is XML bad for big data?

business|bytes|genes|molecules — Sun, 23 Aug 2009 07:31:58 +0100

Image via Wikipedia Mike Driscoll continues his attack against XML for Big Data. He points out three reasons why XML and Big Data are strange bedfellows. XML spawns data bureacracy, which is why JSON exists Size matters and XML is not exactly concise XML is complex and has a cost One of my problems with XML, and this is from someone who loves markup, has always been that it is used in ways it was never intended to be, or at least I hope not. It is a representational format for documents, but ended up becoming the format for all kinds of data standards and worst of all, data transport. He proposes some rules Don’t invent new formats. I think Hari will wholeheartedly agree with this one. This, in particular, is the bane of science. We invent new formats all the time and sometime...

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Technology, disruption and making fortunes

business|bytes|genes|molecules — Sun, 23 Aug 2009 07:10:04 +0100

Image via Wikipedia On Hacker News, I found a link to a rather interesting article in Frontier Economy. In The Mediocre Returns of Extraordinary Technologies the authors note that technologies like the printing press, while extremely disruptive, have not often resulted in fortunes for those involved in the industry, at least not directly. Many reasons are provided, from the short lifecycle of disruptive to mundane, the patent system, etc. But the primary reason, at least in that article, is that prices are driven by cost, not utility. That point, and the general thrust of the article got me thinking. Is monetary success a viable, or even appropriate yardstick to measure, or try for, the success of a technology. When I think of disruptive in my lifetime, I think of the personal computer,...

Genomes that begin with P: A follow-up

Omics! Omics! — Sat, 22 Aug 2009 23:00:00 +0100

I'm really grateful for the comments on my bit about genome assembly, two of whom (one of which is a leading author in genome assembly) pointed out what I (the armchair genomicist) failed to cover and even better getting some first-hand information from the scientist who assembled the published platypus genome. Getting a better education in practical genomics with tuition being a bit of public embarassment; that's a sweet deal.The impact of diploidy was something I'll confess hadn't crossed my mind; I think the topic of different assembly algorithms did briefly flit through. As a bioinformatician, I'm a bit red-faced to have ignored the impact of better algorithms. It is a bit surprising to learn that there is still a bit of to assembly.I also wanted to throw in something else which cross...

testing feed

business|bytes|genes|molecules — Sat, 22 Aug 2009 05:30:34 +0100

(Source: business|bytes|genes|molecules)

Synthetic Biology and getting ahead of ourselves

business|bytes|genes|molecules — Sat, 22 Aug 2009 02:50:53 +0100

Image via Wikipedia I am as big a supporter and believer in the importance of genetic engineering and synthetic biology, and even more so of the importance, potential and near term availability of personal sequencing, but sometimes I think we get ahead of ourselves. …Genetic engineering is now at a point where computer science was around the mid-eighties. The early PCs were limited as to purpose and network. In two and a half decades, the computer has led us into a digial world in which every aspect of lives has been affected. According to Moore’s Law, the performance of computers doubles every 18 months. Genetic engineering is following a similar growth. That blurb is from an article in Edge about The Walkman of Genetic Engineering. The computer is a terrible analogy. Even...

Play the flu video game

VBRC Blog — Fri, 21 Aug 2009 23:58:00 +0100

Play a video game that simulates a flu pandemic at http://www.thegreatflu.com. Watch the red dots spread across the map as you try to minimize the spread by shutting down airports and distributing face masks. The game was developed by Prof. Dr. Ab Osterhaus and the virology department at the Erasmus MC in Rotterdam (see http://www.erasmusmc.nl/overerasmusmc/newsarticles/griepgame_online?lang...). (Source: VBRC Blog)

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PLoS Currents - rapid dissemination of knowledge

Public Rambling — Fri, 21 Aug 2009 20:50:00 +0100

PLoS unveiled recently an initiative they call PLoS Currents. It is an experiment in rapid dissemination of research built on top of Google Knol. Essentially, a community of people dedicated to a specific topic, could use PLoS Currents to describe their ongoing work before it is submitted to a peer review journal. They have focused their initial efforts to Influenza research where the speed of dissemination of information might be crucial. The content of this PLoS Currents: Influenza is not peer reviewed but is moderated by a panel of scientists that will strive to keep the content on topic. There is a FAQ explaining in more detail the initiative. These articles are archived, citable, they can be revised and they should not be considered as peer-reviewed...

Wave test

Blind.Scientist — Fri, 21 Aug 2009 14:19:51 +0100

Let’s see if it works. function initialize() { var wavePanel = new WavePanel("http://wave.google.com/a/wavesandbox.com/"); wavePanel.loadWave("wavesandbox.com!w+RqxqUECK%B"); wavePanel.init(document.getElementById('waveframe')); } (Source: Blind.Scientist)

Data is not document centric

business|bytes|genes|molecules — Fri, 21 Aug 2009 06:25:05 +0100

In recent days I have talked a lot about Big Data and data streams on the web, especially for science. The good news is that there is a lot of good material for inspiration out there these days. The latest source of inspiration is a blog post by Mike Driscoll at Dataspora. In the rise of the data web Mike writes that through our various frameworks we have industrialized the creation of hypertext (as an aside I am playing with Jekyll these days and it rocks) as well as the collection of data, making human data entry much less common. He also points out that while the web we see will be dominated by documents, the web we can't see that is surging with data. This is the data web that fascinates me and many others, a web of data streams which we can orchestrate, slice and dice ...

Open Science meet Open Source

business|bytes|genes|molecules — Thu, 20 Aug 2009 00:59:09 +0100

Gavin Baker at Open Access News, channeling Vivien Marx at Bioinform, writes about plans by PLoS to launch a software section for PLoS Computational Biology and PLoS One, which will include a function for authors to deposit software. The same article also talks about efforts to release large data sets (in context). These are laudable moves. Hopefully those planning out the details will look at various, existing code repositories and data repositories and make sure that they don't work before reinventing the wheel. Posted via email from Flashing Neurons!!! (Source: business|bytes|genes|molecules)

Open Science meet Open Source

business|bytes|genes|molecules — Thu, 20 Aug 2009 00:59:09 +0100

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DNA Origami and lithography

business|bytes|genes|molecules — Thu, 20 Aug 2009 00:17:37 +0100

Artificial DNA nanostructures1, 2 show promise for the organization of functional materials3, 4 to create nanoelectronic5 or nano-optical devices. DNA origami, in which a long single strand of DNA is folded into a shape using shorter 'staple strands'6, can display 6-nm-resolution patterns of binding sites, in principle allowing complex arrangements of carbon nanotubes, silicon nanowires, or quantum dots. However, DNA origami are synthesized in solution and uncontrolled deposition results in random arrangements; this makes it difficult to measure the properties of attached nanodevices or to integrate them with conventionally fabricated microcircuitry. Here we describe the use of electron-beam lithography and dry oxidative etching to create DNA origami-shaped binding sites on technol...

DNA Origami and lithography

business|bytes|genes|molecules — Thu, 20 Aug 2009 00:17:37 +0100

Streams in science are not that far away

business|bytes|genes|molecules — Wed, 19 Aug 2009 07:33:46 +0100

Over the years, I’ve written about the web as a connected entity, with nodes notifying other nodes of an event or action. At various times this has been called the “just in time” web and more recently, in a narrower context, the distributed self. However, it is only in the last several months that I have come to appreciate the inefficiencies of polling and the potential of an event-based, notifications oriented web architecture, and I do believe as we stream more and more scientific data, such architectures are only going to get more common in the sciences, or at least I hope they do. In a recent blog post about Smart Clients, Ilya Grigorik writes As more and more browsers start adopting HTML 5 features I’m hoping to see WebSockets become a reality within the next ...

Rajarshi Guha on Crunching Molecules and Numbers in R

business|bytes|genes|molecules — Wed, 19 Aug 2009 07:24:29 +0100

http://www.slideshare.net/rguha/crunching-molecules-and-numbers-in-r Rajarshi talks about how R can be a powerful tool for cheminformatics and discusses some of the pros and cons. Is this the first Cheminformatics talk at an ACS National Meeting to bring up Hadoop? Probably not, but good to see it there (slide 35). Saptarshi Guha's RHIPE also gets a mention Related articles by Zemanta Adding Hbase to Our Cluster (travishegner.com) Amazon teaches cloud to speak Pig Latin (theregister.co.uk) Posted via email from Flashing Neurons!!! (Source: business|bytes|genes|molecules)

Why do genome assemblies go bad?

Omics! Omics! — Tue, 18 Aug 2009 23:00:00 +0100

Question to ponder: given a genome assembly, how much can we ascertain as to why it didn't fully assemble.I've gotten to thinking about this after reviewing the platypus genome paper. Yeah, it's a year plus old so I'm a bit behind the times, but it's relevant to a grand series of entries that I hope to launch in the very near future. An opinion piece by Stephen J. O'Brien and colleagues in Genome Research (one catalyst for the grand series) argues that the platypus sequence assembly is far less than what is needed to understand the evolution of this curious creature and that the effort was severely hobbled by the lack of a radiation hybrid (or equivalent map).First some basic statistics. The sequencing was nearly entirely Sanger sequencing (a tiny smidgeon of 454 reads were incorporated) y...

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The web as platform: The distributed self

business|bytes|genes|molecules — Mon, 17 Aug 2009 02:02:30 +0100

Been thinking about a bunch about content creation and the web lately (sounds like Cameron Neylon and Google Wave, but not quite as ambitious). Part of it is “new shiny toy syndrome”, but also from the way the web is evolving and my own thoughts around distributed content and presence on the web. Some of those early thoughts around online presence are were written up when I first investigated posterous but some of these have been in my head for a while and recent posts by Steve Rubel and others and discussions on This Week in Google have brought some more nuance to those thoughts, although they’re still incomplete. I’ve always been a proponent of distributed content, where the destination is not as important as the specific object, and the web wit...

A Standard Set of Test Genomes

Omics! Omics! — Sun, 16 Aug 2009 23:00:00 +0100

I was away on vacation, enjoying an Internet-free existence on a tropical isle, when the brouhaha over Stephen Quake's genome sequencing paper blew up. It does appear that the paper used some very sloppy accounting & comparisons for its cost analysis, but some of the reaction to this has been a bit over-the-top (in particular, the needless throwing around of inflammatory personal descriptions).But, it did get me thinking. The real value of this paper is demonstrating the strengths & weaknesses (and specialized clever algorithmics) of Helicos' sequencing instrument. Helicos has struggled to claw their way into the marketplace, but has gotten a few instruments placed. The machine has some interesting properties (more on this later this week) and I'd love to get to try one out, but alas there...

Admin update August 15th, 2009

business|bytes|genes|molecules — Sat, 15 Aug 2009 07:00:35 +0100

I had talked about Posterous before and how I was planning to use it. My experiment is right now on phase 2. I have removed bbgm from my Posterous list, essentially using it more like Tumblr on steroids and making full use of the email features. In addition to using the site as a scrapbook (like I’ve used Tumblr to this point), I am also using it to add pictures and video to various sites. In addition, it’s always a good place to write small notes, etc. I have retired my Tumblr tumblelog (at least for now). A second administrative change is opening up deepaksingh.net, or at least part of it. You can now create accounts for the site, although for most pages permissions are still read-only. If you try and log in you can now create an account, which you can use to edit any pages u...

Wholesale data

business|bytes|genes|molecules — Sat, 15 Aug 2009 01:15:21 +0100

There is a fascinating post on the Sunlight Labs blog arguing that the Government should be a wholesaler of data. They make some very compelling arguments, and I pretty much agree with them. If I had half their eloquence, I would have made a similar argument about scientific data some time ago. But I am going to shamelessly take the ideas in the Sunlight post. Leaving aside some of the questions around what constitutes raw data, many of us have argued that raw scientific data should be made available so that different scientists can look at the data with their own lens and either verify claims, uncover new scientific findings, or provide interfaces that allow others to query the data in all kinds of ways. While we do have ftp servers for genomic data at organizations like the NCBI, it is c...

Plentitude and networks

business|bytes|genes|molecules — Fri, 14 Aug 2009 06:48:11 +0100

Cover of New Rules for the New Economy I don’t always agree with Kevin Kelly, but he is a wonderful writer, and when I do agree with him, it’s usually a very strong agreement. Kevin is re-issuing his 1988 book New Rules for the New Economy in blog form. In a recent post from that he writes about Plentitude. He says In a network, the more opportunities that are taken, the faster new opportunities arise. I find this train of thought fascinating. We are all nodes in a network, a network of scientists and programmers. As a network, do we take opportunities? Does not appear to be the case. Why is that? I think when we do it will be quite fascinating to watch the consequences. (Source: business|bytes|genes|molecules)

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Improvements to the reference management workflow

What You're Doing Is Rather Desperate — Fri, 14 Aug 2009 00:30:22 +0100

I use Google Reader to subscribe to the RSS feeds from journals that interest me (see my public page). I’m also a big fan of CiteULike as a reference management system. For a long time I’ve thought: it would be great if GReader handled journal articles more efficiently. Rather than going from link in GReader -> article at journal -> CiteULike bookmark -> back to GReader, how about “post directly from GReader?” With Google Reader’s new send-to feature, you can do just that. See this forum post for the details. Also, take a look at this how-to for a quick way to post to CiteULike by entering a PubMed PMID, DOI or ISBN identifier in the address bar. Posted in bibliography, research diary, web resources (Source: What You're Doing Is Rather Desperate)

FriendFeed, Facebook and scientific communities

business|bytes|genes|molecules — Wed, 12 Aug 2009 05:48:30 +0100

Yesterday, after a four hour flight and other activites, I found myself opening up Friendfeed on my iPhone and the entire front page was devoted to one topic, the acquisition of my favorite hangout by Facebook, not a place I consider a hangout (although I use it quite a bit to stay in touch with friends and family). There was, understandably, a lot of disappointment and a significant degree of concern among the user base, some to an extreme. I continue to be replaced by the knee jerk reactions of seemingly intelligent people in social networks (in both directions). The scientific community on Friendfeed on the other hand had a much more measured and nuanced response, as evidenced by Cameron’s wonderful blog post. So what does it mean for The Life Scientists. This is a community near ...

The best analogy for the FriendFeed purchase

Blind.Scientist — Tue, 11 Aug 2009 23:53:15 +0100

I don’t like Facebook, the same way I don’t like Orkut. The only reason for me to use Facebook is contact people I don’t see in years, and that facet of it I appreciate. On the other hand I really liked FriendFeed, which is (was) a great service, but didn’t have a commercialization plan, hence it was sold. Anyway, the best analogy I can make of this purchase is: It’s like when that indie, miniscule band that you love and cherish goes mainstream. In a matter of seconds, the whole world knows that band and you don’t like it anymore, because you “discovered” it, because they were “connected” only to you, not the whole world. Now, FriendFeed is Facebook, and Facebook is mainstream, and we scientists need to stay indie, or at least ke...

Translationally optimal codons do not appear to significantly associate with phosphorylation sites

Public Rambling — Tue, 11 Aug 2009 01:47:00 +0100

I recently read an interesting paper about codon bias at structurally important sites that sent me on a small detour from my usual activities. Tong Zhou, Mason Weems and Claus Wilke, described how translationally optimal codons are associated with structurally important sites in proteins, such as the protein core (Zhou et al. MBE 2009). This work is a continuation of the work from this same lab on what constraints protein evolution. I have written here before a short review of the literature on the subject. As a reminder, it was observed that the expression level is the strongest constraint on a protein's rate of change with highly expressed genes coding for proteins that diverge slower than lowly expressed ones (Drummond et al. MBE 2006). It is currently believed that selection against tr...

What we learned last week: August 10th edition

Blind.Scientist — Mon, 10 Aug 2009 20:45:21 +0100

(this will be a weekly post on the most important news of the week, things that caught our eyes here at Blind.Scientist headquarters) - Apparently there is a rich guy on the internet that likes to show off how many computers he has, but doesn’t know a lot about technology and stuff. Anyway, how not to write a post. Never used his website. - Skulpt is a nice project that I really like to see come to fruition. Check it out. - Universal health care, or whatever it will be, in US won’t be approved, because both parties are in the pocket of the (un)health industry. It’s like the joke where the father doctor leaves for vacation and leaves the clinic for his newly graduated son to take care. When he comes back, all his patients are cured, and the father says: “What the hel...

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Paper of the week: INDELible: A Flexible Simulator of Biological Sequence Evolution

Blind.Scientist — Mon, 10 Aug 2009 15:09:40 +0100

The paper of this week touches a subject that I have been involved in the past: sequence simulation. INDELible, by Fletcher and Yang, is a program that is capable of simulating both DNA and amino acid sequences, and it seems to be the complete package to do so. It contains several substitution models and it can even simulate codon substitutions. As the article mentions, the closest comparison to INDELible is DAWG, developed by Reed Cartwright, that seems to be faster. DAWG is a nice program and generates good simulations and has a very well designed code with strong models and quite reliable results. And that’s what you want on a simulation program. You really want is a good implementation of the amino acid/nucleotide substitution pattern and a good model of indel simulation. It seem...

Biologists, programming and house cleaning

business|bytes|genes|molecules — Mon, 10 Aug 2009 04:34:15 +0100

Image by mndoci via Flickr I taught myself a little BASIC in high school; but in those days, living in a small town in the middle of nowhere in India, access to a computer was not exactly easy (I touched one just a handful of times). Later, I got to know some COBOL and eventually FORTRAN. As a physical chemist with a strong interest in quantum mechanics, and numerical methods FORTRAN seemed like a good fit. In grad school, as I moved from mostly wet lab work to writing electronic structure code, and using computational methods to study protein dynamics, structure and photophysics, I was a complete hack. FORTRAN was a tool to express methods, and Perl was fast becoming a tool to script around various applications and munge files. But in those days, outside o...

Testing posterous as a conduit

business|bytes|genes|molecules — Sun, 09 Aug 2009 06:13:14 +0100

Image via CrunchBase Presence, a word not quite often used these days. I’ve always had a different interpretation of presence. I have a portal/wiki, a blog, a tumblelog, and a presence on Twitter, Friendfeed, flickr, YouTube, and Soundcloud Each serves a purpose. The portal/wiki provides a more granular looks at my interests while allowing me to use a platform that enables contributions if I choose to do so and track changes. The blog is the center of my online world in many ways, and where many of my thoughts on science and computing go. The tumblelog is like a scrapbook, providing people a peek into non-so-random stuff that piques my interest, and so on. Then along comes Posterous, which I had initially looked as essentially as a different ap...

Biotechniques: Molecular Biology Techniques Forum

VBRC Blog — Fri, 07 Aug 2009 06:27:02 +0100

Biotechniques is an online forum built to answer questions concerning molecular biology, cell biology, microscopy, and bioinformatics. The page is set up in an easy-to-view, easy-to-navigate manner that allows you to find specific posts, active posts, unanswered questions and browse entire topics. (Source: VBRC Blog)

RSRuby in the IRB console

What You're Doing Is Rather Desperate — Thu, 06 Aug 2009 06:36:52 +0100

R is terrific, of course, for all your statistical needs. But those data structures! “Everything is a list.” Leading to such wondrous ways to access variables as “p <- Meta(gds)$platform", or "last <- mylist[[1]][length(mylist[[1]])]". Sometimes, you want something more familiar. An array, a hash, a hash of arrays. Or, you may need to access R data in the language of your choice – e.g. as part of a Rails project. In Ruby, IRB is your friend. On the right, an IRB session in which we invoke RSRuby, load the GEOquery library from Bioconductor, fetch a dataset from the GEO database and examine the metadata that describes the experiment. Result: a ruby hash of arrays, where the keys are covariate types (”sample, disease.state, description”...

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Young Men & Fire

Omics! Omics! — Tue, 04 Aug 2009 23:00:00 +0100

60 years ago today, 15 young men floated out of a Montana sky onto rugged ground below. They were there to join another already on the scene of a small forest fire. Within a few short hours, only 3 of those men would not be fatally burned by that same fire. As deserved as the festivities are over the spectacular events of July 1969, it's a pity that so little attention has been paid to this tragedy 20 years earlier.I was in college when I first read the definitive account of the Mann Gulch fire, Young Men and Fire by Norman Maclean. Given that I was about at the same age at the time as those smokejumpers, it had a lot of resonance for me. It remains one of my favorite books (along with his other masterpiece, A River Runs Through It, and Other Stories). Someday, I hope to hike the gulch, bo...

300th

YOKOFAKUN — Tue, 04 Aug 2009 23:00:00 +0100

This is my 300th post. This blog started in november 2005 and I want to thank all the people who helped me and contributed to write those posts. I want to thank particularly the Biogang, my followers/following on Twitter and the Life-Scientists on FriendFeed.Here is a timeline of this blog created on dipity.com.Pierre L. on Dipity.This timeline was built without giving my blogger username+ (Source: YOKOFAKUN)

Ignite Seattle 7

business|bytes|genes|molecules — Tue, 04 Aug 2009 07:18:11 +0100

Another Ignite Seattle is now done. This was perhaps my favorite one, with a diverse selection of excellent talks. Here are my slides. Video to follow Big Data & the networked future of Science (at Ignite Seattle 7) View more presentations from Deepak Singh. Related articles by Zemanta Ignite Seattle 7 is Tonight (radar.oreilly.com) Bite sized Big Data (mndoci.com) Lots of data and the network (mndoci.com) (Source: business|bytes|genes|molecules)

Paper of the week: A Quick Guide to Organizing Computational Biology Projects

Blind.Scientist — Tue, 04 Aug 2009 00:11:35 +0100

This is a new series here at the Blind.Scientist headquarters. My team and I will try to feature one scientific publication a week, it might not be hot from the presses or it might not be only about biology and/or bioinformatics. We (my team and I) will try to be eclectic and cover different areas. Alternatively you will find these posts on Research Blogging too. This week we start with a recent publication that appeared on PLoS Computational Biology, titled A Quick Guide to Organizing Computational Biology Projects, by William Stafford Noble (reference and link are on the bottom of the post). It’s a well written publication, that falls under the Education scope of this PLoS, understandably by its title. Mainly it tries to teach some tips and tricks on how to organize your files in a...

Movies 2009

Blind.Scientist — Tue, 04 Aug 2009 00:00:00 +0100

The Bank Job – 3.5/5 Journey into the end of the night – 2/5 How to Lose Friends and Alienate People – 4/5 The Comebacks – 1.5/5 Super-hero Movie – 1.5/5 Moving McAllister – 2/5 Hitman (Unrated Edition) – 3/5 Max Payne – 2.5/5 This Is Spinal Tap (Special Edition) – 3/5 Shattered – 1.5/5 Rocknrolla – 4/5 Traitor – 4/5 Eagle Eye – 3.5/5 The Day the Earth Stood Still – 1/5 Quantum of Solace – 1/5 Role Models – 4/5 Watchmen – 6/5 The Last boy scout – 5/5 Paul Blart, Mall Cop – 3/5 Fired Up – 2.5/5 Shoot them up – 2/5 The International – 3/5 17 again – 2/5 I love you man – 3/5 Shaun of the Dead – 5/5 Hot Fuzz – 5/5 Wolverine: X-Men origins 3...

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Making sense of all that data: Integrating and extracting information from dataspaces

business|bytes|genes|molecules — Mon, 03 Aug 2009 23:28:57 +0100

I have written previously about Trendingtopics.org as a reference site for data analytics using Hadoop and Hive. Pete Skomoroch, who developed the site has written a great follow up article on the Cloudera blog that anyone in the scientific informatics space needs to read. Those same people need to read Chapter 5 in Beautiful Data. There Jeff Hammerbacher writes about the role of the Data Scientist at Facebook. So why should people in the scientific community read those two resources? Big Data is now a fact of life, both in science and otherwise. Our systems, both from the infrastructure and computation standpoint were written for data sets of different sizes. At the same time we are moving towards a world where the need to combine data resources is becoming even more necessary than in the...

Another Lab Cameo

Omics! Omics! — Mon, 03 Aug 2009 23:00:00 +0100

I spent a chunk of a day early last month dusting off my old lab skills. The rationale was that we were losing the senior lab tech who was supporting a lot of the projects I'm involved in. She's actually an old friend from Millennium (we started & left in near synchrony there) who has been lured back to that fold and will be greatly missed (until we steal her back!). Anyway, it looked like we'd have a gap in lab support for some PCR projects. A back-fill position was open, but hiring is never instantaneous. Perhaps some resources could be shifted, perhaps not. So I imposed a bit on my friendship to get a quick refresher in PCR.One interesting factoid is that I have now run PCR in every decade it has existed. In the 80's, when it was still new, some of my undergraduate classes used it. I di...

A Treemap for FriendFeed

YOKOFAKUN — Mon, 03 Aug 2009 23:00:00 +0100

I've resurrected an old Treemap algorithm I described three years ago, and I've used it to plot the activity of the "Life Scientists Room" on FriendFeed.The source of the packing algorithm is available here, and the source of the tool scanning FriendFeed is available here.In the end, here is a clickable treemap of the top 'commentators' in the "Life Scientists Room" of FriendFeed:Two other maps: (Source: YOKOFAKUN)

A proposal for encouraging user contributed annotations to Uniprot

Your bones got a little machine. — Mon, 03 Aug 2009 09:21:56 +0100

Discussion” tab, ala Wikipedia (not pictured). • Each field, or block of related fields, would have an Add/edit button at the top right of the block. (I’ve chosen the Universal Edit Button as an example) Aftertought: Maybe putting these features under tabs isn’t quite the best place, since the existing tabs are ‘actions’ that can be taken rather than ‘extra info’ to be viewed. This UI detail could certainly be refined. This proposal has many wiki-like features (history, attribution, open editing, curation by trusted users and potentially page/section locking) but doesn’t really fit my definition of a wiki since the input format is not free-form wiki-text, but is instead constrained by the interface to enforce the submission of (mostly) st...

Industry Watching: Pharmacovigilance – From monitoring to perpetual analytics

business|bytes|genes|molecules — Sun, 02 Aug 2009 16:46:29 +0100

Image via Wikipedia Pharmacovigilance is an area where a lot of pharma companies are beginning to spend more money and attention and going forward, this will be an area of major emphasis both for the industry and regulatory bodies, especially given recent setbacks. That’s why the work being done at companies like ProSanos is critical. Prosonos’ SafetyWorks product is a web-based system that queries data sources like insurance claims and electronic health records. In addition the system also listens in on other data sources (unsure what these are). These systems, over time, will evolve to monitor CDC data sources, various adverse event reporting systems, both public and private, and additional resources. The challenge will be making sure that there is automation that alerts ...

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Drug synergies tend to be context specific

Public Rambling — Sat, 01 Aug 2009 23:04:00 +0100

A little over a year ago I mentioned a paper published in MSB on how drug-combinations could be used to study pathways. Recently, some of the same authors have now published a study in Nature Biotech analyzing drug combinations under different contexts (i.e. different tissues, different species, different outputs, etc). The underlying methodology of the study is essentially the same as in above mentioned paper. The authors try to study the effect of combining drugs on specific phenotypes. One example of a phenotype could be the inhibition of growth of a pathogenic strain. Different concentrations of two drugs are combined in a matrix form as described in figure 1a (reproduced below) and the phenotype is measured for each case. Two drugs are said to be synergistic if the measured impact on...

The bar is ‘not crackpot’

business|bytes|genes|molecules — Fri, 31 Jul 2009 06:08:18 +0100

Perhaps one of the greatest shifts brought about by the advent of search, specifically the success of Google, and over the last few years, the ability to leverage personal publishing platforms, has been the democratization of information. In other words, it’s no longer sufficient to be a named source, but rather, the key metric is how often someone links to you, and increasingly how often something filters up to the top of todays socially driven streams of data. So why are scientists still stuck in the mentality of the named source? If all that matters is the quality of content, then the specific publication should cease to matter (one reason I love the Article Level Metrics proposed by those at PLoS. Yes, it’s years of tradition, but then so were many of the traditional publis...

Petaflops meet Petabytes

business|bytes|genes|molecules — Fri, 31 Jul 2009 05:12:23 +0100

Image via Wikipedia Dan Reed has written a lot of interesting posts/essays lately, many of which have been covered here. He comes from a world where compute horsepower is king, admittedly a world I cared about for a long time, and still do to this day. But many of us today live in a different world, where the focus on computing isn’t high performance, but data intensive. So it’s interesting when in a recent blog post, Dan writes One of the major lessons from web search and cloud data centers is the power of truly massive scale, near real-time data analysis. When anyone with a cheap cell phone and a web browser can extract data and insights from a non-trivial fraction of the human knowledge base, behavior and culture are transformed. I would like to believe that we can bring ...

A RESTful Web service storing DNA sequences: Jersey, my notebook

YOKOFAKUN — Thu, 30 Jul 2009 23:00:00 +0100

Jersey is the open source JAX-RS implementation for building RESTful Web services. JAX-RS uses java annotations to simplify the development and deployment of web service clients and endpoints. In this post I'll describe how I've implemented a naive RESTful web service for storing and querying a DNA database. This code was tested and deployed under netbeans 6.1.The service is defined in a class (Source: YOKOFAKUN)

How-to: combinations of covariates using Ruby

What You're Doing Is Rather Desperate — Thu, 30 Jul 2009 07:08:38 +0100

I work with people who generate a lot of microarray data. One question that they often ask is: can we find those genes with a two-fold or more change in median expression under two or more different conditions? For example, let’s say that we have 3 conditions: “normal”, “adenoma” and “cancer”. That gives us 3 pairwise comparisons: normal-adenoma, normal-cancer and adenoma-cancer. Here’s a Ruby solution to the problem. First, I installed StatArray, a Ruby gem that provides statistical methods for array objects. It’s not been updated for 3 years, but seems to work. require 'rubygems' require 'statarray' Next, credit to David Burger for posting this code solution for combinations in Ruby. You give it an array of ele...

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Books 2009

Blind.Scientist — Thu, 30 Jul 2009 02:36:00 +0100

List of books read in 2009 – updated regularly 1 – The Max (Hard Case Crime) 2 – Gentlemen (33 1/3) 3 – Celine Dion’s Let’s Talk About Love: A Journey to the End of Taste (33 1/3) 4 – Musicophilia: Tales of Music and the Brain, Revised and Expanded Edition 5 – Born Standing Up: A Comic’s Life 6 – The Dogs of Riga 7 – Hold Tight 8 – Mystic River 9 – The White Lioness 10 – Long Lost 11 – Echo Burning (Jack Reacher) 12 – And Then There Were None 13 – Fake I.D. (Hard Case Crime) 14 – The Shock Doctrine 15 – Cocaine Nights 16 – Cocaine Nights Related articles by Zemanta How To Make 2009 Your Best Blogging Year (Source: Blind.Scientist)

Couldn't help but laugh at this ,metagenome project

Omics! Omics! — Wed, 29 Jul 2009 23:00:00 +0100

I would have thought this to be an April's Fool prank, except I came across the dataset while browsing the NCBI Short Read Archive. It did have me laughing out loud.Metagenomic Analysis with Galaxy: Windshield Genomics and BeyondAnd in case one thought the title was jargon or a brand name...we asked the followingquestions: “When I drive through Pennsylvania in June my windshieldgets quite dirty with all these bugs. Yet do I know what they are?How many beetles versus butterflies? Is there a difference betweenday and night? Is there a difference between Pennsylvania andConnecticut?” So we scraped the windshield, isolated genomic DNA,and subjected it to 454 FLX sequencing. We then uploaded the datainto Galaxy and attempted answering these questions. In the endPennsylvania turned out to be...

Lots of data and the network

business|bytes|genes|molecules — Wed, 29 Jul 2009 03:44:44 +0100

Big Data and the networked future of science; not only is that the title of my talk at Ignite Seattle 7 next week, but also was the working title of my talk at VA Tech. I strongly believe that the future of the life sciences will include not only large data sets, but the need to merge and co-analyze diverse data sources. The size and complexity of these projects and the skills required means we need to think about new ways of addressing these data volumes. These challenges are being recognized across the board. In a recent abstract from a paper on NetSolve/D, the authors (including Jack Dongarra) The persistent mood of exhilaration in the research community over exponential increases in the capacity of computational resources has been tempered recently by the realization that a torrential...

Movies 2009

Blind.Scientist — Wed, 29 Jul 2009 02:39:00 +0100

Bite sized Big Data

business|bytes|genes|molecules — Tue, 28 Jul 2009 03:03:00 +0100

Image by Hugger Industries via Flickr Just after I moved to Seattle after over five years in San Diego (the longest I’ve ever stayed in one place for a stretch), I got a chance to attend an event that convinced me that I had made the correct decision. Ignite Seattle was fun, geeky, creative and had great energy and has since become a key attraction at many a geek event. The two chances I have had to speak there were among the most fun experiences of my life. Due to travel, I missed the last Ignite Seattle, but this time I plan to be there, especially since I was lucky enough to get another opportunity to speak. Here’s the Title and Abstract that I submitted Big Data and the networked future of science New instruments, sensors, distributed scientific collaboration, informal p...

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Just say no to perspective pie charts!

Omics! Omics! — Mon, 27 Jul 2009 23:00:00 +0100

>Several papers in a row tripped over one of my pet peeves. Why does anyone who cares about their data use a perspective pie chart?Pie charts in general get little respect in the visualization community (Tufte hates them), but while I don't love them I don't hate them either. The scheme is intuitive and widely understood -- the area (and pie angle) of each slice is proportional to its share of the total. This is one class of objection: area is a harder visual concept to compare than lengths. The other is that these waste dimensions and pixels -- why use two dimensions and lots of pixels to display information which can be shown in one dimension with many fewer pixels. While pixels are not gold, why not maximize their value?But there's no excuse for perspective pie charts. These abomination...

Just what does a genome cost?

Omics! Omics! — Sun, 26 Jul 2009 23:00:00 +0100

Scientists are rarely trained in finance, and even more rarely comfortable with it. In an ideal world, experiments just happen and somehow it all gets covered. But the reality is that experiments cost money.Perhaps nowhere in biology has this been so at the front of attention as with genome sequencing, particularly since the cost has been marching down. But, cost has also turned out to be a murky area. Numbers are thrown around without always having clear evidence.Today, George Church was quoted as saying the cost is around $5K and would soon be $1K. This is very exciting -- but how real is it? Not only am I nervous that this is an exon resequencing cost, but even if it's for a complete human genome shotgun I wonder how obtainable it really is? Is this cost "fully loaded" or just a raw mat...

Drawing a circular genome. Chapter 2: java swing

YOKOFAKUN — Sun, 26 Jul 2009 23:00:00 +0100

This post follows my previous post Ajax/PHP/Mysql/Canvas Drawing a circular genome, my notebook. The problem here, is drawing a circular genomic map that might contain a huge number of data and using an asynchronous method to fetch and display the data. Here, the server returning some JSON data is the same as in the last post but I now use a Java Swing client to fetch and display the data. Here (Source: YOKOFAKUN)

Don't translate this ! Security with Spring, my notebook

YOKOFAKUN — Sun, 26 Jul 2009 23:00:00 +0100

In my previous post titled "SpringFramework/BeanFactory My notebook" I showed how to use the Spring Framework to manage a set of java beans with a xml file and a BeanFactory.Now, let's add a drop of Security in our model. Let's say you're working for a big paranoid pharma company where the user "lindenb" is not allowed to use the class spring.Translator with the standard genetic code. A naive (Source: YOKOFAKUN)