MedWorm: Bioinformaticians

Inside the Variation Toolkit: Tools for Gene Ontology

YOKOFAKUN — Tue, 31 Jan 2012 05:00:00 +0100

GeneOntologyDbManager is a C++ tool that is part of my experimental Variation Toolkit. This program is a set of tools for GeneOntology, it is based on the sqlite3 library. Download Download the sources from Google-Code using subversion:.... svn checkout http://variationtoolkit.googlecode.com/svn/trunk/ variationtoolkit-read-only ... or update the sources of an existing installation... cd (Source: YOKOFAKUN)

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Does Illlmina Also Have A Homopolymer Problem?

Omics! Omics! — Mon, 30 Jan 2012 05:00:00 +0100

One of the most widely-publicized error modes with Ion Torrent and 454 sequencing has been the challenge of correctly counting the number of bases in homopolymer runs. Because these chemistries use non-terminating nucleotides, polymerase is free to add as many as possible. Unfortunately, the signal linearity breaks down, making it difficult to correctly count. Ion Torrent today released a note on homopolymers, but rather than plowing this well-trod ground it goes for a less publicized problem: Illumina having a more specific challenge in this department. The note is available on the Ion Community, free registration required.Read more » (Source: Omics! Omics!)

Inside the variation toolkit: VCF2XML

YOKOFAKUN — Sat, 28 Jan 2012 05:00:00 +0100

vcf2xml is C++ tool that is part of my Variation Toolkit. It transforms a "Variant Call Format document" to XML, so it can be later processed with xslt, xquery, etc... Dependencies libxml http://xmlsoft.org/ Download Download the sources from Google-Code using subversion:.... svn checkout http://variationtoolkit.googlecode.com/svn/trunk/ variationtoolkit-read-only ... or update the (Source: YOKOFAKUN)

Insert your VCFs in a sqlite database.

YOKOFAKUN — Sat, 28 Jan 2012 05:00:00 +0100

vcf2sqlite is C++ tool that is part of my Variation Toolkit. It inserts a "Variant Call Format document" (VCF) into a sqlite3 database. Download Download the sources from Google-Code using subversion:.... svn checkout http://variationtoolkit.googlecode.com/svn/trunk/ variationtoolkit-read-only ... or update the sources of an existing installation... cd variationtoolkit svn update ... and (Source: YOKOFAKUN)

Wiider postmortem

Your bones got a little machine. — Sat, 28 Jan 2012 03:00:54 +0100

I always intended to write this postmortem earlier … now three years after development ceased, I’m finally getting around to it. Warning – retrospective rambling ahead. In mid 2007, Nintendo released the Opera-powered browser for their Wii gaming console which they called the Internet Channel. For many people, including myself, this was the first time they had been able to use “Internet on the TV”. Because of the typical viewing distance, low resolution for CRT-based televisions, and the unique navigation interface using the Wiimote, many web sites were functional but not particularly comfortable to use. Many sites targeted at desktop PCs were too complex and heavyweight for the Internet Channel, fonts were often too small such that cumbersome zooming and scr...

de-Bruijn assembler

Bioinformatics Latest News — Fri, 27 Jan 2012 05:00:00 +0100

In the last post I talked about the overlap-layout-consensus (OLC) way of Genome assembly. The approach which is (really!) getting popular these days is the other one, de-Bruijn-graphs (DBG). It is based on the simple idea of converting the hard problem of finding Hamiltonian to relatively simpler Eulerian for assembling biological sequences. There is a beautiful tutorial like introduction co-authored by the 'father' of this idea, Prof. Pevzner. To put it naively, in contrast with OLC approach where one represents the reads as vertex in graph which are connected if the end of the read representing the first vertex overlaps with the start of the second one, DBG approach has the overlapping parts of the reads as the vertices and edges representing th...

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Reproducible research: three links that made me think

What You're Doing Is Rather Desperate — Fri, 27 Jan 2012 01:20:45 +0100

I’m constantly amazed, bemused and troubled by how little published scientific research is genuinely reproducible, in that you or I (or even the original authors) could go back and check the results. Three examples from around the Web converged in my mind this week. Software availability A BioStar user asks: where is the software for the method described in a Science article, “A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection.” No-one can find it on the Web; the best we can do is a press release from 2010 stating that the software “should soon be available.” Why do the so-called flagship journals and their reviewers have so little interest in the methods used to generate data shown in papers? It’s beyond my c...

Roche Guns For Illumina

Omics! Omics! — Wed, 25 Jan 2012 05:00:00 +0100

Due to a business dinner & general exhaustion, I turned in early last night & was caught unaware this morning of the big news: Roche is making a hostile takeover bid for Illumina. Ugh!Read more » (Source: Omics! Omics!)

Science Online 2012 on Twitter

Notes from the biomass — Mon, 23 Jan 2012 22:36:29 +0100

Science Online 2012, held in at the NC state university in Raleigh, NC, last week was a transforming event. The 450 attendees were a colorful mix of science writers, journalists, researchers, educators and artists. Apparently, the ratio of scientists dropped in its 6th installment. But the love of Science in the air would have graced any proper scientific meeting. Much of it has already been praised in readable form and can be accessed in a wiki repository. So why was Science Online 2012 so great? The reliable WLAN, the conference hall, the sessions run by the usual suspects, more or less prepared? I fail to answer that question precisely but coming back I realized I changed my views on many issues in science communication profoundly. When I wrote it up, it sounded as shallow as th...

Sequencing Technology Fireworks

Omics! Omics! — Tue, 10 Jan 2012 05:00:00 +0100

I actually awoke today expecting an exciting press release, but I sure wasn't prepared for the big announcements from Ion and Illumina. Not that they were totally unexpected, but there's a huge difference between speculation and announced products (which, of course, are hugely different from ones you can actually buy!)Read more » (Source: Omics! Omics!)

A CGI-version of samtools tview.

YOKOFAKUN — Sat, 07 Jan 2012 05:00:00 +0100

I've created a lightweight CGI-based web-application for samtools tview. This C++ program named ngsproject.cgi uses the samtools api, it allows any user to visualize all the alignments in a given NGS project. The projects and their BAMS are defined on the server side using a simple XML document. e.g: /home/lindenb/samtools-0.1.18/ (Source: YOKOFAKUN)

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Ion Torrent Pairs: To What End?

Omics! Omics! — Sat, 07 Jan 2012 05:00:00 +0100

Ion Torrent quietly released a set of paired end datasets over the holiday break. This is a bit embarassing for me, as in my last post on Ion I stated the platform "will probably never have paired ends" and in fact Ion had already announced the protocol. Oy! I also missed their mate pair protocol being released, though the document itself is another victim of Ion's incredibly counterproductive security policy. If you don't own a PGM, you can't access the document -- never mind if you are trying to plan for a potential buy or are preparing a library for a friend/collaborator to run. Read more » (Source: Omics! Omics!)

The Variation Toolkit

YOKOFAKUN — Thu, 05 Jan 2012 05:00:00 +0100

During the last weeks, I've worked on an experimental C++ package named The Variation Toolkit (varkit). It was originally designed to provide some command lines equivalent to knime4bio but I've added more tools over time. Some of those tools are very simple-and-stupid ( fasta2tsv) , reinvent the wheel ("numericsplit"), are part of an answer to biostar, are some old tools (e.g. bam2wig) that have (Source: YOKOFAKUN)

Hamiltonian Assembler

Bioinformatics Latest News — Thu, 05 Jan 2012 05:00:00 +0100

Just came across Andrew's Hamiltonian Cycle finder (HCF) get: wget https://raw.github.com/ahh/ahh-toys/master/ham.sh simple check: bash ham.sh a b b c c a [followed by Ctrl-D should produce] a b c based purely on shell commands and thought of testing it out as a Genome assembler. The genome assembly problem is closely related to finding the shortest common superstring (S) of a given set of strings (s1, s2… sn). The superstring S corresponds to the genome and the set of strings being the short sequence reads produced by the sequencing machines. The popular ways of approaching this problem are OLC and DBG (overlap-layout-consensus and de-bruijn-graph). OLC approach is similar to HCF or the popular textbook example, the tr...

2011 blog stats courtesy of WordPress.com

What You're Doing Is Rather Desperate — Sun, 01 Jan 2012 00:14:16 +0100

The kind people at WordPress.com have prepared a 2011 annual report for this blog. Click here to see the complete report. Filed under: this blog Tagged: 2011, summary, wordpress.com (Source: What You're Doing Is Rather Desperate)

A Fundamental Breakthrough in Protein Folding

Trapped in the USA — Wed, 28 Dec 2011 06:13:02 +0100

In my humble opinion, the biggest paper in protein folding from the last few years just got published in the wee hours of 2011. It is Protein 3D Structure Computed from Evolutionary Sequence Variation from Debora Marks, Lucy Colwell and colleagues (and when I say colleague I mean Chris Sander, which you should all know as a co-author of DSSP). This paper proves the tremendous result that the key structural contacts in a protein structure can be derived from a multiple sequence alignment. And that these contacts are sufficient to generate reliable structures of the protein. And big proteins at that. I heard on the grapevine that this paper had a difficult passage to publication. I was both surprised and not surprised by this. I was surprised because this is such a fundamental result, it ...

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Year's End

Omics! Omics! — Wed, 28 Dec 2011 05:00:00 +0100

I hoped this year to push myself to blog more frequently and regularly. Clearly I did better than some years, but not up to the standard I had hoped for. I've also realized that I missed noting some significant personal milestones.Read more » (Source: Omics! Omics!)

Sequencing for relics from the Sanger era part 1: getting the raw data

What You're Doing Is Rather Desperate — Thu, 22 Dec 2011 04:28:44 +0100

Sequencing in the good old daysIn another life, way back in the mists of time, I did a Ph.D. Part of my project was to sequence a gene from a bacterium, which encoded an enzyme involved in nitrate metabolism. It took the best part of a year to obtain ~ 2 000 bp of DNA sequence: partly because I was rubbish at sequencing, but also because of the technology at the time. It was an elegant biochemical technique called the dideoxy chain termination method, or “Sanger sequencing” after its inventor. Sequence was visualized by exposing radioactively-labelled DNA to X-ray film, resulting in images like the one at left, from my thesis. Yes, that photograph is glued in place. The sequence was read manually, by placing the developed film on a light box, moving a ruler and writing down the...

Books Read 2011

Trapped in the USA — Mon, 19 Dec 2011 22:30:34 +0100

I started this year with the good intention of writing a paragraph or three for each book I read. A short review so to speak. I managed for about 15 books up to April. It’s too much work to write about what I just read. Easier to read something new. So here’s my reading list for this year (managed to read a lot of technical shit): 1. Stendhal, The Red and the Black 2. Steig Larson, The Girl who kicked the Hornet’s Nest 3. Neil Howe and William Strauss, The Fourth Turning 5. Edith Wharton, “Age of Innocence”. 6. Gary Taubes, “Why we get Fat” 7. Nathan Haren & Mike Cliffe Jones, “Beyond Blogging” 8. Jules Verne, “Voyage au Centre du Monde” 9. Rino Breerbaart, “Song Logic” 11. Mario Vargas Llosa, “Aunt Julia and the Scriptwriter” 12. Henry James, �...

Magic Numbers and unit conversions in Structural Biology

Trapped in the USA — Wed, 14 Dec 2011 21:00:55 +0100

If you end up doing any kind of energy calculation in proteins or organic chemistry – and that includes messing around with Molecular Dynamic trajectories – you may end up dealing with actual numbers. And that means you’ll have to get your head around physical units and their conversions. I’ve spent days trying to figure out magic numbers in equations and source-code. Diving into the guts of someone else’s source-code is not the nicest place to figure such things out. Do it enough, and you’ll start seeing the same numbers pop up everywhere. As I’ve never seen anyone bother to describe some very common magic numbers in biochemistry, I’ll list a bunch of them right here. First let’s get acquainted with the standard units: po...

#arseniclife: the genome

What You're Doing Is Rather Desperate — Wed, 14 Dec 2011 04:35:32 +0100

It’s about one year since the science story dubbed #arseniclife hit the headlines. November 30th saw the release of a draft genome sequence for Halomonas sp. GFAJ-1, the bacterium behind the furore. As Iddo pointed out on Twitter, sequencing the DNA from GFAJ-1 is itself strong evidence against arsenate in the DNA backbone, since the sequencing chemistry would be highly unlikely to work in that case. However, if like me you think that a new microbial genome provides the most fun to be had in bioinformatics [*], you’ll be excited by the availability of the data. In this post then: where to get it, some very preliminary analysis and some things that you might like to to with it. Projects for your students, perhaps. [*] note to self: why, then, am I working on colorectal cancer? ...

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Reflecting on a Year of Ion Torrent

Omics! Omics! — Fri, 09 Dec 2011 05:00:00 +0100

Ion Torrent released three more datasets this morning, all generated on their 318 chip. One's from E.coli but two are human genomic samples. With approximately 1.2Gbp of raw data coming from these 318 chips (fron around 6 million quality filtered reads per chip), they are starting to move up the food chain in human genomics from pure amplicon sequencing to more complex small targeted resequencing efforts.Read more » (Source: Omics! Omics!)

New Look, Mobile Friendly

Trapped in the USA — Thu, 08 Dec 2011 00:41:04 +0100

I’ve been meaning to do this for a while, I’ve updated the look of the blog. The previous design was inspired by an old design of über minimalist Ev Bogue. Back then I was wandering around the world as a nomadic minimalist. I’ve since been folded back in academia and it’s time for a change. The new look has two goals: 1. Emphasise the article nature of most of my (longish) posts 2. Responsive-Web-Design Resize the window and make it real narrow. You will see the design collapse into a linear layout. Perfect for reading on a mobile† device. †I really mean iPhones, but I need to stay in the good books of @pansapien. (Source: Trapped in the USA)

A Friday round-up

What You're Doing Is Rather Desperate — Thu, 01 Dec 2011 23:36:06 +0100

Just a brief selection of items that caught my eye this week. Note that this is a Friday as opposed to Friday, lest you mistake this for a new, regular feature. 1. R/statistics ggbio A new Bioconductor package which builds on the excellent ggplot graphics library, for the visualization of biological data. R development master class Hadley Wickham recently presented this course on R package development for my organisation. I was on parental leave at the time, otherwise I would have attended for sure. 2. Bioinformatics in the media DNA Sequencing Caught in Deluge of Data I described this NYT article as a “surprisingly-good intro article“. Michael Eisen described it as “kind of silly“. I think we’re both right. Michael’s perspective is that of an expert i...

Suggest some new terms for the EDAM Ontology for Bioinformatics

YOKOFAKUN — Thu, 01 Dec 2011 05:00:00 +0100

EDAM is an ontology of general bioinformatics concepts, including topics and data types, formats, identifiers and operations. Is your specific subject of research present in this ontology (e.g "RNA-Seq") ? go and have a look at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM. If it is not, feel free to suggest a new term in the form below. Your term might be included in the next (Source: YOKOFAKUN)

Special Topic Issue "Webscience in medicine"

Medical Ecosystem for Personalized Event-Based Surveillance — Tue, 29 Nov 2011 08:05:00 +0100

A Call for papers has been released for a special topic issue on Webscience in medicine. The special topic will appear within the Journal "Methods of information in Medicine". (Source: Medical Ecosystem for Personalized Event-Based Surveillance)

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Boring, monotonous day-to-day tasks? That’s synonymous with bioinformatics.

What You're Doing Is Rather Desperate — Thu, 24 Nov 2011 05:18:38 +0100

In response to this question, I can only point out that J.C.R. Licklider figured it out over 50 years ago: Despite the fact that there is a voluminous literature on thinking and problem solving, including intensive case-history studies of the process of invention, I could find nothing comparable to a time-and-motion-study analysis of the mental work of a person engaged in a scientific or technical enterprise. In the spring and summer of 1957, therefore, I tried to keep track of what one moderately technical person actually did during the hours he regarded as devoted to work. Although I was aware of the inadequacy of the sampling, I served as my own subject. It soon became apparent that the main thing I did was to keep records, and the project would have become an infinite regress if the ke...

Processing json data with apache velocity.

YOKOFAKUN — Sun, 20 Nov 2011 05:00:00 +0100

I've written a tool named "apache velocity" which parse json data and processes it with "Apache velocity" (a template engine ). The (javacc) source code is available here: https://github.com/lindenb/jsandbox/blob/master/src/sandbox/VelocityJson.jj Example Say you have defined some classes using JSON: [ { "type": "record", "name": "Exon", "fields" : [ {"name": "start" (Source: YOKOFAKUN)

OSGi and Eclipse RCP Talk

eric.jain.name — Thu, 17 Nov 2011 22:50:40 +0100

I gave a talk at the Seattle Java User Group this week, where I talk about two technologies I use at work: The OSGi module system, and the Eclipse Rich Client Platform. Giving this talk was a good experience, and the audience was great. You can watch the talk below. (Source: eric.jain.name)

"VCF annotation" with the NHLBI GO Exome Sequencing Project (JAX-WS)

YOKOFAKUN — Wed, 16 Nov 2011 05:00:00 +0100

The NHLBI Exome Sequencing Project (ESP) has released a web service to query their data. "The goal of the NHLBI GO Exome Sequencing Project (ESP) is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to (Source: YOKOFAKUN)

The infidelity of the theoretical protein backbone

Trapped in the USA — Tue, 15 Nov 2011 20:23:07 +0100

Problems in protein simulations are often reduced to one of two categories: do we have a sufficiently accurate model of atomic interactions? have we sufficiently explored the conformational space of our proteins? If you talk to molecular modellers, they will try to tell you the problem lies wholly in conformational sampling. It is an article of their faith that force-fields are good enough. Our erstwhile modeller can then claim that the problem lies not in software but in hardware. It’s just that their computers are too slow to finish their simulations properly. Well, I beg to differ. One major flaw in atomic force-fields, which has been swept under the carpet, is that atomic force-fields fail to properly model the protein backbone. And they’ve failed to do so, for ...

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Some English pronunciation tips

Trapped in the USA — Mon, 14 Nov 2011 11:59:06 +0100

Although I learnt English as a second language, I now wear it like a well-worn glove. But in science, there are tons of made-up poly-syllabic words, and I occassionally trip over some of them, such as: equilibrate, equilibrium and equilibration. However, I’ve been learning a bunch of languages the last few years, and through doing that, it’s thrown English pronunciation in relief. I’m starting to get a conscious handle on English pronunciation, and I’ve discovered some useful rules that were not apparent to me before: English is an accented language. There is one emphasized syllable in every polysyllabic word, unlike say, Chinese or French where there are no syllable stresses. In Chinese each syllable is delineated quite clearly, giving a staccato feel, wher...

Some English pronounciation tips

Trapped in the USA — Thu, 10 Nov 2011 06:55:47 +0100

Although I learnt English as a second language, I now wear it like a well-worn glove. But in science, there are tons of made-up poly-syllabic words, and I occassionally trip over some of them, such as: equilibrate, equilibrium and equilibration. However, I’ve been learning a bunch of languages the last few years, and through doing that, it’s thrown English prounciation in relief. I’m starting to get a conscious handle on English prounciation, and I’ve discovered some useful rules that were not apparent to me before: English is an accented language. There is one emphasized syllable in every polysyllabic word, unlike say, Chinese or French where there are no syllable stresses. In Chinese each syllable is delineated quite clearly, giving a staccato feel, wherea...

MedEx 2011

Medical Ecosystem for Personalized Event-Based Surveillance — Tue, 08 Nov 2011 08:10:00 +0100

On October 28, 2011 the Second International Workshop on Webscience and Information Exchange (MedEx 2011) took place in Glasgow. The audience had the opportunity to learn more about the facets and research questions related to webscience in medicine and healthcare. Three full papers and five position papers were presented covering a wide spectrum of research problems in medical natural language processing and webscience. Among others, two papers from the M-Eco context have been introduced.In her keynote, Wendy Chapman provided insights into her vision of enabling collaboration and sharing in clinical natural language processing. The second keynote was held by Sophia Ananiadou on advances of biomedical text mining for semantic search. The position papers provided lots of discussion points s...

The paper about BioStar has been published in "PLoS Computational Biology"

YOKOFAKUN — Tue, 01 Nov 2011 04:00:00 +0100

The article describing BioStar has been published in PLoS Computational Biology: BioStar: An Online Question & Answer Resource for the Bioinformatics Community Laurence D. Parnell, Pierre Lindenbaum, Khader Shameer, Giovanni Marco Dall'Olio, Daniel C. Swan, Lars Juhl Jensen, Simon J. Cockell, Brent S. Pedersen, Mary E. Mangan, Christopher A. Miller, Istvan Albert. 2011 PLoS Comput Biol 7(10 (Source: YOKOFAKUN)

Fitting Out

Omics! Omics! — Thu, 27 Oct 2011 04:00:00 +0100

One of the attractions of my new shop was the possibility to see a biotech company built from the ground up. Each of my previous companies had been a long-standing concern by the time I got there; even Codon Devices had a year plus under its belt and some equipment already mothballed. The new venture moved into its first lab space last week, and as you can see from the picture all we have at the moment there are bare walls.Read more » (Source: Omics! Omics!)

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A reference genome with or without the 'chr' prefix

YOKOFAKUN — Fri, 21 Oct 2011 04:00:00 +0100

The name of the chromosomes in the fasta files for the human genome are prefixed with 'chr' : $ grep ">" hg19.fa >chr1 >chr2 >chr3 >chr4 >chr5 >chr6 (...) The FAIDX index for this fasta file looks like this: chr1 249250621 6 50 51 chr2 243199373 254235646 50 51 chr3 198022430 502299013 50 51 chr4 191154276 704281898 50 51 chr5 180915260 899259266 50 51 chr6 171115067 1083792838 50 51 (...) . (Source: YOKOFAKUN)

Running a local JABAWS server for Jalview on Ubuntu (11.04 Natty)

Your bones got a little machine. — Fri, 14 Oct 2011 03:52:52 +0100

The excellent Jalview sequence alignment visualization and editing tool has the ability to send a set of sequences to a multiple sequence alignment web service (“JABAWS”) and receive the results in a new alignment window. This is really convenient when you are doing lots of sequence analysis, and Geoff Barton’s group at the University of Dundee provide a JABAWS server that Jalview will use by default. But maybe the Dundee server is down. Or maybe you think your local machine will do things faster. Or maybe you work on über secret sequences in some Faraday cage bunker with no permanent network connection. In each of these cases, you may want to run your own local JABAWS server and use that instead. In this case, read on. Download the JABAWS war file (direct link here)...

MiSeq Made Easy?

Omics! Omics! — Tue, 11 Oct 2011 04:00:00 +0100

The first computer I ever tried to program was built from a kit by my brother and father. The DATAC-1000 was a single-board machine, with that single printed circuit board about the area of a large laptop (image on page 9). Sporting a grand 1K of RAM, it was a grand machine. User input-output was entirely through a set of binary touchpads and LEDs, though a cassette tape interface enabled storing and reading programs. If I helped any with it, I might have sorted the resistors since I had just learned the color code. The machine sported the same processor as some other machines of the time, such as the KIM-1 and the PET and even something called an Apple.Read more » (Source: Omics! Omics!)

Swimming, Running, Hunting, and Meditating: the Evolutionary Origin of Mystical States

Trapped in the USA — Mon, 10 Oct 2011 12:27:57 +0100

I’ve wondered often at how mystical states came about, states of mind that takes us out of the every day, such as the samadhi of buddhist meditation, or the zone of the long-distance runner. Assume, for argument sake, that such mystical states are an intrinsic part of our human heritage, then they must have evolved from a mental substratum dating back to a more primordial existence. The question then arises as to what possible use our distant quasi-monkey ancestors might have had for mystical-like states or mind. Or to rephrase it another way, is there some kind of biological function that would require the evolution of mystical-like state of mind? To explore this, we need a reasonable map of the evolution of humans from our common ancestor with other apes. First though, we need...

Knime4Bio: a set of custom nodes for the interpretation of NGS data with KNIME

YOKOFAKUN — Fri, 07 Oct 2011 04:00:00 +0100

Our paper has just been published in Bioinformatics :-) http://bioinformatics.oxfordjournals.org/content/early/2011/10/07/bioinformatics.btr554.abstract Knime4Bio: a set of custom nodes for the interpretation of Next Generation Sequencing data with KNIME. Pierre Lindenbaum, Solena Le Scouarnec, Vincent Portero and Richard Redon Summary: Here, we describe Knime4Bio, a set of (Source: YOKOFAKUN)

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Grouping mutations/Gene=f(sample)

YOKOFAKUN — Wed, 05 Oct 2011 04:00:00 +0100

GroupByGene is a small C++ tool grouping the data: CHROM POS REF GENE SAMPLE by gene=f(sample). This tool is available on github:https://github.com/lindenb/ccsandbox/blob/master/src/groupbygene.cpp. Example: $ cat input.tsv #CHROM POS REF ALT GENE SAMPLE chr1 10 A T gene1 indi1 chr1 10 A T gene1 indi2 chr1 11 C G gene1 indi2 chr2 110 C G gene2 indi3 chr3 210 A T gene3 indi1 chr3 211 C T gene3 (Source: YOKOFAKUN)

Verticalize: printing the input stream vertically.

YOKOFAKUN — Wed, 05 Oct 2011 04:00:00 +0100

A useful tool: verticalize is a small C++ tool printing the input stream vertically. The source is available on github : https://github.com/lindenb/ccsandbox/blob/master/src/verticalize.cpp. An Example with 1000genomes.org : $ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.sites.vcf.gz"|\ gunzip -c | grep -v "##" |\ verticalize | head -n 30 >>> (Source: YOKOFAKUN)

Surveillance Workshop at GMDS

Medical Ecosystem for Personalized Event-Based Surveillance — Fri, 30 Sep 2011 06:21:00 +0100

On September 28, 2011, the workshop "From indicator-based to event-based surveillance" took place in conjunction with the GMDS Jahrestagung in Mainz. We had four interesting presentations. Tim Eckmanns gave an overview on indicator- and event based systems and showed the delays in traditional reporting on the EHEC outbreak in 2011. Jas Mantero from ECDC spoke about the event-based surveillace as performed by ECDC. Jens Linge from JRC presented the MediSys System as an example of an event-based system. Kerstin Denecke (L3S) introduced the M-Eco projet. The audience was very interested in the topic and asked motivating questions. All in all a nice workshop in the sunny city of Mainz. (Source: Medical Ecosystem for Personalized Event-Based Surveillance)

Thinking Outside the Box or Just Plain Nuts?

Omics! Omics! — Wed, 28 Sep 2011 04:00:00 +0100

Please take the title in the spirit it is intended: as a bit lighthearted. Seeing the object pictured and reading the accompanying blog post from one of Jonathan Eisen's graduate students. It's an unusual solution to a common problem, and gave me a good chuckle.Read more » (Source: Omics! Omics!)

Boston's Boris Bikes

Omics! Omics! — Tue, 27 Sep 2011 04:00:00 +0100

When I discovered that my new gig would temporarily in Boston, I realized I had an opportunity to try out Boston's new bikeshare program. Started this summer, Hubway consists of racks of bikes in public places which can be used for short hops around town. I like my folding bike, but on some rush hour trains it is very hard to find space for it, especially with some train conductors who are more interested in giving dirty looks than serving their passengers. Plus, it's now quite dark on the last leg of my commute, and even if I had some really slick lights I don't like riding even short distances in the dark.Read more » (Source: Omics! Omics!)

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Medical Ecosystem for Personalized Event-Based Surveillance — Tue, 27 Sep 2011 03:19:00 +0100

Nelson Award Nominee @ Hypertext 2011 We were pleased to be nominated for the Nelson Award at Hypertext 2011 for our paper entitled, A Transfer Approach to Detecting Disease Reporting Events in Blog Social Media, Avaré Stewart, et.al.We continue our work of tackling the burden of manually labelling data and address the problems associated with building a supervised learner to classify frequently evolving, and variable blog content. We automatically classify outbreak reports to train a supervised learner, and the knowledge acquired from the learning process is then transferred to the task of classifying blogs.For more details about our work, please refer to the following link: http://dl.acm.org/citation.cfm?id=1996001 (Source: Medical Ecosystem for Personalized Event-Based Surveillance)

PostScript as a Programming Language for Bioinformatics: mynotebook

YOKOFAKUN — Mon, 26 Sep 2011 04:00:00 +0100

"PostScript (PS) is an interpreted, stack-based programming language. It is best known for its use as a page description language in the electronic and desktop publishing areas."[wikipedia]. In this post, I'll show how I've used to create a simple and lightweight view of the genome. Introduction: just a simple postscript program The following PS program fills a rectangular gray shape; You (Source: YOKOFAKUN)

Joining genomic annotations files with the tabix API.

YOKOFAKUN — Fri, 23 Sep 2011 04:00:00 +0100

Tabix is a software that is part of the samtools package. After indexing a file, tabix is able to quickly retrieve data lines overlapping genomic regions (see also my previous post about tabix). Here, I wrote a tool named jointabix that joins the data of a (chrom/start/end) file with a file indexed with tabix. I've posted the code on github at: https://github.com/lindenb/samtools-utilities/blob/ (Source: YOKOFAKUN)

Transitions

Omics! Omics! — Sun, 18 Sep 2011 04:00:00 +0100

I went to an Infinity going-away lunch last week. We head off to some favorite local restaurant and order a modest (but delicious) meal on the company dime. The departee makes an impromptu speech, there are goodbyes and handshakes and usually a number of pleas to stay, both fictitious and heartfelt. Those staying wonder what could lure someone away from the very safe and green pastures of the company. I've been to many such lunches with Millennium and Infinity; with Codon the lunches tended to be group affairs as people were laid off in batches. Read more » (Source: Omics! Omics!)

Illumina Calls for a Flag on the Play

Omics! Omics! — Wed, 14 Sep 2011 04:00:00 +0100

Continuing my sports analogies, but switching games, in my coverage of the benchtop sequencer war today. Alas, I can't refer to instant replay, as the usual set of procrastination excuses has resulted in this being filed very late after I was made aware of it (first by a comment in the blog, then by a friendly chap from Illumina alerting me). In any case, Illumina has responded to Ion Torrent's claims on long reads and overestimated MiSeq quality, and mostly done so by crying "Foul!".Read more » (Source: Omics! Omics!)

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The Wikipedia Template:Infobox_biodatabase is now integrated in DBPedia

YOKOFAKUN — Sun, 11 Sep 2011 04:00:00 +0100

In January 2011, I started the project Template:Infobox_biodatabase. The goal of this project is the annotation of the biological databases in wikipedia using an infobox. The pages annotated with this template have now been integrated into DBpedia 3.7 and it is now possible to query the data through a SPARQL endpoint. (Note: during the process of writing the new pages in wikipedia, a few articles (Source: YOKOFAKUN)

Customizing "C printf" to print a FASTA sequence.

YOKOFAKUN — Fri, 09 Sep 2011 04:00:00 +0100

The GNU C library lets you define your own custom conversion specifiers for printf template strings. In the current post, I will show how to add a new modifier for printf to print a fasta sequence. Say we have a C structure holding a FASTA sequence: typedef struct fasta_t { char* name; char* sequence; }Fasta; The new output conversion is registered with register_printf_specifier. (Source: YOKOFAKUN)

Interacting with bioinformatics webservers using R

What You're Doing Is Rather Desperate — Thu, 08 Sep 2011 12:49:42 +0100

In an ideal world, all bioinformatics tools would be made available via the Web as a web service with an API, as well as a standalone package to download for local use. This is rarely the case and sometimes, even where one or the other is available, factors such as cost come into play. So we resort to web scraping; writing code to interact with the code that lies behind a web server so as to submit queries, retrieve and parse results. Normally, I’d use something like Ruby’s Mechanize library for this purpose. However, where the purpose is to retrieve delimited data for analysis using R, I figured it was time to try and achieve the entire process within R. So here’s how I used the RCurl and XML packages to interact with the WHAT IF server, which provides tools for the anal...

Parsing a BAM file with javascript, yes we can. (Node.js and V8)

YOKOFAKUN — Tue, 06 Sep 2011 04:00:00 +0100

Node.js is an event-driven I/O server-side JavaScript environment based on V8, Google's open source JavaScript engine. In the current post I will describe how I've used Node/V8 to parse a BAM file. Here I've used node v0.5.5 and my code is hosted in a new git repository bionode. Designing a C++ native extension for Node.js wrapping the bgzf format BAM files are stored using the bgzf format. We (Source: YOKOFAKUN)

Merging two XML files using the libxml streaming API.

YOKOFAKUN — Tue, 06 Sep 2011 04:00:00 +0100

I just wrote a program appending one or more XML files to another XML file using the libxml streaming API. This program named mergexml is available on github at: mergexml.Usage$ mergexml -hmergexml: Pierre Lindenbaum PHD. 2011.Compilation: Sep 6 2011 at 19:54:22.Usage: mergexml [options] -i database.xml xml1, xml2, ....xmlnOptions: -i (required) -o (default:stdout) --replace replace xml-in (Source: YOKOFAKUN)

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Genetic Education:

Omics! Omics! — Wed, 31 Aug 2011 23:00:00 +0100

A study by the American Society of Human Genetics (ASHG) is published today suggesting that few U.S. states have adequate standards in place for genetics education. I forgot to ask for a link to the article that would go live post-embargo, but it should be on the website of the journal (CBE Life Sciences Education)Read more » (Source: Omics! Omics!)

Will Max-Seq Gain Traction?

Omics! Omics! — Tue, 30 Aug 2011 23:00:00 +0100

At the beginning of the month, I had dinner with J Adams from Azco Biotech and some friends/colleagues of his and talked over the Max-Seq. And yes, I did let them pick up the bill -- J wouldn't let me pay for myself. In Sequence did a nice piece on it the next week, so again I've blown an opportunity to scoop them. Then somehow, between vacations and other distractions, this piece was stuck in blogger limbo. But, there are some details I don't see there and some color I think worth adding.Read more » (Source: Omics! Omics!)

Wishing I Had Been A Referee: A Renaissance for Tagamet?

Omics! Omics! — Sat, 27 Aug 2011 23:00:00 +0100

Back from vacation & watching another wave of Hurricane Irene soak the area (curiously, the windiest times so far seem to be breaks in the rain). August has not seen much attention paid to this space (indeed, I have one piece that has gestated nearly the whole month), so time to put the shoulder to the wheel. Just before my vacation, a pair of papers showed up in Science Translational Medicine which describe two attempts at drug re-positioning by transcriptional profiling. The key concept is to take expression profiles for diseases and try to find drugs which appear to generate the opposite transcriptional pattern, with the theory that the drug could nudge the disease pattern back to a normal state. This is an idea which has been kicking around for a while, and at one time was...

Monitoring PubMed retractions: updates

What You're Doing Is Rather Desperate — Tue, 16 Aug 2011 05:51:03 +0100

PubMed cumulative retractions 1977-presentThere’s been a recent flurry of interest in retractions. See for example: Scientific Retractions: A Growth Industry?; summarised also by GenomeWeb in Take That Back; articles in the WSJ and the Pharmalot blog; and academic articles in the Journal of Medical Ethics and Infection & Immunity. Several of these sources cite data from my humble web application, PMRetract. So now seems like a good time to mention that: The application is still going strong and is updated regularly I’ve added a few enhancements to the UI; you can follow development at GitHub I’ve also added a long-overdue about page with some extra information, including the fact that I wrote it :) Now I just need to fix up my Git repositories. Currently there’...

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A FUSE-based filesystem reproducing the NCBI Taxonomy hierarchy.

YOKOFAKUN — Fri, 12 Aug 2011 23:00:00 +0100

In this post I will show how I've used FUSE to create a new loadable filesystem for Linux, reproducing the tree of the NCBI Taxonomy. From the Fuse Homepage:With FUSE it is possible to implement a fully functional filesystem in a userspace program. Features include:Simple library APISimple installation (no need to patch or recompile the kernel)Secure implementationUserspace - kernel interface (Source: YOKOFAKUN)

Wikipedia OpenSearch and semantic bash completion

YOKOFAKUN — Tue, 09 Aug 2011 23:00:00 +0100

I wrote a tool that use the opensearch API for mediawiki to display the results of a query in wikipedia:$ opensearch Charles DarwCharles_Darwin Charles Robert Darwin FRS (12 February 1809 – 19 April 1882) was an English...Charles_Darwin_University Charles Darwin University (CDU) is an Australian public university wi...Charles_Darwin%27s_health For much of his adult life, Charles Darwin's (Source: YOKOFAKUN)

Quick tip: bash completion for Bioinformatics

YOKOFAKUN — Mon, 08 Aug 2011 23:00:00 +0100

The default behavior for the completion can be extended by creating a new file: ${HOME}/.bash_completion in your home. For example, you can write your own Bash Completion for samtools, bwa or your favourite tool by adding the following line in "${HOME}/.bash_completion": complete -f -X '!*.@(bam|sam|fasta|fa|fa.gz|fastq.gz|fasta.gz)' samtools bwa Open a new bash and type: $ samtools index (Source: YOKOFAKUN)

Names in Collision

Omics! Omics! — Sun, 07 Aug 2011 23:00:00 +0100

I will claim that I saw this coming, in that I've toyed with the basic skeleton of this post before. But, I hadn't gotten around to it -- but how could I miss this opportunity. On a mailing list devoted to SAM, someone asked about a related topic to SAM, and one of the experts on the board replied with an electronic head-scratchingRead more » (Source: Omics! Omics!)

BioRuby development: feedback on using Git

What You're Doing Is Rather Desperate — Fri, 05 Aug 2011 03:15:57 +0100

Everyone likes constructive feedback. I received a couple of great comments on my previous post, which warrant a brief discussion. @vlandham points out that when the main BioRuby repository updates, you’ll want to update your local repository. Using git, you do that by adding a remote which points to the original repository, from which you can fetch updates and merge with your local version: git remote add upstream https://github.com/bioruby/bioruby.git # fetch/merge only when main repo updates git fetch upstream git merge upstream master This is described at the GitHub help page Fork A Repo. Michael points to an article titled A successful Git branching model. It suggests that when developing new features you create a feature branch (also called topic branch). This can help with t...

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A beginner’s guide to BioRuby development

What You're Doing Is Rather Desperate — Thu, 04 Aug 2011 13:31:35 +0100

I’m the “biologist-turned-programmer” type of bioinformatician which makes me a hacker, not a developer. Most of the day-to-day coding that I do goes something like this: Colleague: Hey Neil, can you write me a script to read data from file X, do Y to it and output a table in file Z? Me: Sure… (clickety-click, hackety-hack…) …there you go. Colleague: Great! Thanks. I’m a big fan of the Bio* projects and have used them for many years, beginning with Bioperl and more recently, BioRuby. And I’ve always wanted to contribute some code to them, but have never got around to doing so. This week, two thoughts popped into my head: How hard can it be? There isn’t much introductory documentation for would-be Bio* developers The answer to the firs...

Ion Throws A Long Punch At MiSeq

Omics! Omics! — Wed, 03 Aug 2011 23:00:00 +0100

The benchtop sequencer wars are heating up! Illumina and Life are engaged in a fierce war of pamphlets and datasets to convince the world that they have the edge. I won't attempt to give a complete play-by-play, but hit on the latest developments, which includes Ion releasing a dataset of 250+ bp reads.Read more » (Source: Omics! Omics!)

The GPCR-G complex: the canonical structure of Cell Signaling (with interactive guide)

Trapped in the USA — Mon, 01 Aug 2011 23:27:19 +0100

embed_a1_dict = { "pdb_id":"3sn6", "canvas_tag":"embed_a1_tag", "view_id":"view:u74775", "text_height":120, } embed_a2_dict = { "pdb_id":"3sn6", "canvas_tag":"embed_a2_tag", "view_id":"view:5xd1fr", "text_height":80, } embed_a3_dict = { "pdb_id":"1azt", "canvas_tag":"embed_a3_tag", "view_id":"view:nid9qp", "text_height":80, } Perhaps you’ve heard of the new structure of the GPCR-G complex. It’s a seminal breakthrough, and I concur with Curious Wavefunction in that it’s worthy of a Nobel prize. So noobs, why is it important? According to some estimates, some 30% of our proteins are membrane proteins and the reason that they are so many is that membrane proteins are where most of the signal processors between our cells are found. Our multi-cellularity d...

ISMB coverage on Twitter? It’s possible there was…

What You're Doing Is Rather Desperate — Mon, 01 Aug 2011 04:38:17 +0100

Peter writes: I wonder if part of the drop off is live bloggers moving to platforms like Twitter? I can tell you it seemed like there were almost as many tweets for one SIG (#bosc2011) as for the whole of #ISMB / #ECCB2011, and I personally didn’t post anything to FriendFeed but posted lots on Twitter. Well, there’s a problem with using Twitter for analysis of conference coverage. Let’s try searching for ISMB-related tweets using the twitteR package: library(twitteR) ismb <- searchTwitter("ismb", 1000) length(ismb) # [1] 30 If we can't archive, how can anyone else?30? Are we using twitteR properly? Running the same search at the Twitter website gives roughly the same results, plus this unhelpful message. I like Twitter – as a real-time communicatio...

The Metaphysical Countrygirl

Trapped in the USA — Mon, 01 Aug 2011 02:57:44 +0100

You, functional space variants in voltage, the only light Transitory effect of Love several different lights Sustain Sustain them you sustain them. ~ Omar Pérez, 2010 translated by Krisitin Dykstra Gentlemen: a little gift for the ladies who prefer Tesla coils to hair-rollers (Source: Trapped in the USA)

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Using the Freebase and the Bioportal Widgets to create a semantic object.

YOKOFAKUN — Sun, 31 Jul 2011 23:00:00 +0100

The following HTML code uses:a Widget from the NCBO Bioportal for the Protein-protein interaction OntologyAnd two Widgets from Freebase, linking to the proteins, the genes and the diseases.After completion, it generates a JSON object describing a semantic object:{"subject":"http://www.freebase.com/view/en/nsp3","predicate":"http://purl.org/obo/owl/MI#MI_0407","value":"http://www.freebase.com/view (Source: YOKOFAKUN)

Memory-Mapping the Human Genome with 'mmap': my notebook

YOKOFAKUN — Sun, 31 Jul 2011 23:00:00 +0100

In this post, I've explored how to use a memory-mapped file to handle the 3Go of the Human Genome sequence as if it was entirely loaded in memory.Via wikipedia: "A memory-mapped file is a segment of virtual memory which has been assigned a direct byte-for-byte correlation with some portion of a file or file-like resource. This resource is typically a file that is physically present on-disk... In (Source: YOKOFAKUN)

Storing some SNPs using the leveldb library. My notebook.

YOKOFAKUN — Sat, 30 Jul 2011 23:00:00 +0100

In this post I'll describe how I've used the leveldb API, a C++ key-value database, to store some SNPs (key=rs,value=sequence). "LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.". A benchmark for this engine is available here: http://code.google.com/p/leveldb/source/browse/trunk/doc/benchmark.html.Download & install (Source: YOKOFAKUN)

How Many Toes Does Ion Have Left?

Omics! Omics! — Thu, 28 Jul 2011 23:00:00 +0100

I've previously complained about Ion Torrent's bungling and secrecy when it comes to educating their current and potential future users about key technical information. I've recently come across yet another botch, one that underscores that attempting to control information in the Internet age only serves to distract from the goal of ensuring access to correct information.Read more » (Source: Omics! Omics!)

I can’t resist a word cloud: now using R!

What You're Doing Is Rather Desperate — Thu, 28 Jul 2011 10:11:36 +0100

Top 1000 words in FriendFeed comments, ISMB 2008-2011The wordcloud package is word clouds for R with a difference: they look great. Of course, having just analysed online coverage of the ISMB conference, I had to run all 6 906 comments from the 2008-2011 meetings through some code. If you followed along via the Sweave code, I went as far as generating the data frame of comments, ismb.comments, then pulled the comment text into a new data frame using: data.frame(ismb.comments$body) It was then simply a case of following along with the excellent example code from the post Word Cloud in R, over at One R Tip A Day, limiting myself to the 1000 most-used words. Watch out, the TermDocumentMatrix() function from the tm package uses quite a lot of memory. Result shown at right: click image for full...

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Analysis of ISMB coverage at FriendFeed: 2008 – 2011

What You're Doing Is Rather Desperate — Thu, 28 Jul 2011 02:40:17 +0100

ISMB/ECCB 2011 was held between July 15-19 this year and as in previous years, FriendFeed was used to cover the meeting. Last year, I wrote a post about how to use R to analyse the coverage. I was planning something similar for 2011 when I thought: we have 4 years of ISMB at FriendFeed now – why not look at all of them? So I did. Read on for the details. 1. First – an apology In my post from last year, I included some R code which will grab a FriendFeed feed in JSON format using the API and convert it to an R list. I would have used it again this year, except that the ISMB 2008 feed is no longer a complete archive of the 2008 meeting. This is, unfortunately, my fault – but all is not lost. I decided to leave FriendFeed earlier this year and began by deleting the se...

Tschuess, Shuttle!

Omics! Omics! — Wed, 27 Jul 2011 23:00:00 +0100

Clearly with a week having passed since touchdown, my farewell to the space shuttle program is grossly overdue. I actually missed watching the event live, as I was off on a camping trip in some beautiful New Hampshire woods. Atop of the usual excuses, it's been a bit hard to figure out what I could write that was different than so much that has been written. It would seem that every major media outlet opined on the subject, and most did a decent job in hitting the key points. Read more » (Source: Omics! Omics!)

Controlling IGV through a Port: my notebook.

YOKOFAKUN — Tue, 26 Jul 2011 23:00:00 +0100

A protocol for interacting with the The Integrative Genomics Viewer (IGV) is described here: http://www.broadinstitute.org/igv/PortCommands. So, you can save some pictures of a genomic region without interacting with IGV.Via a shell script$ cat script.shmkdir -p /tmp/igvsleep 2echo "snapshotDirectory /tmp/igv"sleep 2echo "goto chr3:100"sleep 2echo "snapshot"sleep 2echo "goto chr3:200-300"sleep (Source: YOKOFAKUN)

A mysql full-text parser searching for some SNPs

YOKOFAKUN — Mon, 25 Jul 2011 23:00:00 +0100

A mysql full-text parser server plugin can be used to replace or modify the built-in full-text parser.This post a full-text parser plugin named bioparser that extracts the rs#### id from a text.The sourceThe source of this plugin is available on github at:https://github.com/lindenb/bioudf/blob/master/src/bioparser.c.The work horse of the plugin is a simple function bioparser_parse scanning the (Source: YOKOFAKUN)

The samtools C API: creating a WIG file for the genome coverage

YOKOFAKUN — Sun, 24 Jul 2011 23:00:00 +0100

I wrote a tool which uses the samtools API to generate a WIG file for the genome coverage. This tool, bam2wig, as well as some other tools using this library are available in the following git repository:https://github.com/lindenb/samtools-utilitiesMy code is based on this original C source hosted on: http://samtools.sourceforge.net/sam-exam.shtml. (I hope I understood this API as many functions/ (Source: YOKOFAKUN)

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Getting out gene list from Ensembl web query results with WWW::Mechanize

Bioinformatics Latest News — Wed, 20 Jul 2011 04:00:00 +0100

Seems like the Ensembl API is not providing a way to get list of results (?) for web query, thus decided to write a simple perl script. So to get list of gene hits for Ensembl query 'histone h2a histone cluster 1' one can simply run: perl getensidmech.pl 'histone h2a histone cluster 1'and the quick and dirty code getensidmech.pl using WWW::Mechanize is there at http://research-code-base-animesh.googlecode.com/svn/trunk/code_lic/getensidmech.pl :) (Source: Bioinformatics Latest News)

Drawing a SVG timeline with the http://data.bnf.fr data

YOKOFAKUN — Tue, 19 Jul 2011 23:00:00 +0100

The National French Library has recently started to releaseits data as RDF/XML. Here, I've played with the biographies of the famous French writers to create a simple timeline.Unfortunately, this timeline is too large to be displayed here. :-)However, here is the java code I used to generate this map as a SVG document: See also: Freebase and the History of Sciences That's it,Pierre (Source: YOKOFAKUN)

Intuition arises out of Mathematical Intractability

Trapped in the USA — Mon, 18 Jul 2011 13:51:53 +0100

In conclusion, all I want to add to Curious’s post is that chemist rely on their intuition specifically because the mathematics in quantum chemistry does not admit easily solvable equations, or reliable low-order approximations. The intuition is needed simply because a useful mathematical solution is not tractable. Similar problems plague many sub-disciplines in physics but the physicists have a much better PR machine. (Source: Trapped in the USA)

An interactive 'dialog' generating a SAM Flag

YOKOFAKUN — Sun, 17 Jul 2011 23:00:00 +0100

The following shell script uses the dialog utility to generate a numeric Sam flag.$ sh selectsam.sh ┌───────────────────────SAM FLAGS──────────────────────────┐ │ SELECT FLAGS │ │ ┌──────────────────────────────────────────────────────┐ │ │ │ [X] 1 Read Paired │ │ │ │ [ ] 2 Read (Source: YOKOFAKUN)

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I give up

What You're Doing Is Rather Desperate — Fri, 15 Jul 2011 04:26:35 +0100

It’s what – 10 years or more? – since we began to wonder when web technologies such as RSS, wikis and social bookmarking sites would be widely adopted by most working scientists, to further their productivity. The email that I received today which began “I’ve read 3 interesting papers” and included 1 .doc, 3 .docx and 4 .pdf files as attachments is indicative of the answer to this question, which is “not any time soon.” I’ve given up trying to educate colleagues in best practices. Clearly, I’m the one with the problem, since this is completely normal, acceptable behaviour for practically everyone that I’ve ever worked with. Instead, I’m just waiting for them to retire (or die). I reckon most senior scientists (and they...

I can't save you, but I can help you: reverse-complementing a DNA in OpenOffice

YOKOFAKUN — Thu, 14 Jul 2011 23:00:00 +0100

People in my lab are using "Microsoft Word" to edit and annotate their sequences. Just like Neil, I can't save them but I can help them: here is an OpenOffice / LibreOffice macro reverse-complementing the current selected text. open libreoffice/openofficeOpen menu "Tools / Macros / Organize macros / Basic...Select "My Macros/Standard" and click on "New"Copy+paste my macro hereClick on the top (Source: YOKOFAKUN)

A text alignment viewer using the samtools API

YOKOFAKUN — Wed, 13 Jul 2011 23:00:00 +0100

I wrote a modified version of samtools tview. The original code uses the curses API to display an interactive sequence viewer.I wanted to generate this kind of screen for a large number of positions and I wanted to be able to redirect the output to a unix pipeline so I changed the original code in order to only handle an extensible 2-dimensional array of characters. The code I wrote is available (Source: YOKOFAKUN)

Ion's Gaggle of New Accessory Products

Omics! Omics! — Mon, 11 Jul 2011 23:00:00 +0100

Ion Torrent had a press release announcing a number of new components to the platform, as well as shipping of the 316 chip and a drop in price of the original 314 chip to $99 (alas, the announcement was not synchronized with updating the online store, so no details could be checked -- such as the price of the 316 chips).Read more » (Source: Omics! Omics!)

PacBio's Foray Against the German E.coli Outbreak

Omics! Omics! — Sun, 10 Jul 2011 23:00:00 +0100

I recently remarked that it was surprising that PacBio had not jumped on the German E.coli outbreak strain, given CEO Eric Schadt's professed interest in biosurveillance. Dr. Schadt was kind enough to spend a half hour discussing the topic with me last week, in the wake of PacBio releasing de novo assemblies of this strain and 11 other pathogenic E.coli strains (6 having never previously been sequenced) on the PacBio DevNet website. Dr. Schadt also has a detailed blog post on the project. In both the blog post and our conversation yesterday he explained why PacBio wasn't in the forefront of this effort but still decided to jump in. Dr. Schadt was certainly aware of the outbreak; he was in Germany at a conference when the public alarm was building. But initi...

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Storing SNPs in a HDF5 file: my notebook

YOKOFAKUN — Fri, 08 Jul 2011 23:00:00 +0100

I discovered the benefits of using twitter in 2008, the day Deepak Singh replied to one of my tweets related to the storage of a large number of genotypes.Since that day, I've tried to use the HDF5 library, without any success (there's a large disheartening documentation/API on the HDF5 site and the API seems to be only used by a small number of geeks). Furthermore, HDF5 is a technology used by (Source: YOKOFAKUN)

R: calculations involving months

What You're Doing Is Rather Desperate — Thu, 07 Jul 2011 13:32:38 +0100

Ask anyone how much time has elapsed since September last year and they’ll probably start counting on their fingers: “October, November…” and tell you “just over 9 months.” So, when faced as I was today with a data frame (named dates) like this: pmid1 year1 month1 pmid2 year2 month2 21355427 2010 Dec 21542215 2011 Mar 21323727 2011 Feb 21521365 2011 Jun 21297532 2011 Feb 21336080 2011 Mar 21291296 2011 Apr 21591868 2011 Jun ... How to add a 7th column, with the number of months between “year1/month1″ and “year2/month2″? R has lots of methods for date/time calculations, many of which seem notoriously difficult to get your head around. One answer for my problem came, as so often, from ...

Second M-Eco User Workshop

Medical Ecosystem for Personalized Event-Based Surveillance — Mon, 04 Jul 2011 08:40:00 +0100

On May 26, the second M-Eco user workshop took place. Again, representatives of WHO, INVS, ECDC as well as from the Mekong Basin Disease Surveillance Oragnisation attended the meeting. he consortium presented the first prototype and several evaluation experiments have been performed. The user feedback will be considered in the secon phase of the project. (Source: Medical Ecosystem for Personalized Event-Based Surveillance)

The Neo4j REST API. My notebook

YOKOFAKUN — Sun, 03 Jul 2011 23:00:00 +0100

Neo4j is a open-source graph engine implemented in Java. This post is my notebook for the Neo4J-server, a server combining a REST API and a webadmin application into a single stand-alone server.Download & extract Neo4JDownload Neo4J from here$ tar xfz neo4j-community-1.4.M04-unix.tar.gz$ rm neo4j-community-1.4.M04-unix.tar.gz$ cd neo4j-community-1.4.M04/Start the Neo4J Server#edit the config (Source: YOKOFAKUN)

Workshop at GMDS conference

Medical Ecosystem for Personalized Event-Based Surveillance — Tue, 28 Jun 2011 07:24:00 +0100

The M-Eco consortium will held a workshop on the topic "From indicator-based to event-based surveillance" at the Annual Meeting of the German Sociaty of Medical Informatics and Society of Epidemiology. The workshop will be held on September 28 at the Johannes-Gutenberg Universität in Mainz. More details are available:here (Source: Medical Ecosystem for Personalized Event-Based Surveillance)

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The java library for BigBed and BigWig: my notebook

YOKOFAKUN — Mon, 27 Jun 2011 23:00:00 +0100

Jim Robinson and his team, from the Broad Institute/IGV, have recently released a java library parsing the BigBed and the BigWig formats. Here is my notebook for this API.Download and compile the libraryThe sources are hosted at: http://bigwig.googlecode.com/.$ svn checkout http://bigwig.googlecode.com/svn/trunk/ bigwig-read-only$ cd bigwig-read-only$ antBuildfile: build.xmlcompile: [mkdir] (Source: YOKOFAKUN)

Bioinformatician 2.0 ( JeBiF Workshop 2011 )

YOKOFAKUN — Mon, 27 Jun 2011 23:00:00 +0100

Here is the presentation I gave for the JeBiF Workshop 2011 (jobs and careers in bioinformatics).Bioinformatician 2.0 View more presentations from Pierre Lindenbaum Pierre Legrain (CEA) and Franck Molina, CNRS talking about working in Bioinformatics in the industry and/or academia. (Source: YOKOFAKUN)

MiSeq Aims for Ion Torrent

Omics! Omics! — Thu, 23 Jun 2011 23:00:00 +0100

Illumina has released a MiSeq dataset for E.coli MG1655 on its website. Accompanying the FASTQ and BAM files is a presentation, the first half of which compares the performance to big brother HiSeq. The second half is an explicit comparison against the available Ion Torrent. Read more » (Source: Omics! Omics!)

A first peek at data from an Ion 316 chip

Omics! Omics! — Mon, 20 Jun 2011 23:00:00 +0100

Ion Torrent has made available an E.coli DH10B fragment dataset for the 316 chip, which is expected to be generally available early next month. I've theoretically had access to the data since Saturday, but a series of events (computer-free weekend, a crashed home computer, a personal day & a good but unbloggable conference) have meant that ambitious plans to analyze it are still in progress. So, what I discuss below is either from Ion's provided information or other sources, so take it with appropriate caution.Read more » (Source: Omics! Omics!)

Two administrative notes

Omics! Omics! — Mon, 20 Jun 2011 23:00:00 +0100

Two administrative items:First, sometimes comments are getting moderated very late. I do pledge this is not an attempt on my part to bury negative commentary. Rather, it appears that sometimes when I thought I had moderated comments via my Android phone it hasn't succeeded. Second, I am trying out the new smartphone-friendly layout option for Blogger. Please let me know if you are reading this on a smartphone and hate the new layout.Read more » (Source: Omics! Omics!)

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Woman drowned in molten chocolate

Trapped in the USA — Mon, 20 Jun 2011 13:37:50 +0100

Oh, to be a performance artist in NYC. Beguiling mix of textures, facial transmorgification, guttural colors, and drowning. Cocoally good: Chocolate, 2010 from MARTYNKA WAWRZYNIAK on Vimeo. (Source: Trapped in the USA)

A couchdb-like application using apache JETTY and BerkeleyDB. My notebook

YOKOFAKUN — Sat, 18 Jun 2011 23:00:00 +0100

This is my notebook for the Jetty API. Jetty provides an Web server and javax.servlet container. It can be embedded in devices, tools, frameworks, application servers, and clusters. I find it more easier for developping and testing a new web application as it doesn't require some deployement descriptors, some configuration files, a web container, etc... like in apache tomcat. As I will show below (Source: YOKOFAKUN)

E.coli Outbreak Genomics

Omics! Omics! — Tue, 14 Jun 2011 23:00:00 +0100

The E.coli outbreak in Germany continues to be a major news item. It is looking increasingly doubtful that the source of the infection will be conclusively traced, as the German authorities have already named and then backed off two suspects, Spanish cucumbers and German bean sprouts. These activities have not been without repercussions; Spanish agriculture has been hard hit and exports of European produce in general are reportedly hurting. On the genomics front, the outbreak has demonstrated how quickly bacterial genomics can be run on the current class of instrumentation. BGI Europe knocked off the sequence in a series of Ion Torrent runs in 3 days, and a group at University of Muenster worked at similar speed with the Ion setup as well. Later, sequences have come ...

Sorting and Joining some Genotypes with Hadoop.

YOKOFAKUN — Tue, 14 Jun 2011 23:00:00 +0100

This post describes how I've used hadoop to merge two large files produced by our Affymetrix-Axiom Genotyping platform.(Note: working with the last version of hadoop has been a headache: it contains some classes with the same name: ('org.apache.hadoop.mapreduce.Reducer' and 'org.apache.hadoop.mapred.Reducer' ), many classes have been deprecated ( org.apache.hadoop.mapred.JobConf ) but they are (Source: YOKOFAKUN)

XSLT+SVG= "It Came from Outer Space" (anaglyphs)

YOKOFAKUN — Sun, 12 Jun 2011 23:00:00 +0100

"It Came from Outer Space", Universal's first film to be filmed in 3-D.Just like with the "Gimp", Inkscape , a SVG editor, can manage some layers:Each layer will appear in the SVG document as an element svg:g with an attribute: inkscape:groupmode="layer" under the root element svg:svg. I've written a XSLT stylesheet that converts the SVG image to an Anaglyph image. The stylesheet is available on (Source: YOKOFAKUN)

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Startups, tenure and real-world systems

business|bytes|genes|molecules — Sun, 12 Jun 2011 06:44:50 +0100

Tweet Earlier today I visited DBMS Musings to read Daniel Abadi’s blog post on peer review, but ended up re-reading an older post. In the post Daniel talks about why he is doing a startup pre-tenure. I am not an academic, neither have I ever started a company, although I’ve been in both environments, so I can’t quite speak from experience here, but the post caught my attention at multiple levels. What makes this interesting is that Daniel has spent time on getting his company off the ground himself, with active involvement, and the resulting leave of absence limits his ability to do things junior faculty are expected to do, like publish. He admits that there is little precedent and that it’s a gamble. So why go on? Admittedly, this is computer science, but the key ...

An extension for Inkscape processing a sequence from Genbank

YOKOFAKUN — Thu, 09 Jun 2011 23:00:00 +0100

Let's create a new extension for inkscape by recycling an old XSLT stylsheet producing a SVG image ! For example, we're going to use this xslt stylsheet: https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/ncbi/gb2svg.xsl that transforms a Genbank XML INSDSeq to SVG. It is downloaded into the extension directory; ${HOME}/.config/inkscape/extensions/gb2svg.xslNow let's tell (Source: YOKOFAKUN)

Vectorial drawing with the UCSC Genome browser and inkscape

YOKOFAKUN — Thu, 09 Jun 2011 23:00:00 +0100

Select a view in the UCSC genome browser. Export it (top menu) it as Encapsulated Postscript (EPS)Import the EPS file in inkscape'Ungroup' the objects and have fun.That's it.Pierre (Source: YOKOFAKUN)

Handling a BigWig file from Java+JNI : my notebook

YOKOFAKUN — Mon, 06 Jun 2011 23:00:00 +0100

In a previous post I've shown how to use a Java JNI interface to control a NCURSES panel from a java program.I'll show here how to use java JNI to call the C methods developped by Jim Kent's team at UCSC to handle a BigWig file.The Makefile for compiling the following sources is defined below:Export the LD_LIBRARY_PATH:export LD_LIBRARY_PATH=/path/to/current/directoryDownload Jim Kent's sources (Source: YOKOFAKUN)

If you have too much data, then “good enough” is good enough

business|bytes|genes|molecules — Mon, 06 Jun 2011 19:16:36 +0100

Tweet I would suggest that all my friends in the world of bioinformatics read this fabulous article by Pat Helland. Pat’s on of the leading experts in distributed transactions and knows more about databases than most of us put together. His ACM article goes into some the tradeoffs and changes in mindset that need to me made when working with data that changes and comes from different sources, and all so o ften has ambiguity associated with it. It also tells you a little but about the differences in SQL and NoSQL systems when it comes to transaction semantics and in a way that meets complete sense. Perhaps the most interesting part of the article was the section on “Mulligan stew” where we also provides the example of building a heterogeneous catalog. A product catalog...

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The Arsenic Bug, Revisited

Omics! Omics! — Sat, 04 Jun 2011 23:00:00 +0100

As has been covered in many outlets, Science has released eight technical comments on the arsenic-loving bacterium issue along with a response by the authors, which I commented on when it appeared. A good summary of the comments can be found at In The Pipeline, and Fejes.ca has a good take on it as well. The quick summary is that various technical and theoretical issues are presented by the critics, and the NASA team dismisses all of them by standing by their data and interpretations. Read more » (Source: Omics! Omics!)

Pubmed: sorting the articles on the number of times they've been cited

YOKOFAKUN — Fri, 03 Jun 2011 23:00:00 +0100

In 2008 I used www.eigenfactor.org/ to sort a set of Pubmed articles on the impact factor of the journal. In the current post I will show I've used NCBI ELink to sort the articles on the number of times they've have been cited in some other articles in pubmed-central.The NCBI ELink API checks for the existence of an external or link from a list of one or more primary IDs. It can (Source: YOKOFAKUN)

The Pain: Installing Matplotlib in Snow Leopard on a Mac

Trapped in the USA — Fri, 03 Jun 2011 06:58:46 +0100

I’ve said it before, and I’ll say it again, python combined with matplotlib is one of the most potent tools for scientific computation. But gee, why does it have to be so hard to install it on my Macbook with Snow Leopard? I’ve finally figured it out how to install it on my computer with some measure of understanding. So here are some tips. If you really want to get it working RIGHT NOW, I suggest you use macports, and just do sudo port install py26-matplotlib which will install a separate version of python2.6 in the ‘/opt/local’ directory. However, everything will work. The down side of this approach is that other packages that you install through a .dmg will fail to find that version of python installed in ‘/opt/local’. Alas, the standard...

agile redUX

Inforbiomatica — Thu, 02 Jun 2011 17:39:51 +0100

I blogged (more) recently (than here) at balancedteam.org on agile redUX: http://www.balancedteam.org/2010/12/20/agile-redux/ (Source: Inforbiomatica)

Finding the truth is a waste of time, scientists say

What You're Doing Is Rather Desperate — Thu, 02 Jun 2011 02:29:42 +0100

Before bioinformatics, I worked in both biochemistry and microbiology labs, including a stint in the field of extremophile biology. So like many other people, I’ve been following the “arsenic life” story with great interest. It seems that far more has been written about the publication, the manner of its announcement, the ensuing online debate and the personalities involved than about the principal scientific question: can arsenate substitute for phosphate in biological molecules? My opinion, for what it’s worth, is that the Science paper presented no compelling evidence for covalently-bound As in DNA and that the editors should have asked the authors either to do better experiments or tone it down. Now, Nature News reports that the criticisms are in, the authors ha...

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Playing with the Gimp server: my notebook

YOKOFAKUN — Mon, 30 May 2011 23:00:00 +0100

In the following post, I'll show how the Gimp can be used as a server that will read and execute some statements in the scheme programming language. The scheme script will be used to downlad, resize and filter an image from the web.Starting the Gimp ServerGo in menu Filters→Script-Fu→Start ServerThe original image(3156 x 2538)Barbara McClintock in the lab at Cold Spring Harbor in 1947The (Source: YOKOFAKUN)

Computing and abstractions revisited

business|bytes|genes|molecules — Sun, 29 May 2011 17:05:22 +0100

Tweet Computing is critical. Computing is not important. Two seeming contradictory statements, but I’ll point to Google. Their success is built on computing, lots of it. The end user doesn’t care. They get information back. They don’t have to set up clusters and queries. They just search. While that’s a gross oversimplication for science, there are aspects of computing productivity that just don’t make sense anymore. I was reminded of this point by a question on Biostar about setting up MPI. There are different level of skill sets required and I might be one of the first to argue that a computational scientist should understand their tool, the computer. But at what level? In the end I love abstractions and productivity. The more you have to spend time setti...

Cancer classification using Google prediction API

Bioinformatics Latest News — Sun, 29 May 2011 12:42:00 +0100

Google's prediction API is now available to everyone with nice tutorial on how to get going :) so I decided to check its performance using gene expression values for 5 selected genes using online-feature-selection from the classic AML/ALL dataset (training/test).The dataset needed to be formatted (training/test) and copied to Google storage to get the default scripts working. Coming to the results, well the training step:./oauth-train.sh mlani/top5_tr.csvgave a performance of about 3/4:./oauth-check-training.sh mlani/top5_tr.csv{ "kind": "prediction#training", "id": "mlani/top5_tr.csv", "selfLink": "https://www.googleapis.com/prediction/v1.2/training/mlani/top5_tr.csv", "modelInfo": { "modelType": "classification", "classificationAccuracy": 0.75 }, ...

Purity in the atomic force-fields of molecular dynamics simulations

Trapped in the USA — Sun, 29 May 2011 05:56:51 +0100

In the protein modeling community, there is a split between those who pursue a more “physics-based” approach, and those pursue a more “empirical-based” approach. Nothing highlights this better than the acrimonious debate between atomic force-fields and statistical potentials. These force-fields are used in everything from protein folding studies, ligand-binding studies and protein-protein interaction studies. From a brutally pragmatic point of view, the successes in protein folding and homology modeling show that empirical force-fields have galloped far ahead. Still, the purists leer down on empirical force-fields, as they pray themselves to sleep at night that the test of time will expose empirical force-fields for the dirty statistic aberrations that they are. ...

Cancer classification using Google prediction API

Bioinformatics Latest News — Sun, 29 May 2011 04:00:00 +0100

Google's prediction API is now available to everyone with nice tutorial on how to get going :) so I decided to check its performance using gene expression values for 5 selected genes using online-feature-selection from the classic AML/ALL dataset (training/test). The dataset needed to be formatted (training/test) and copied to Google storage to get the default scripts working. Coming to the results, well the training step: ./oauth-train.sh mlani/top5_tr.csvgave a performance of about 3/4: ./oauth-check-training.sh mlani/top5_tr.csv { "kind": "prediction#training", "id": "mlani/top5_tr.csv", "selfLink": "https://www.googleapis.com/prediction/v1.2/training/mlani/top5_tr.csv", "modelInfo": { "modelType": "classification", "classificationAccuracy": 0.75 &...

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Data, software, and money

business|bytes|genes|molecules — Sun, 29 May 2011 00:38:14 +0100

Tweet Steve O’Grady has written a blog post about a recent talk he gave at OSBC. In the post he welcomes the Age of Data. The talk covers two topics of great interest, software and data. In the context of the life sciences I have worked on both the “data as a product” side and on the packaged software side. He notes that none of the top “software” companies in the world are of recent vintage. These are companies making money from selling software (a really difficult business in the sciences). He argues that data driven products is where the market is. The success of Google and others is a testament to this, but in the sciences the entire model of data as product has never worked. I would argue that this is partly cause we’ve always sold the data itself ...

Paying a Painful 75% Secrecy Tax

Omics! Omics! — Wed, 25 May 2011 23:00:00 +0100

In a post a while back, I mentioned that my Ion Torrent sequencing project was stalled because my service provider couldn't get some of the key kits, despite an Ion representative posting that no such shortages existed. I've been remiss in updating that; last Tuesday the kits showed up and Monday I got my data -- and a bit of a shock.Read more » (Source: Omics! Omics!)

Predicting kinase specificity from phosphorylation data

Public Rambling — Wed, 25 May 2011 17:37:00 +0100

Over the past few years, improvements in mass-spectrometry methods have resulted in a big increase in throughput for the identification of post-translational modifications (PTMs). It is even hard to keep up with all the phosphoproteomics papers and the accumulation of phosphorylation data. Most often, improvements in methods result in interesting challenges and opportunities. In this case, how can we make use of this explosion in PTM data ? I will try to explore a fairly straightforward idea, on how to use phosphorylation data to predict kinase substrate specificity. I'll describe here the general idea and just the first stab at it to show that I think it can work. The inspiration for this is the work by Neduva and colleagues that have show that we can search for enriched m...

MiSeq's First Light

Omics! Omics! — Sun, 22 May 2011 23:00:00 +0100

Someone was kind enough to send me a copy of a poster by Illumina reporting results from the MiSeq. Now, to be very upfront, by someone I mean "a person from a PR firm contracted by Illumina" and "kind enough" that she was doing her job. I don't have illusions about motive here, the author list is all from Illumina or Epicentre, but this was a poster presented at the recent Cold Spring Harbor Biology of Genomes meeting. It certainly isn't peer-reviewed data, but it is something. Of course, we can't know to what degree these are cherry-picked results. If you want to be really cynical, call it messaging and not data. Yes, I've taken some flak in the comments recently about how favorable my coverage of Ion has been, and I'm trying to adjust. �...

Jargon: The Art of Naming Things

Trapped in the USA — Sun, 22 May 2011 21:47:20 +0100

I like jargon but jargon, like anything else, can be used for good, or for evil. Whilst there are plenty of writing guides that rail against the use of jargon, such advice would make us miss out on the richness that carefully minted technical terms add to the language. Our language would be poorer without words such as entropy or DNA or tectonic plates. Still, an eternally recurring complaint is that academic articles are unreadable because they are riddled with jargon, prose-killing, soul-sucking jargon. But is jargon the real problem? Perhaps it’s merely the sloppy use of jargon. I don’t believe that all science writers out there are deliberately using jargon to obfuscate their thoughts. It’s just that no-one’s really framed a way for them to use jargon effectiv...

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PERL one liner to generate 1000 base genome

Bioinformatics Latest News — Sun, 22 May 2011 04:00:00 +0100

perl -e '@b=qw/A T G C/;print ">Genome\n";while($l<1000){print @b[int(rand(4))];$l++;}' (Source: Bioinformatics Latest News)

Syntax highlighting of R code at WordPress.com

What You're Doing Is Rather Desperate — Fri, 20 May 2011 07:57:46 +0100

If your WordPress blog is hosted at WordPress.com (like this one), you may know that source code in posts is formatted and highlighted using a shortcode, as explained here. Until recently, R was not on the list of supported languages (neither was Perl), but I noticed today that both of them are now supported. This may have happened months ago and I just wasn’t aware of it. I spent a merry hour or so updating my old posts in the R category, so the code should now feature pretty colours. Let me know if you spot any errors that I may have introduced inadvertently. I guess this is in some sense recognition that R is now used quite widely and that usage is growing. Filed under: programming, R, statistics, this blog Tagged: shortcode, syntax highlighting, wordpress (Source: What You're Doi...

Friday fun with: Google Trends

What You're Doing Is Rather Desperate — Fri, 20 May 2011 01:55:17 +0100

Some years ago, Google discovered that when people are concerned about influenza, they search for flu-related information and that to some extent, search traffic is an indicator of flu activity. Google Flu Trends was born. Google Trends: bronchitisIllness is sweeping through our department this week and I have succumbed. It’s not flu but at one point, I did wonder if my symptoms were those of bronchitis. Remembering Google Flu Trends, I thought I’d try my query for “bronchitis” at Google Trends, where I saw the chart shown at right. Interesting. Clearly seasonal, peaking around the latest and earliest months of each year. Winter, for those of you in the northern hemisphere. Next: select USA and Australia as regions download the data in CSV format (I chose fixed sca...

Forums: Open Beats Closed Hands Down

Omics! Omics! — Wed, 18 May 2011 23:00:00 +0100

Around the Internet, there are a number of communities in which scientists can swap useful information. SEQAnswers is a very useful site I frequent; BioStar is one I don't but probably should. Life Technologies has set up a community around Ion Torrent, and the contrast between that and SEQAnswers is a useful one.SEQAnswers has a straightforward access policy. Anyone can view content, but to post or reply you must register for a membership. This approach appears to have been very successful, as there is a healthy number of individuals posting to the site. You can browse around and figure out if the site applies, plus search engines such as Google can steer individuals in. SEQAnswers boasts a number of authors of major second generation sequencing analys...

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How to: create a partial UCSC genome MySQL database

What You're Doing Is Rather Desperate — Wed, 18 May 2011 04:54:10 +0100

File under: simple, but a useful reminder UCSC Genome Bioinformatics is one of the go-to locations for genomic data. They are also kind enough to provide access to their MySQL database server: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A However, users are given fair warning to “avoid excessive or heavy queries that may impact the server performance.” It’s not clear what constitutes excessive or heavy but if you’re in any doubt, it’s easy to create your own databases locally. It’s also easy to create only the tables that you require, as and when you need them. As an example, here’s how you could create only the ensGene table for the latest hg19 database. Here, USER and PASSWD represent a local MySQL user and password with full privileg...

Friday fun projects

What You're Doing Is Rather Desperate — Sat, 14 May 2011 06:13:46 +0100

What’s a “Friday fun project”? It’s a small computing project, perfect for a Friday afternoon, which serves the dual purpose of (1) keeping your programming/data analysis skills sharp and (2) providing a mental break from the grind of your day job. Ideally, the skills learned on the project are useful and transferable to your work projects. This post describes one of my Friday fun projects: how good is the Sydney weather forecast? There’ll be some Ruby, some R and some MongoDB. Bioinformatics? No, but some thoughts on that at the end. 1. Define the problem Step 1 in any project is to define the problem. The question “how good is a weather forecast?” might be addressed in many ways. Obviously, we need to collect two kinds of data: predictions and o...

Oh Would It Be Fun to Debug Strobe Sequencing!

Omics! Omics! — Fri, 13 May 2011 23:00:00 +0100

Through the course of a month, I easily sketch out (on average) a dozen plus experimental designs in the context of my day job. Of course, only a very few of these are ever executed; many never get shown to another soul. By constantly pondering how I might tackle questions, I can keep in practice and present plans which are reasonably well thought-out. It also helps to have thought through things; sometimes a rejected plan will suddenly look like a gem due to some other result or change in priorities.Atop that, I also sketch up a few which have nothing to do with my day job. Partly it is fun, and partly it is a way to exercise the process on areas I can be certain of my objectivity. A related exercise is to sketch out a business plan; I end up doing that a few times a year. Nev...

Blogger glitch

Omics! Omics! — Thu, 12 May 2011 23:00:00 +0100

Blogger experienced an outage which I found out about today. This caused my last post to disappear; any posts or comments in a certain time period were lost.Thanks go out to the anonymous reader who posted a comment wondering where my last post went. Blogger (Google) did not notify me of the issue. The really disconcerting part is the Google cached version of the post was missing as well -- this suggested something very odd going on.I often write posts directly in Blogger, so I don't have a backup. This was an exception & I did actually have the rough draft, which I would have posted if the old one wasn't restored. (Source: Omics! Omics!)

Ion's Growing Pains

Omics! Omics! — Tue, 10 May 2011 23:00:00 +0100

A recent In Sequence article indicated that Ion Torrent is enjoying strong initial sales. This bodes well for continued evolution and improvement of the technology, as LIFE will continue to smell revenues and opportunity. Ion has announced a number of improvements, but most aren't scheduled to arrive until the near future.The challenge is for LIFE to keep executing on their plan. Already some issues have arisen; my own Ion experiment at a service provider is stalled due to a back-ordered template prep reagent (two weeks and counting!). This is a key reason to do pilots on emerging technologies with non-critical (but interesting) samples; I was bitten last fall by another backorder bug (that time, the paired end SOLiD reagents). Of course, this time it is even more complicated, ...

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Analyzing exome data with KNIME

YOKOFAKUN — Tue, 10 May 2011 23:00:00 +0100

A presentation I gave last week in my lab Analyzing Exome Data with KNIME View more presentations from Pierre Lindenbaum (Source: YOKOFAKUN)

Towards mastery: deliberative practice, flow and personality traits

Trapped in the USA — Mon, 09 May 2011 13:53:27 +0100

By now, you’ve probably come across the factoid that you need 10,000 hours of practice to master any activity (thanks Malcolm Gladwell). Although it’s good that people are finally getting over the idea of a shortcut to success, this oft-quoted figure of 10000 hours does not really answer the question whether mastery is innate or acquired. After all, plenty of people have plodded away at activities for more than 10000 hours without getting to any recognizable level of mastery. It’s a topic that I’ve read around a lot in and here I’d like to throw down some connections between practice, neural plasticity, flow and innate psychological traits. Deliberative practice In “Talent is Overrated,” Geoff Colvin argues that it’s not just any kind of ...

Ion Torrent's Data Quality Is Pretty Good (and Better Than Ion Claims)

Omics! Omics! — Sat, 07 May 2011 23:00:00 +0100

One of the key questions around Ion Torrent, as with all new platforms, is what is the sequence data quality like. Now, that can be a loaded question but I'll ask a slight variant on it: how truthful (or accurate) is Ion at estimating base quality?Quality scores are a useful adjunct to sequencing data and are commonly expressed as phred scores, which are the integer part of -10*log10 of the error probability. Any base caller needs to estimate these and many downstream programs, from aligners to assemblers to variant callers, rely on these quality values for their operations. In many cases, the individual quality scores are combined to generate some joint estimate of the error (I built one such model at Codon). These error probabilities come not from an infallible source, but ar...

Which numbers did I use this time?

Omics! Omics! — Fri, 06 May 2011 23:00:00 +0100

Noted screenwriter William Goldman's second memoir on the film industry is titled "Which Lie Did I Tell?". The title is not a quote from Goldman, but rather what another movie industry said after getting off a long phone call he had taken in Goldman's presence. I'm a bit nervous I inadvertently strayed in that direction in my last item on Pacific Biosciences.I was relying on memory for my numbers & in the course of writing things I think I also revised those downwards, not out of malice but rather an attempt to be conservative. As a correspondent pointed out, the first pass accuracy on the first commercial system is claimed to be 85%, not 80% as I stated. On the number of reads, I failed to update for the newer SMRT cells which are out; I said 10K and it...

Changes

business|bytes|genes|molecules — Fri, 06 May 2011 03:02:36 +0100

Tweet As some you have probably noticed via a prior tweet and a LinkedIn profile change, I have a new role at AWS, getting back to my product management roots. This gives me a chance to get up close and personal with infrastructure, thinking about the types of applications and workloads people are running, high performance computing, etc. I love product, and it’s good to be back. Will definitely mean a reduction in travel and speaking engagements, but mostly result in being more picky about those. Maybe this means that c2cbio will make a semi-comeback. We’ll see. In the meantime, I am excited. (Source: business|bytes|genes|molecules)

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Books Read March/April 2011

Trapped in the USA — Tue, 03 May 2011 12:11:33 +0100

9. Rino Breerbaart, “Song Logic” Reading “Song-logic”, a book of essays of music by Rino Breebaart, I felt a slight twinge of jealousy. Ever since I can remember, I have always wanted to write about my own transcendent experiences in music listening. In these hypothetical essays, I would break down my experiences with stylish wit and irresistible acumen. That I haven’t is clear, but if I did then they would look something like these essays. To write great music criticism, you have to have a sharp ear, a theorizing bent and a poetic tongue. But most of all, you need a sympathetic heart. These essays are written in a mature tone, suffused with a generosity that is absent in much criticism out there. There is no snark, just an honest attempt at trapping the ...

How Many More Machines will PacBio Sell This Year?

Omics! Omics! — Sun, 01 May 2011 23:00:00 +0100

Amongst last week's news is the item that Pacific Biosciences has officially launched their SMRT sequencing platform. I'd too eye-deep in various projects to figure out how off schedule that is (I think nearly a year from their original target), but now it is launched. Read more » (Source: Omics! Omics!)

In defense of 'Omics

Public Rambling — Thu, 28 Apr 2011 21:29:00 +0100

High-throughput studies tend to have a bad reputation. They are often derided as little more than fishing expeditions. Few have summarized these feelings as sharply as Sydney Brenner: "So we now have a culture which is based on everything must be high-throughput.I like to call it low-input, high-throughput, no-output biology"Having dealt with these type of data for so long, I am often in the strange position of having to defend the approaches. As I was in a real need to procrastinate, I decide to try to write some of these thoughts down. Error rates One of the biggest complaints directed at large-scale methods is that they have very high error rates. Usually these complaints come from scientists interested in studying system X or protein Y, that dig into these datasets...

Multiple Widget Embedding for Jolecule

Trapped in the USA — Thu, 28 Apr 2011 02:27:49 +0100

Finally, I've got the Jolecule widgets working properly. That is, multiple widgets working on the same page. That took some fugly global-variable name-mangling meta-programming code. But hey, it's javascript, so you are supposed to write fugly code. What this means is that you can create annotated views for different proteins, then hot-link it back on your blog/website/journal-article to have fast loading interactive protein widgets. I've also added a handy "link" button below every text box of the annotated views, where you can grab the appropriate embedding HTML code for your annotated views. If you install multiple widgets, there will be some renaming to be had. If you are embedding the second widget, you will have to change: embed1_dict => embed2_dict...

mapping people I'm following on twitter: (KML, java, geonames.org)

YOKOFAKUN — Wed, 27 Apr 2011 23:00:00 +0100

I wrote a java tool to map the people I'm following on twitter. This tool invokes the twitter API to fetch the profiles of my contacts and it uses the geonames web services to guess the geolocation of the places.The source code is available on github at https://github.com/lindenb/jsandbox/blob/master/src/sandbox/TwitterToKML.java.the build.xml is here.Compilationant twitterkml#get your twitter-id (Source: YOKOFAKUN)

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dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions

YOKOFAKUN — Wed, 27 Apr 2011 23:00:00 +0100

People from the "Human Genetics Center" in Houston have compiled a new resource named dbNSFP and described in http://www.ncbi.nlm.nih.gov/pubmed/21520341.Hum Mutat. 2011 Apr 21. doi:10.1002/humu.21517.dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions. Liu X, Jian X, Boerwinkle E.They have compiled the "prediction scores from four new and popular (Source: YOKOFAKUN)

Playing with the HTML5 File API: translating a Fasta file.

YOKOFAKUN — Thu, 21 Apr 2011 23:00:00 +0100

In the current post, I'm using the new HTML5 File Api. This new API can read the content of a file on the client side without needing a remote server. Let me repeat this: YOU DO NOT NEED A SERVERYOU DO NOT NEED TO COPY AND PASTE THE CONTENT OF THE FILE IN A TEXTAREA.As an example, the following code reads a whole DNA fasta file stored on your computer and translate each DNA sequence to a protein. (Source: YOKOFAKUN)

Lists of URLs are so 1990s

What You're Doing Is Rather Desperate — Wed, 20 Apr 2011 14:08:18 +0100

Subtitle: “Why some projects are not worth your valuable time and skills.” Let’s wrap up this exploration of how to extract URLs associated with NAR Database articles. I’m tempted to start with the summary: don’t bother – just Google it. If you want that, skip to the end. First: forget PubMed. This query: "Nucleic Acids Res"[JOUR] "Database issue"[ISS] is all well and good except that between 1998 and 2004, the NAR Database Issue was not named “Database issue”; it just has a volume number, like the other issues. If you insist on trying to extract URLs from PubMed abstracts, be prepared for frustration. They include every valid variant imaginable (with/without a leading “http://”) and many invalid variants (b...

Factoids (and using R as a simple calculator)

What You're Doing Is Rather Desperate — Wed, 20 Apr 2011 02:16:11 +0100

Wikipedia defines factoid as “a questionable or spurious—unverified, incorrect, or fabricated—statement presented as a fact, but with no veracity.” Last night I was enjoying a TV documentary series, The Story of Science, when I heard a startling factoid, namely: If the “empty space” inside the atoms that make up people were removed, the entire human population would fit inside a sugar cube. What the? Can we improve the veracity of this factoid? Atoms Let’s start with atoms. Assuming that atoms are spherical, with a central nucleus which is also spherical, we can calculate atomic and nuclear volumes. A Google search for average diameter of an atomic nucleus suggests that the “average” nuclear diameter is 1e-14 metres, ~ 10 000 times less than...

MedWorm: Bioinformaticians

Inside the Variation Toolkit: Tools for Gene Ontology

Does Illlmina Also Have A Homopolymer Problem?

Inside the variation toolkit: VCF2XML

Insert your VCFs in a sqlite database.

Wiider postmortem

de-Bruijn assembler

Reproducible research: three links that made me think

Roche Guns For Illumina

Science Online 2012 on Twitter

Sequencing Technology Fireworks

A CGI-version of samtools tview.

Ion Torrent Pairs: To What End?

The Variation Toolkit

Hamiltonian Assembler

2011 blog stats courtesy of WordPress.com

A Fundamental Breakthrough in Protein Folding

Year's End

Sequencing for relics from the Sanger era part 1: getting the raw data

Books Read 2011

Magic Numbers and unit conversions in Structural Biology

#arseniclife: the genome

Reflecting on a Year of Ion Torrent

New Look, Mobile Friendly

A Friday round-up

Suggest some new terms for the EDAM Ontology for Bioinformatics

Special Topic Issue "Webscience in medicine"

Boring, monotonous day-to-day tasks? That’s synonymous with bioinformatics.

Processing json data with apache velocity.

OSGi and Eclipse RCP Talk

"VCF annotation" with the NHLBI GO Exome Sequencing Project (JAX-WS)

The infidelity of the theoretical protein backbone

Some English pronunciation tips

Some English pronounciation tips

MedEx 2011

The paper about BioStar has been published in "PLoS Computational Biology"

Fitting Out

A reference genome with or without the 'chr' prefix

Running a local JABAWS server for Jalview on Ubuntu (11.04 Natty)

MiSeq Made Easy?

Swimming, Running, Hunting, and Meditating: the Evolutionary Origin of Mystical States

Knime4Bio: a set of custom nodes for the interpretation of NGS data with KNIME

Grouping mutations/Gene=f(sample)

Verticalize: printing the input stream vertically.

Surveillance Workshop at GMDS

Thinking Outside the Box or Just Plain Nuts?

Boston's Boris Bikes

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PostScript as a Programming Language for Bioinformatics: mynotebook

Joining genomic annotations files with the tabix API.

Transitions

Illumina Calls for a Flag on the Play

The Wikipedia Template:Infobox_biodatabase is now integrated in DBPedia

Customizing "C printf" to print a FASTA sequence.

Interacting with bioinformatics webservers using R

Parsing a BAM file with javascript, yes we can. (Node.js and V8)

Merging two XML files using the libxml streaming API.

Genetic Education:

Will Max-Seq Gain Traction?

Wishing I Had Been A Referee: A Renaissance for Tagamet?

Popular topics at the BioStar Q&A site

Monitoring PubMed retractions: updates

A FUSE-based filesystem reproducing the NCBI Taxonomy hierarchy.

Wikipedia OpenSearch and semantic bash completion

Quick tip: bash completion for Bioinformatics

Names in Collision

BioRuby development: feedback on using Git

A beginner’s guide to BioRuby development

Ion Throws A Long Punch At MiSeq

The GPCR-G complex: the canonical structure of Cell Signaling (with interactive guide)

ISMB coverage on Twitter? It’s possible there was…

The Metaphysical Countrygirl

Using the Freebase and the Bioportal Widgets to create a semantic object.

Memory-Mapping the Human Genome with 'mmap': my notebook

Storing some SNPs using the leveldb library. My notebook.

How Many Toes Does Ion Have Left?

I can’t resist a word cloud: now using R!

Analysis of ISMB coverage at FriendFeed: 2008 – 2011

Tschuess, Shuttle!

Controlling IGV through a Port: my notebook.