Computer Science posts
- February 5, 2010
- 06:53 AM
- 52 views
Classic paper: Montagues and Capulets in Science
by Duncan Hull in O'Really?
In preparation for a joint seminar I’ll be doing with Midori Harris here at the EBI, here’s a classic paper [1,2] on the social problems of building biomedical ontologies. This paper is worth reading (or re-reading) because it makes lots of relevant points about the use and abuse of research and how people misunderstand each [...]... Read more »
Goble, C., & Wroe, C. (2004) The Montagues and the Capulets. Comparative and Functional Genomics, 5(8), 623-632. DOI: 10.1002/cfg.442
- February 5, 2010
- 02:37 AM
- 56 views
10 Websites With The Best Information on Depression
by Dr Shock in Dr Shock MD PhD
After searching for websites about depression (‘‘depression,’’ ‘‘depression treatment,’’ and ‘‘depression help’’) with a popular search engine: Google, the authors of this work carefully examined the websites. The websites were evaluated on accountability, interactivity, esthetics, readability and content quality. They also used the brief DISCERN as a content quality indicator for general consumers. They found [...]
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Zermatten, A., Khazaal, Y., Coquard, O., Chatton, A., & Bondolfi, G. (2010) Quality of web-based information on depression. Depression and Anxiety. DOI: 10.1002/da.20665
- February 4, 2010
- 11:59 AM
- 35 views
VarScan 2 Released on SourceForge
by Daniel Koboldt in Massgenomics
Accurate variant detection in massively parallel sequencing data is a significant bioinformatics challenge. Not only do new sequencers offer unprecedented breadth (whole genome) and depth (30x or more), but they suffer coverage biases and error rates that make variant calling difficult. Last year, we published VarScan, our in-house algorithm for SNP and indel detection on [...]... Read more »
Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L. (2009) VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (Oxford, England), 25(17), 2283-5. PMID: 19542151
- February 4, 2010
- 03:51 AM
- 42 views
Forty years of hackers at the movies
by David Bradley in Sciencetext
There are two definitions of “hacker” the first is the one we geeks mean when we call someone a hacker – a person skilled in using technology, particularly computers, who enjoys understanding the inner workings of that technology, perhaps for personal education. The second is the colloquial definition that refers to someone engaged in breaking [...]Post from: David Bradley's Sciencetext Tech TalkForty years of hackers at the movies
... Read more »
Damian Gordon. (2010) Forty years of movie hacking: considering the potential implications of the popular media representation of computer hackers from 1968 to 2008. Int. J. Internet Technology and Secured Transactions, 2(1/2), 59-87. info:/
- February 3, 2010
- 10:53 AM
- 36 views
Story behind the science: #PLoS Genetics "Evolutionary mirages" paper
by Jonathan Eisen in The Tree of Life
So there is this cool new paper out in PLoS Genetics: Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers. and I have wanted to write about it for a week or so. You see, the paper is about something I have been interested in for most of my career - how the particular processes by which mutations occur can sometimes be biased (i.e., some types of mutations are more common than others) and that these biases can create highly ordered patterns in genomes and in turn that observation of these ordered patters can sometimes be misinterpreted as being the result of adaptation. Mistaken claims of adaptation in genomics are a favorite topic of mine - and let me to create (with tongue in cheek) a new omics word - Adaptationomics.Anyway - so I really really like this paper. But there is a week bit of a problem in writing about it. You see, it is by my brother, Michael Eisen, a Prof. at UC Berkeley (and a student in his lab Richard Lusk). And, well, I don't want to say anything wrong or stupid about the paper since, well, my brother will be pissed off. And so I have not written about it yet. But then I realized the best way to write about this one is to simply ask my brother for the "Story behind the science" for the paper, as I have been doing for some other recent papers.If you want a summary of the paper, here it is in their own words:Authors summary: Because mutation is a random process, most biologists assume that apparently non-random features of genome sequences must be the result of natural selection acting to create and preserve them. Where this is true, genome sequences provide a powerful means to infer aspects of molecular, cellular, and organismal biology from the signatures of selection they have left behind. However, recent analyses have shown that many aspects of genome structure and organization that have traditionally been attributed to selection can often arise from random processes. Several groups—including ours—studying the sequences that specify when and where genes should be produced have identified common, seemingly conserved, architectural features, based on which we have proposed new models for the activity of the complex molecular machines that regulate gene expression. However, in the work described here we simulate the evolution of these regulatory sequences and show that many of the features that we and others have identified can arise as a byproduct of random mutational processes and selection for other properties. This calls into question many conclusions of comparative genome analysis, and more generally highlights what Michael Lynch has called the “frailty of adaptive hypotheses” for the origins of complex genomic structures.Conclusions: Lynch has eloquently argued that biologists are often too quick to assume that organismal and genomic complexity must arise from selection for complex structures and too slow to adopt non-adaptive hypotheses. Our results lend additional support to this view, and extend it to show that indirect and non-adaptive forces can not only produce structure, but also create an illusion that this structure is being conserved. We do not doubt that many aspects of transcriptional regulation constrain the location of transcription factor binding sites within enhancers. Indeed a large body of experimental evidence supports this notion, and we remain committed to identifying and characterizing these constraints. But if this process is to be fueled by comparative sequence analysis, as we believe it must be, it is essential that we give careful consideration to the neutral and indirect forces that we now know can produce evolutionary mirages of structure and function.I must say I love the title lead in "Evolutionary mirages" which is another but much better way of saying "Adaptationism is a bad thing". Anyway, before I get in any more trouble, here are some words about the paper from the Senior Author, Michael Eisen, my brother. Questions by me (I know, not very creative ones - but they will have to do):1. Why did you do this work?This paper started out as a control. My lab is interested in understanding how the enhancers that control gene expression work - focusing on those that control early development in Drosophila. In 2008, we published a paper showing that when we put enhancers from a distantly related family of flies into Drosophila melanogaster embryos, they drive patterns of expression that are identical to the endogenous D. melanogaster enhancers, even though they have almost no conservation of primary DNA sequence. But since they have the same function, they must have something in common - and so we compared the configurations of transcription factor binding sites in orthologous enhancers across different evolutionary timescales looking for something they shared.What we found is that binding sites in all of these enhancers occur in clusters. They are closer to each other than one would expect if they were scattered randomly in the ~1,000 bp of an enhancer. And, what's more, sites that were close to each other were far more likely to be conserved. Surely, we thought, this could be no accident. So we proposed that enhancers are organized into compact clusters of sites for one or more factors - and that these "mini modules" are the primary unit of enhancer function.But as we worked to extend these analyses to whole genomes, we sought a more rigorous, quantitative assessment, of just how improbably different levels of binding site clustering were. Like pretty much everyone in the field, we had used a null model in which binding sites were scattered randomly in an enhancer. But, I've been working with genomes long enough to know that nothing is ever truly random - and that all kinds of adaptive and non-adaptive processes create patterns in genome sequences that confound simple analyses. I wanted to come up with a null model for the distribution of sites within in an enhancer that was more realistic.To do this I turned to my graduate student Rich Lusk, a card-carrying population geneticist trained at the University of Chicago. Rich was proud of his status as one of the few members of the lab who didn't work on flies - but I convinced him to put aside the abstract models of binding site evolution in yeast and work on developing a real null model for our studies of enhancer evolution.The idea was to simulate enhancers evolving without any constraint on the organization of transcription factor binding sites they contain, and to see what happens. But this did not mean letting enhancers evolve neutrally - their extreme functional conservation demonstrates that they are under fairly strong constraint. Since it is pretty clear that these enhancers are responding to the same transcription factors in all of these species, Rich's simulations required that enhancers maintain their binding site composition - but placed no constraints on how the sites were organized relative to each other.And what we found was striking. Even with no explicit selection on binding site organization - these evolved enhancers had lots of structure! Binding sites were clustered together, and, the closer together sites were, the more conserved they were -- just like they were in real enhancers. In made us realize pretty quickly that the patterns we had latched onto - and which many other people were describing in different systems - might not be an evolutionary signature contraint on the organization of sites within in enhancers, but simply a byproduct of selection on binding site composition. If you want details, read the paper! But this has radically altered the way that we look at enhancer evolution.2. How did you come up with the title.Rich and I were writing the paper, and we had some really long, hideous, boring title. In writing the paper, the idea that things are not always what they appear to be was at the forefront of my mind. I was thinking about how desperate we and other people in the field were to figure out how enhancers work - it's a vexing problem that has defied decades of work - and how we all hoped that evolutionary analysis was going to rescue us - and how quickly and eagerly we latched on to the first signs of a signal - and how that was just like a mirage you see in the desert....3. Any interesting background? (see 1)4. When did the work start?About a year ago. We had been thinking about this for a while, but only when Rich focused on it did things get rolling.5. Why PLoS Genetics? Did PLoS Biology reject it?PLoS Genetics was our first choice. PG has become the premier journal for evolutionary genetics - it routinely publishes the most interesting and important work in the field, and everyone reads it. While every paper I've sent there has been heavily scrutinized, the editorial process has been fair (though sometimes agonizingly slow....), and each review has been thoughtful and many (including in this case) helped to vastly improve the paper.... Read more »
Lusk, R., & Eisen, M. (2010) Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers. PLoS Genetics, 6(1). DOI: 10.1371/journal.pgen.1000829
- January 27, 2010
- 11:01 AM
- 75 views
Evolving Robots
by Bryan in Imaging Geek
Creationists often like to claim that complex traits cannot arise from the "simple" processes of mutation and selection. They often claim that these processed are not even observable (even though we've been observing them since we began breeding plants and animals).
Anyone with even a basic grasp of science knows the above claims are pure BS, but not being content with simply being right, some scientists have now gone the extra mile and used evolution to make ROBOTS.
And not just any robots - robots that walk, hunt each other, evolve their shape, and which are even altruistic - a distinctly mammalian trait. All of that was evolved; starting with nothing more than a collection of parts and a simple mutation/selection algorith.... Read more »
Floreano, D., & Keller, L. (2010) Evolution of Adaptive Behaviour in Robots by Means of Darwinian Selection. PLoS Biology, 8(1). DOI: 10.1371/journal.pbio.1000292
- January 27, 2010
- 05:52 AM
- 41 views
Looking at Peer-to-Peer Optimization Methods
by Tomas Rawlings in CatBot Blog
P2P algorithms can offer robustness and communication efficiency over more centralised GRID methods. So authors compared to p2p algorithms performance searching in large-scale and unreliable networks.
read more... Read more »
Balázs Bánhelyi, Marco Biazzini, Alberto Montresor, and Márk Jelasity. (2009) Peer-to-Peer Optimization in Large Unreliable Networks with Branch-and-Bound and Particle Swarms. Lecture Notes In Computer Science, 87-92. info:/
- January 21, 2010
- 05:05 AM
- 77 views
Blogging a Book about Bio-Ontologies
by Duncan Hull in O'Really?
If you wanted to write a guide to Biomedical and Biological Ontologies [1], especially the what, why, when, how, where and who, there are at least three choices for publishing your work:
Journal publishing in your favourite scientific journal.
Book publishing with your favourite academic or technical publisher.
Self publishing on a web blog with your favourite blogging [...]... Read more »
Yu, A. (2006) Methods in biomedical ontology. Journal of Biomedical Informatics, 39(3), 252-266. DOI: 10.1016/j.jbi.2005.11.006
- January 20, 2010
- 06:51 AM
- 68 views
"A Local Maxima method and a Fair Dispersion Normalization for extracting Multi-Word Units from corpora" by Ferreira and Pereira
by David Brenes in Nobody's Papers
Because of my research I’m interested in term correlation not just in pairs but in groups of ‘n’ terms (ngrams). Looking for some statistic measures and explanations about the advantages and implementations of Log-Likelihood measures I reached:
Joaquim Ferreira da Silva, & Gabriel Pereira Lopes (1999). A Local Maxima method and a Fair Dispersion Normalization for
extracting multi-word units from corpora Sixth Meeting on Mathematics of Language
In this paper the authors present a new algorithm for extracting MultiWords Units (MWU) which corresponds with what I called ngrams before.
This algorithm, called LocalMaxs, finds the best MWU from a given sentence finding which MWU has a higher value than any of it’s antecessors (MWUs with less words) and succesors (MWUs with more words), that is a local maxima just as in any other mathematical function.
What I was really interested into was in “how can I know how appropriate is a MWU?”. Here is where the pure statistical knowledge is needed and the second part of the paper.
In this second part they make a very helpful and understandable introduction to a serious of statistical measures. The only problem is all of these measures are thought to evaluate a pair of terms, not a group of ‘n’ terms.
The authors then propose a simple way to generalize the measures from bigram to a ngram (MWU). They consider a ngram just as a bigram being the first term of the bigram the first “x” terms of the MWU and the second term of the bigram the last”n - x” terms.
As an example, consider we have the MWU “michael jordan nba statistics”. We could consider this ngram as a bigram formed by the “terms” “michael jordan nba” and “statistics”.
Of course, depending where you cut (what they call the dispersion point) the MWU you can have different “bigrams” with very different statistical relevance. In our example we could have the bigram [“michael” “jordan nba statistics”], [“michael jordan” “nba statistics”] or [“michael jordan nba” “statistics”].
To solve this dispersion point problem and obtain a simple statistic value they make the arithmetical average of the value of every possible “bigram”.
As if all of this was not enough to justify the reading of this paper every statistical measure is explained with a mathematical formula (not simple, but very helpful) which make all the paper easily reproducible and implementable for your own system.
In fact, I have implemented all of them for a brief evaluation in my own environment. You can download my implementation and play with it. I think I didn’t make any mistake, but if you find something wrong, please let me know it.
In every PHP file are included the required functions and there’s always a function which receives the ngram to evaluate and a text string which will act as a little corpus to find the ngram occurences. It shoud be easy improve it in a more sofisticated way, but my intention was giving a simple implementation of the mathematic formula.... Read more »
Joaquim Ferreira da Silva, & Gabriel Pereira Lopes. (1999) A Local Maxima method and a Fair Dispersion Normalization for extracting multi-word units from corpora . Sixth Meeting on Mathematics of Language. info:/
- January 15, 2010
- 08:11 AM
- 102 views
Bio2RDF: Large Scale, Distributed Biological Knowledge Discovery
by Duncan Hull in O'Really?
Michel Dumontier was visiting the EBI this week, here’s the details of his seminar Bio2RDF and Beyond! Large Scale, Distributed Biological Knowledge Discovery (slides embedded below) for anyone interested who missed it:
Abstract: The Bio2RDF.org [1] project aims to transform silos of bioinformatics data into a distributed platform for biological knowledge discovery. Initial work focused on [...]... Read more »
BELLEAU, F., NOLIN, M., TOURIGNY, N., RIGAULT, P., & MORISSETTE, J. (2008) Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. Journal of Biomedical Informatics, 41(5), 706-716. DOI: 10.1016/j.jbi.2008.03.004
- January 7, 2010
- 03:06 AM
- 103 views
Internet Use Has No Negative Influence on Well-being
by Dr Shock in Dr Shock MD PhD
A recent meta-analysis examined the relationship between various Internet uses and well being. The studies published until know is mostly about the discussion whether using Internet for communication with e-mail replaces other forms of communication such as using the phone, chat or face to face contact. Contact through e-mail, facebook, twitter and such replaces real [...]
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Huang, C. (2009) Internet Use and Psychological Well-being: A Meta-Analysis. CyberPsychology , 2147483647. DOI: 10.1089/cpb.2009.0217
- January 6, 2010
- 12:23 PM
- 87 views
Finding Recurrent CNVs in Cancer
by Daniel Koboldt in Massgenomics
Copy number aberrations (CNAs) represent one of the most prevalent genetic alterations in cancer cells. There is considerable interest in finding CNAs that affect the same chromosomal region in multiple tumor samples. Recurrent CNA (RCNA) implies the presence of key cancer genes; on chromosome 7, for example, we often see amplification of the region containing [...]... Read more »
Zhang Q, Ding L, Larson DE, Koboldt DC, McLellan MD, Chen K, Shi X, Kraja A, Mardis ER, Wilson RK.... (2009) CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. Bioinformatics (Oxford, England). PMID: 20031968
- January 4, 2010
- 02:40 AM
- 153 views
The Dangers of Facebook
by Dr Shock in Dr Shock MD PhD
The threats of the popular social network Facebook are:
Identity theft
Threats to personal safety such as stalking or threatening either online or in real life
Social risks through participating in minority groups or stigmatized groups
How do people differ in self-disclosure and what kind or how much of information has a high risk for these treats?
In a recent [...]
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Nosko, A., Wood, E., & Molema, S. (2009) All about me: Disclosure in online social networking profiles: The case of FACEBOOK. Computers in Human Behavior. DOI: 10.1016/j.chb.2009.11.012
- January 2, 2010
- 01:48 AM
- 174 views
how to speak your mind, literally.
by Greg Fish in weird things
Talking brains have been a staple of science fiction and comic books, usually taking the role of villains using their considerable intellect to destroy or conquer the world and implying that nerds with access to money and weapons can be really dangerous. The Brain from the DC Comics’ series Doom Patrol was essentially a raw [...]... Read more »
Guenther, F., Brumberg, J., Wright, E., Nieto-Castanon, A., Tourville, J., Panko, M., Law, R., Siebert, S., Bartels, J., Andreasen, D.... (2009) A Wireless Brain-Machine Interface for Real-Time Speech Synthesis. PLoS ONE, 4(12). DOI: 10.1371/journal.pone.0008218
- December 30, 2009
- 08:00 AM
- 144 views
Computer skills linked to math talent
by David Bradley in Sciencetext
Businesses and the economy as a whole rely increasingly on computing, but many potential users are not entirely confident of the technology. A research study published in January suggests that an individual’s computer self-efficacy is influenced by their competence in mathematics. I asked the author Assistant Professor of Management Information Systems Franklin Morris of The [...]Post from: David Bradley's Sciencetext Tech TalkComputer skills linked to math talent
... Read more »
R. Franklin Morris, Jr., & Evelyn H. Thrasher. (2010) Implications for e-commerce: the influence of math and computer confidence on computer self-efficacy. International Journal of Electronic Marketing and Retailing, 3(1), 15-37. info:/
- December 29, 2009
- 02:03 PM
- 92 views
Story Behind the Nature Paper on 'A phylogeny driven genomic encyclopedia of bacteria & archaea' #genomics #evolution
by Jonathan Eisen in The Tree of Life
Today is a fun day for me. A paper on which I am the senior author is being published in Nature (yes, the Academic Editor in Chief of PLoS Biology is publishing a paper in Nature, more on that below ..). This paper, entitled, "A phylogeny driven genomic encyclopedia of bacteria and archaea" represents a culmination of years of work by many people from multiple institutions. Today in this blog I am going to do my best to tell the story behind the paper - about the people and the process and a little bit about the science.
First, a brief bit about the science in the paper. In this paper, we (mostly people at the Joint Genome Institute, where I have an Adjunct Appointment -- but also people in my lab at UC Davis and at the DSMZ culture collection) did a relatively simple thing - we started with the rRNA tree of life as a guide. Then we identified branches in the bacterial and archaeal portions of this tree where there were no genome sequences available (or in progress) (this was done mostly by Phil Hugenholtz, Dongying Wu and Nikos Kyrpides) Next we searched for representatives of these "unsequenced" branches in the DSMZ culture collection (a collection of bacteria and archaea that can be grown in the lab). And we identified in total some 200 of these. And then the DSMZ (under the direction of Hans-Peter Klenk) grew these organisms and sent the DNA to the Joint Genome Institute. And then JGI turned on their genome sequencing muscle and sequenced the genomes of the organisms in the DNA samples. And finally, we spent a good deal of time then analyzing the data asking a pretty simple question - are there any general benefits that come from this "phylogeny driven" approach to sequencing genomes compared to what one might find with sequencing just any random genome (after all, any genome sequence could have some value)? The paper, describes what we found, which is that there are in fact many benefits that come from sequencing genomes from branches in the tree for which genomes are not available.
More on the details of the science below. But first, I want to note that this paper was truly an amazing team effort, with all sorts of people from the JGI in particular, going above and beyond the call of duty to make sure it happened and worked well. And the Department of Energy has been truly phenomenal in my opinion in supporting this project which in the end is not explicitly about "energy" per se but is really about providing a reference set of genomes that should improve the value of all microbial genome data.
Anyway, now for the story behind the story. And be prepared, because this is a bit long. But I think it is important to place this work in a bigger context both in terms of my background as well as some of the background of other people in the project. If you can't wait for more on the GEBA project then perhaps you should go to some of these links:
Videos of talks I have given on the project:
"Genomic Encyclopedia of Bacteria and Archaea (GEBA)"- Jonathan ...
Recent talk I gave at the Sackler NAS "Microbes and Health" meeting
Podcast of interview of me for ASM's Meet the scientist
Stories about GEBA
Nature News from 11.17.2009
Stories about our paper
Nature News
GenomeWeb "GEBA Researchers Publish Results from Dozens of Bacterial, Archaeal Genomes"
Ars Technica article "Presenting a genomic encyclopedia of bacteria (and archaea" by John Timmer
Iddo Friedberg blogged about it
The OpenHelix Blog on it
Leonardo Martins blogs about it here and helps translate a Spanish story about the project
R&D magazine has a post based on the press releases here
NY Times story by Carl Zimmer here.
FriendFeed Discussions here (includes a thread about Nature using a Creative Commons license)
And I will post more links as they come up. Below what I try to provide is some of the story behind the story:
My personal interest in applied uses of phylogenetics stage 1: undergraduate preparation at Harvard
As this paper is primarily about an applied use of phylogenetics (in selecting genomes for sequencing), I thought it would be worth going into some of how I personally became a bit obsessed with applied uses of phylogenetics. For me, my obsession began as an undergraduate at Harvard where I got exposed to the value of phylogeny as a tool from many many angles including but not limited to:
Freshman year taking a course taught by Stephen Jay Gould where Wayne and David Maddison were Teaching Assistant's and where they were demoing their new phylogenetics software called MacClade
Sophomore year taking a conservation biology class with Eric Fajer and Scott Melvin where I was exposed to the concept of "phylogenetic diversty" as a tool in assessing conservation plans
Junior year working in the lab of Fakhri Bazzaz with people like David Ackerly and Peter Wayne who made use of phylogeny as a key tool in their research projects
Senior year and the year after graduating where I worked in the lab of Colleen Cavanaugh using rRNA based phylogenetic analysis to characterize uncultured chemosynthetic symbionts. I note it was in Colleen's lab that I also became obsessed you could say with microbes and why they rock.
My personal interest in applied uses of phylogenetics stage 2: graduate school at Stanford
All of this and more gave me a strong passion for phylogeny as a tool. And so when I went to graduate school at Stanford (originally to work with Ward Watt on butterflies, but then I switched to working in Phil Hanawalt's lab on the "Evolution of DNA repair genes, proteins and processes"). And while in that lab I become pretty much obsessed with three things, all related to phylogeny.
First, I was interested in whether the rRNA tree of life, which I had used in my studies in Colleen Cavanaugh's lab (and in my first paper in J. Bacteriology, which, thanks to ASM, is now in Pubmed Central and free at ASM's site too), was robust or, as some critics argued, was not that useful. This was a critical question since the best way to study the phylogeny of microbes at the time, and also the best way to study uncultured microbes, was to leverage the ability to clone rRNA genes by PCR and then to build evolutionary trees of those rRNA genes. As part of my graduate work, I did a study where I compared the phylogenetic trees of rRNA to trees of another gene from the same speci... Read more »
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.... (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. DOI: 10.1038/nature08656
- December 29, 2009
- 11:38 AM
- 124 views
SNP Discovery in NGS Data, Atlas-SNP2, and VarScan
by Daniel Koboldt in Massgenomics
A paper in this month’s Genome Research sheds light on predictors of sequencing error in next-generation sequencing. Using data from both 454 and Illumina platforms, Shen et al applied logistic regression models to identify sequence- and platform-related factors that contribute to substitution (SNP) errors.
The results, I think, offer new insight into the challenge of accurate [...]... Read more »
Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA.... (2009) A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome research. PMID: 20019143
- December 29, 2009
- 01:43 AM
- 109 views
More coverage of the GEBA "Phylogeny Driven Genomic Encyclopedia"
by Jonathan Eisen in The Tree of Life
Additional discussion of recent paper... Read more »
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.... (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. DOI: 10.1038/nature08656
- December 25, 2009
- 10:00 AM
- 117 views
An interesting approach to camera calibration
by hr0nix in Sex, drugs and applied science
Camera calibration is a process of determining intrinsic (like principal point or focal length) and extrinsic (position and orientation in space) parameters of a camera, which is often described by the pinhole camera model. In computer vision we usually perform calibration by analyzing images taken from camera. The most widely used approach to camera calibration is based on this paper by Zhengyou Zhang. It involves chessboard (or some other planar calibration pattern) and consists of the following steps:
Find a chessboard (bigger is better). Note that it should have distinct width and height (measured in chessboard squares) which should both be even (otherwise you will be unable to determine chessboard orientation given its picture).
Find a “calibration dude”.
Calibration dude takes a chessboard and waves it in front of the camera attached to a computer with calibration software installed. Calibration software takes about 20 images with distinct chessboard orientations (camera orientation remains the same, of course), finds inner corners of the chessboard on every image and then uses them together with information about real-world size of chessboard to determine intrinsic camera parameters.
Calibration dude puts chessboard on the floor in a way camera still can see it. Calibration software than takes one more image from camera, finds chessboard corners on it (again) and calculates camera position assuming that some predefined chessboard corner is located at the coordinate system origin and chessboard sides are oriented towards coordinate system axes. Of course, any other chessboard orientation can be specified in software, but this one is the most simple.
What problems do we have there? First of all, camera can see no floor at all, so we can’t just put chessboard on it during step 4. Instead we need to set it up somewhere else, not on the ground level. We should then carefully measure its position and orientation and pass them as an input to the calibration tool.
What if we have more than one camera seeing no floor, and those cameras are not overlapping? In this case we should repeat process described above for each camera, carefully measuring chessboard position in the world coordinate system every time. In fact, it’s a pain in the ass. Calibrating multiple cameras that way can be really slow and error-prone.
Much more interesting approach to multiple non-overlapping camera calibration was proposed in this paper. Its key idea is to fix chessboard position (put it at the origin) and move mirror instead. Cameras will see chessboard reflection in that mirror and use reflected image for calibration. Of course, some questions arise.
Is it legal to determine intrinsic camera parameters using reflected chessboard image? Answer is simple: yes. Authors prove that common calibration techniques give same result (except of coordinate system handedness) when applied to mirrored images.
Don’t we need to know position and orientation of the mirror when calibrating extrinsic parameters? No, we don’t. It turns out that every mirrored chessboard image imposes constraint on the position and orientation of the real camera. And if we have five (or more) such images, we can reconstruct position and orientation without any knowledge of mirror position.
This approach can save a lot of time and help to reduce part of the calibration error that arises from incorrect chessboard position and orientation determination. But it has it’s own drawbacks, of course. First of all, mirror is rather heavy. It’s not easy to manipulate it if your calibration dude is not a beefcake. Next, it’s hard to change orientation of the calibration pattern in frame from one snapshot to another when using mirror. It has to be in the field of view of the camera, and oriented such that the pattern’s image is reflected into the camera. These requirements may result in little variation in the pattern orientations as seen by the camera in the mirror and lead to solution degeneration.
Despite the drawbacks, this approach has the potential to increase speed of the multiple camera calibration process a lot. We will probably try it in 2010.
Ram Krishan Kumar, Adrian Ilie, Jan-Michael Frahm, & Marc Pollefeys (2008). Simple calibration of non-overlapping cameras with a mirror 2008 IEEE Conference on Computer Vision and Pattern Recognition
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Ram Krishan Kumar, Adrian Ilie, Jan-Michael Frahm, & Marc Pollefeys. (2008) Simple calibration of non-overlapping cameras with a mirror. 2008 IEEE Conference on Computer Vision and Pattern Recognition. info:/
- December 24, 2009
- 08:04 AM
- 86 views
Story Behind the Nature Paper on 'A phylogeny driven genomic encyclopedia of bacteria & archaea' #genomics #evolution
by Jonathan Eisen in The Tree of Life
Discussion of the background to a recent Nature paper ... Read more »
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.... (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. DOI: 10.1038/nature08656
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