Computer Science posts
- September 1, 2010
- 01:00 PM
- 330 views
The "Bad" Language of Physics
by S.C. Kavassalis in The Language of Bad Physics
One of the things I sometimes find myself writing about is the “bad” language used by physicists. Sometimes we say Riemannian when we really should say psuedo-Riemannian, sometimes we call something a metric when it really is a line element – the kind of nitpicky pet-peeves that practically everyone has about literature in their field. Today, I’m going to be talking about the bad language in physics in a totally different context however.... Read more »
Regge, T. (1961) General relativity without coordinates. Il Nuovo Cimento, 19(3), 558-571. DOI: 10.1007/BF02733251
Galassi, M. (1993) Lapse and shift in Regge calculus. Physical Review D, 47(8), 3254-3264. DOI: 10.1103/PhysRevD.47.3254
Kheyfets A, LaFave NJ, & Miller WA. (1990) Null-strut calculus. II. Dynamics. Physical review D: Particles and fields, 41(12), 3637-3651. PMID: 10012308
ALPER ÜNGÖR, & ALLA SHEFFER. (2002) PITCHING TENTS IN SPACE-TIME: MESH GENERATION FOR DISCONTINUOUS GALERKIN METHOD. International Journal of Foundations of Computer Science , 13(2). info:/10.1142/S0129054102001059
- August 31, 2010
- 09:00 PM
- 11 views
The Bad Language of Physics
by S.C. Kavassalis in The Language of Bad Physics
One of the things I sometimes find myself writing about is the “bad” language used by physicists. Sometimes we say Riemannian when we really should say psuedo-Riemannian, sometimes we call something a metric when it really is a line element – the kind of nitpicky pet-peeves that practically everyone has about literature in their field. Today, I’m going to be talking about the bad language in physics in a totally different context however.
Teepee Lattices, Future-Pointing Wigwams ........ Read more »
Regge, T. (1961) General relativity without coordinates. Il Nuovo Cimento, 19(3), 558-571. DOI: 10.1007/BF02733251
Galassi, M. (1993) Lapse and shift in Regge calculus. Physical Review D, 47(8), 3254-3264. DOI: 10.1103/PhysRevD.47.3254
Kheyfets A, LaFave NJ, & Miller WA. (1990) Null-strut calculus. II. Dynamics. Physical review D: Particles and fields, 41(12), 3637-3651. PMID: 10012308
ALPER ÜNGÖR, & ALLA SHEFFER. (2002) PITCHING TENTS IN SPACE-TIME: MESH GENERATION FOR DISCONTINUOUS GALERKIN METHOD. International Journal of Foundations of Computer Science , 13(2). info:/10.1142/S0129054102001059
- August 30, 2010
- 03:44 PM
- 56 views
Hacking Commercial Quantum Cryptography Systems by Illumination
by Olexandr Isayev in isayev.info
Quantum hackers have performed the first 'invisible' attack on two commercial quantum cryptographic systems. By using lasers on the systems — which use quantum states of light to encrypt information for transmission — they have fully cracked their encryption keys, yet left no trace of the hack.... Read more »
Lydersen, L., Wiechers, C., Wittmann, C., Elser, D., Skaar, J., & Makarov, V. (2010) Hacking commercial quantum cryptography systems by tailored bright illumination. Nature Photonics. DOI: 10.1038/NPHOTON.2010.214
Feihu Xu, Bing Qi, & Hoi-Kwong Lo. (2010) Experimental demonstration of phase-remapping attack in a practical quantum key distribution system. Preprint. arXiv: 1005.2376v1
- August 26, 2010
- 07:20 PM
- 39 views
Improved Protein Minimotif Prediction for Drug Development
by Michael Long in Phased
Sanguthevar Rajasekaran (University of Connecticut, United States), Martin Schiller (University of Nevada Las Vegas, United States), and coworkers have improved upon Minimotif Miner computer software for predicting functional relationships among proteins, relevant to drug discovery. This news feature was written on August 26, 2010.... Read more »
Rajasekaran, S., Mi, T., Merlin, J. C., Oommen, A., Gradie, P., & Schiller, M. R. (2010) Partitioning of Minimotifs Based on Function with Improved Prediction Accuracy. PLoS ONE, 5(8). DOI: 10.1371/journal.pone.0012276
- August 26, 2010
- 04:55 PM
- 47 views
Galaxy, a stride towards reproducible computational research
Galaxy started out as a very useful tool to do genomics research that was reproducible and sharable. One of my pet peeves in reading research papers that use genomic analysis or online genomics resources is the materials and methods sections. Often the methods and parameters used are mentioned only in a very cursory manner, if [...]... Read more »
Goecks, J., Nekrutenko, A., Taylor, J., & Galaxy Team, T. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology, 11(8). DOI: 10.1186/gb-2010-11-8-r86
- August 25, 2010
- 06:50 PM
- 52 views
Correlating Drug Side Effects, Biochemical Pathways, and Diseases
by Michael Long in Phased
The computational model of Izhar Wallach, Navdeep Jaitly, and Ryan Lilien (Unversity of Toronto, Canada) will accelerate drug development, and help scientists understand the origin of adverse drug side effects. This news feature was written on August 25, 2010.... Read more »
Wallach, I., Jaitly, N., & Lilien, R. (2010) A Structure-Based Approach for Mapping Adverse Drug Reactions to the Perturbation of Underlying Biological Pathways. PLoS ONE, 5(8). DOI: 10.1371/journal.pone.0012063
- August 25, 2010
- 08:00 AM
- 42 views
Resolving conflicts to make finding a job easier
by David Bradley in Sciencetext
Politicians might tell you that, “the ongoing evaluation of global joblessness data can be represented by a negative slope on the current employment hysteresis”. Unemployment is on the rise, in other words. So, it’s rather timely that a powerful “meta job search” engine is being developed by Austrian and UK computer scientists. Tabbasum Naz of [...]Post from: David Bradley's Sciencetext Tech TalkResolving conflicts to make finding a job easier
... Read more »
Tabbasum Naz, Jürgen Dorn, & Alexandra Poulovassilis. (2010) Configurable meta-search in the job domain. Int. J. Web Engineering and Technology, 6(1), 33-57. info:/
- August 23, 2010
- 09:05 PM
- 55 views
A Web Server for Identifying the "Hot Spot" of Protein-Protein Interfaces
by Michael Long in Phased
Narcis Fernandez-Fuentes (University of Leeds, United Kingdom) and coworkers' web server will greatly accelerate the development of drugs which target protein-protein interfaces. This news feature was written on August 23, 2010.... Read more »
Segura Mora, J. S., Assi, S. A., & Fernandez-Fuentes, N. (2010) Presaging Critical Residues in Protein interfaces-Web Server (PCRPi-W): A Web Server to Chart Hot Spots in Protein Interfaces. PLoS ONE, 5(8). DOI: 10.1371/journal.pone.0012352
- August 20, 2010
- 04:10 PM
- 70 views
Genome-Scale Epigenetic Marker Detection Across Populations
by Michael Long in Phased
Lior Pachter (University of California at Berkeley, United States) and coworkers have developed MetMap software for uncovering epigenetic data hidden by standard MethylSeq analysis, which will advance our understanding of the role of epigenetics in human health and medicine. This news feature was written on August 20, 2010.... Read more »
Singer, M., Boffelli, D., Dhahbi, J., Schoenhuth, A., Schroth, G. P., Martin, D. I. K., & Pachter, L. (2010) MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations. PLoS Computational Biology, 6(8). DOI: 10.1371/journal.pcbi.1000888
- August 20, 2010
- 04:26 AM
- 54 views
What’s the point of the semantic web?
by sciencebase in Sciencebase Science Blog
I was scanning journal tables of contents as usual this week and it occurred to me that there must be a better way to find relevant and timely research information that would be of interest to Sciencebase readers…and, of course, out pops the following title: Technically approaching the semantic web bottleneck Sounded, perfect…kind of…but what’s [...]What’s the point of the semantic web? is a post from: Sciencebase Science Blog
... Read more »
Nikolaos Konstantinou, Dimitrios-Emmanuel Spanos, Periklis Stavrou, & Nikolas Mitrou. (2010) Technically approaching the semantic web bottleneck. Int. J. Web Engineering and Technology, 6(1), 83-111. info:/
- August 16, 2010
- 12:50 PM
- 76 views
Octopusomics
Let’s take a minute to talk about connectomics. No, not genomics. No, not metabolomics. Not any of the other -omics, but connectomics. It’s a new-ish field that the computational neuroscience geek in all of us can love. By way of introduction, the “connectome” is the “network of elements and connections forming the human brain” (according [...]... Read more »
Sporns, O., Tononi, G., & Kötter, R. (2005) The Human Connectome: A Structural Description of the Human Brain. PLoS Computational Biology, 1(4). DOI: 10.1371/journal.pcbi.0010042
Yoonsuck Choe, Louise C Abbott, Giovanna Ponte, John Keyser, Jaerock Kwon, David Mayerich, Daniel Miller, Donghyeop Han, Anna Maria Grimaldi, Graziano Fiorito.... (2010) Charting out the octopus connectome at submicron resolution using the knife-edge scanning microscope. BMC Neuroscience, 11(Supplement 1), 136-137. info:/10.1186/1471-2202-11-S1-P136
MAYERICH, D., ABBOTT, L., & McCORMICK, B. (2008) Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain. Journal of Microscopy, 231(1), 134-143. DOI: 10.1111/j.1365-2818.2008.02024.x
White, J., Southgate, E., Thomson, J., & Brenner, S. (1986) The Structure of the Nervous System of the Nematode Caenorhabditis elegans. Philosophical Transactions of the Royal Society B: Biological Sciences, 314(1165), 1-340. DOI: 10.1098/rstb.1986.0056
MORI, S., & ZHANG, J. (2006) Principles of Diffusion Tensor Imaging and Its Applications to Basic Neuroscience Research. Neuron, 51(5), 527-539. DOI: 10.1016/j.neuron.2006.08.012
- August 12, 2010
- 08:00 AM
- 64 views
Who on Earth uses Flickr?
by David Bradley in Sciencetext
Flickr.com, in case you didn’t know, is an online photo repository, it’s now part of Yahoo, but nevertheless remains an incredibly popular site for sharing photos and creating galleries. It also acts as a neat resource for finding Creative Commons images for use on blogs and other sites. Flickr describes itself thus: You take photos. [...]Post from: David Bradley's Sciencetext Tech TalkWho on Earth uses Flickr?
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Amir Dotan, & Panayiotis Zaphiris. (2010) A cross-cultural analysis of Flickr users from Peru, Israel, Iran, Taiwan and the UK. Int. J. Web Based Communities, 6(3), 284-302. info:/
- August 11, 2010
- 07:09 PM
- 64 views
A Foundation for Next-Generation Analysis Tools
by Daniel Koboldt in Massgenomics
The emergence of next-generation sequencing has presented numerous significant challenges to the bioinformatics community. NGS instruments have given rise to a new generation of software tools for the alignment, assembly, management, and visualization of incredible amounts of data. New algorithms have also been developed to assess coverage, assess genomic copy number, call variants (SNPs/indels), and [...]... Read more »
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M.... (2010) The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome research. PMID: 20644199
- August 10, 2010
- 06:46 PM
- 58 views
The Wednesday Post (11/08/2010)
by thomastu in Disease of the Week
Looking at protein folders A recent Nature letter looks at the properties of human protein folders and how they can design better programs to do it automatically (Photo taken by Thomas Tu) My mother was always vaguely disdainful of me playing computer games as a child (… and as an adult). But it turns out [...]... Read more »
Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. DOI: 10.1038/nature09304
- August 5, 2010
- 10:04 AM
- 94 views
Humans beat computers in predicting protein structures
by The Curious Wavefunction in The Curious Wavefunction
I was going to first describe Rosetta in a post, but a rather cool paper related to the program which appeared in Nature yesterday makes me jump the gun.In a nutshell, Rosetta tries to predict the structure of proteins from amino acid sequence by inserting fragments from known protein structures and doing many rounds of side chain torsional angle and rigid-body energy optimization. It uses a scoring function to rank the resulting structures that uses empirically derived hydrogen bonding, hydroph........ Read more »
Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. DOI: 10.1038/nature09304
- August 5, 2010
- 08:24 AM
- 79 views
Foldit: Innovative Biology for Gamers
by GrrlScientist in This Scientific Life
Guessing how a protein will fold up based on its DNA sequence is often too difficult for even the most advanced computer programs. Now biochemists and computer scientists at my alma mater, the University of Washington, have collaborated to create Foldit, an online computer game where computer players do the work. ... Read more »
Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. DOI: 10.1038/nature09304
- August 4, 2010
- 11:18 AM
- 79 views
Come on feel the PyroNoise
by Nicholas Loman in Pathogens: Genes and Genomes
454 sequencing technology has revolutionised the field of microbial ecology by providing a means to sequence tens of thousands of partial 16S rDNA sequences quickly and efficiently. However, this new capacity brought new problems to a field fraught with potential sources of bias. Early analyses of microbial communities using 454 data tended to overstate the [...]... Read more »
Quince, C., Lanzén, A., Curtis, T., Davenport, R., Hall, N., Head, I., Read, L., & Sloan, W. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods, 6(9), 639-641. DOI: 10.1038/nmeth.1361
- July 27, 2010
- 11:17 AM
- 95 views
Twenty Million Papers in PubMed: A Triumph or a Tragedy?
by Duncan Hull in O'Really?
A quick search on pubmed.gov today reveals that the freely available American database of biomedical literature has just passed the 20 million citations mark*. Should we celebrate or commiserate passing this landmark figure? Is it a triumph or a tragedy that PubMed® is the size it i... Read more »
Halevy, A., Norvig, P., & Pereira, F. (2009) The Unreasonable Effectiveness of Data. IEEE Intelligent Systems, 24(2), 8-12. DOI: 10.1109/MIS.2009.36
Torvik VI, & Smalheiser NR. (2009) Author Name Disambiguation in MEDLINE. ACM transactions on knowledge discovery from data, 3(3). PMID: 20072710
Islamaj Dogan R, Murray GC, Névéol A, & Lu Z. (2009) Understanding PubMed user search behavior through log analysis. Database : the journal of biological databases and curation. PMID: 20157491
- July 27, 2010
- 10:34 AM
- 97 views
Can Computers Help Scientists With Their Reading?
by Rob Mitchum in ScienceLife
The public perception of science in action typically involves a person in a white coat pouring brightly-colored fluids in and out of test tubes. Sure, a little bit of that does go on in a laboratory. But before the glassware is broken out, a lot of less glamorous stuff has to happen. Every experiment is [...]... Read more »
Evans, J., & Rzhetsky, A. (2010) Machine Science. Science, 329(5990), 399-400. DOI: 10.1126/science.1189416
- July 26, 2010
- 02:18 AM
- 66 views
The neural response to emotional robots
When it comes to robotics, Japan is way ahead of the rest of the world. Reality is quickly catching up with science-fiction as robots are being used and developed for increasingly complex behaviours. There are now Japanese robots that function as security guards, trainers for professional skills, and even pets and social companions.Robots are taking over roles that were once thought to make humans unique. An archetypal example of this is the use of robots for cognitive therapy. Robots are ........ Read more »
Thierry Chaminade1,2*, Massimiliano Zecca3,4,5, Sarah-Jayne Blakemore6, Atsuo Takanishi, Chris D.Frith1, Silvestro Micera, Paolo Dario, Giacomo Rizzolatti, Vittorio Gallese11, & Maria Alessandra Umilta. (2010) Brain Response to a Humanoid Robot in Areas Implicated in the Perception of Human Emotional Gestures. PLoS ONE. info:/
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