Even under the best of circumstances, the process of writing can be challenging for both professional and novice writers alike. For novice writers such as university students, the difficulties associated with writing can be further exacerbated when it is combined with their tendency to procrastinate and delay starting a paper till the night before it is due. Unfortunately, it seems that regardless of what an instructor may say or do, many students still inevitably get caught in an endless loop o........ Read more »
Twidale, M.B., Gruzd, A.A. . (2008) Writing in the Library: exploring tighter integration of digital library use with the writing process. Information Processing , 44(2), 558-580. info:/10.1016/j.ipm.2007.05.010
The Open Biomedical Ontologies (OBO)  are a set of reference ontologies for describing all kinds of biomedical data shared in a centralised OBO Foundry. Every year, users and developers of these ontologies gather from around the globe for a workshop at the EBI near Cambridge, UK. Following on from the first workshop two years [...]... Read more »
Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L., Eilbeck, K., Ireland, A., Mungall, C.... (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology, 25(11), 1251-1255. DOI: 10.1038/nbt1346
If you join Twitter in response to a major emergency situation, you’re more likely to become a long-term adopter of the technology. Many early users shared nothing more than the minutiae of their everyday lives on the personal micro-blogging service. However, the Mumbai Taj Hotel terrorist attack, the Hudson River plane crash, California wildfires, Australian [...]Post from: David Bradley's Sciencetext Tech TalkThere’s a tweeting emergency
... Read more »
Amanda Lee Hughes, & Leysia Palen. (2009) Twitter adoption and use in mass convergence and emergency events. Int. J. Emergency Management, 6(3/4), 248-260. info:/
Nature-inspired design: this phrase makes me think of shark-skin swimsuits, velcro, and an endless assortment of coffee tables using natural knots and tree branches. There is logic behind design reliant upon natural elements. After all, organisms have been undergoing evolution for millions of years for the sake of efficiency. If anyone knows how to [...]... Read more »
Andrew Adamatzky, & Jeff Jones. (2009) Road planning with slime mould: If Physarum built motorways it would route M6/M74 through Newcastle. International Journal of Bifurcation and Chaos. arXiv: 0912.3967v1
Katifori, E., Szöllősi, G., & Magnasco, M. (2010) Damage and Fluctuations Induce Loops in Optimal Transport Networks. Physical Review Letters, 104(4). DOI: 10.1103/PhysRevLett.104.048704
Tero A, Takagi S, Saigusa T, Ito K, Bebber DP, Fricker MD, Yumiki K, Kobayashi R, & Nakagaki T. (2010) Rules for biologically inspired adaptive network design. Science (New York, N.Y.), 327(5964), 439-42. PMID: 20093467
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 »
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 [...]
Related posts:Assess Health Information Online Three........ Read more »
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
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
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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:/
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 high........ 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
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 ........ 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
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:/
If you wanted to write a guide to Biomedical and Biological Ontologies , 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 »
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 al........ 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:/
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  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
There have been many new developments in quantum computing during the last few years, but last Sunday a paper appeared in Nature Chemistry that shows how far the area really has come. It seems that now things are getting really interesting: American and Australian scientists just built a quantum circuit that calculated the energy Eigenvalues [...]... Read more »
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 [...]
Related posts:Internet Cool Tools for Physicians This is an excellent book for physicians to read...
Will Online Chat Al........ Read more »
Huang, C. (2009) Internet Use and Psychological Well-being: A Meta-Analysis. CyberPsychology , 2147483647. DOI: 10.1089/cpb.2009.0217
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
The threats of the popular social network Facebook are:
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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Are Facebook Users D........ Read more »
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
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
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:/
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