Here are this week’s journal picks.
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You can see all the picks in citeulike:
MizBee: A Multiscale Synteny Browser (http://dx.doi.org/doi:10.1109/TVCG.2009.167)
Miriah Meyer, Tamara Munzner, Hanspeter Pfister et al. IEEE Transactions on Visualization and Computer Graphics, Vol. 15, No. 6. (23 October 2009), pp. 897-904.
Whole exome capture in solution with 3Gbp of data (http://dx.doi.org/doi:10.1186/gb-2010-11-6-r62)
Matthew Bainbridge, Min Wang, Daniel Burgess et al. Genome Biology, Vol. 11, No. 6. (2010), R62.
I am not familiar with Belgian history and its current problems and it seems it is too touchy issues to bring this up with people. So I am just investigating what is going on. Sure I can understand the problems better if I can understand Dutch but my Dutch is limited to familiar science topics. But it seems that the eventual split is possible even though it will not strengthen neither part; but it will satisfy the nationalism of some Flanders. How deeply is the passion rooted? The problem seems to be extremely deep. I just realized that it is almost impossible for Americans, Canadians and in some sense Japanese to understand the complexity of European histories. Japanese history is mostly internal up to 150 years ago except several very ancient critical events. US and Canada both experienced civil wars but not as bad as other countries. Continue Reading
Journal of Negative Results in BioMedicine is ready to receive manuscripts on all aspects of unexpected, controversial, provocative and/or negative results/conclusions in the context of current tenets, providing scientists and physicians with responsible and balanced information to support informed experimental and clinical decisions.
Abstract: The drug concentration was slightly higher than mice under investigation could tolerate therefore all individuals did not survive for two weeks…
The great PhD scam: Jordan Ellenberg
“We dangle our three magic letters before the eyes of these predestined victims, and they swarm to us like moths to an electric light. They come at a time of life when failure can no longer be repaired easily and when the wounds it leaves are permanent . . . “
Deception is universal.
Deception was defined by Vrij in 2001 as “a successful or unsuccessful deliberate attempt, without forewarning, to create in another a belief which the communicator considers to be untrue” (Vrij 2001). Another good definition of deception was proposed by de Waal in 1992: “Deception can be defined as the projection, to one’s own advantage, of an inaccurate or false image of knowledge, intentions, or motivations” (de Waal 1992). Lastly, Byrne defines deception functionally as “acts from the normal repertoire of the agent, deployed such that another individual is likely to misinterpret what the acts signify, to the advantage of the agent” (Byrne 1997).
Carolyn Ristau investigated a particularly interesting deceptive behavior in the piping plover’s “broken wing display” (Ristau 1996). The piping plovers deceive predators approaching their nest by feigning an injured wing and hopping farther and farther from the nest, leading the predator away from their young. If the predator begins to pursue them and gets close enough to catch them, they immediately take flight and escape from the danger. If the predator still approaches the eggs, the piping plover will continue to mimic a broken wing in an attempt to lure the predator away from the nest. What is most fascinating is that the piping plover recognizes different types of dangerous intruders. It distinguishes between predators that may eat its eggs or young, and animals like cows that may simply crush the eggs with no intent to eat them. In the case of a cow nearing the nest, the piping plover remains in its nest until the cow is close and it then flutters into the cow’s face, startling it into running away from the nest. This suggests that not only does the piping plover consciously intend to deceive; it understands when deception does not work to protect its offspring.
Thomas Friedman wrote something similar in his book about the social and industrial paradigm shift in the 20th century. He did not specifically discussed about Japan. But Kurokawa concisely summed up the possible cause of the stagnation of Japan, which enjoyed the unprecedented economic growth after its defeat of the WWII. Individuals can easily chose their own action on the face of change. The changing the fundamental social and economic structures that have worked so well previously is very difficult. Continue Reading
2008 Quinn et al; licensee BioMed Central Ltd.
BMC Genomics. 2008; 9: 404.
Published online 2008 August 28. doi: 10.1186/1471-2164-9-404.
Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome
GS FLX assembliesA previous version of the Newbler assembler used in performing the assemblies has been described previously , and the overall structure and phases of the assembler used here follows the structure described in that paper; however, the algorithms used for the specific phases of assembly have been upgraded. The upgraded Newbler assembler identifies pairwise overlaps between reads, and then uses them to construct multiple alignments of contiguous regions of the dataset. Boundaries where the read-by-read alignments diverge or converge (such as at the boundaries of repeat regions) define breaks in the contig multiple alignments (also called branch points). The resulting data structure consists of a graph, where each node is a contiguous multiple alignment, undirected edges exist between the 5′ and 3′ ends of the contig nodes, and reads form alignments along paths of the graph. The assembler builds this multiple alignment graph using an adjustable greedy algorithm of taking a ‘query’ read, finding the pairwise overlaps to it, constructing a multiple alignment of those overlaps, then choosing a subsequent ‘query’ read from the overlapped reads that are only partially aligned so far (thereby extending the multiple alignment). If any pairwise overlap alignments conflict with the current multiple alignment graph, corrective algorithms use the conflicting alignments to either ignore the new pairwise overlap (if the graph is more consistent) or to correct the constructed multiple alignment (if the new pairwise overlap identifies a misalignment in the graph). These overlaps and multiple alignment algorithms use a combination of nucleotide-space (i.e., the bases of the reads) and flow-space (i.e., the 454 flowgram signal intensities of the reads), where available, to perform the multiple alignment construction.Following the construction of the multiple alignment graph, a series of ‘detangling’ algorithms are used to simplify the complex regions of the graph, such as overly collapsed regions shorter than the length of the reads (i.e., parts of reads that happened to be near-identical to each other by chance, and so produced overlaps that collapsed into a single multiple alignment region). The nodes in the resulting graph after detangling are considered to be the ‘contigs’ by the assembler, and those longer than 500 bp are output as the ‘large contigs’ of the assembly (those longer than 100 bp are output in the set of ‘all contigs’).If paired end reads are included in the data set (either 454 or Sanger paired ends), then an additional scaffolding step is performed after detangling, to create chains of contig nodes using the paired end information. The pairs from each library where both halves of the pair occur in the same contig are used to calculate expected pair distances for the library. The scaffolding algorithm then performs a greedy algorithm of identifying pairs of nodes where at least two paired end reads have their halves aligned at the ends of the pair of nodes, with the correct alignment direction and expected distance from each other. In addition, the set of paired end reads aligned at those two contig ends must support the unambiguous chaining of the two nodes as immediate neighbors in a scaffold, with fewer than 10% of the paired end reads aligning to other contig nodes in the assembly. The chains of contig nodes found by this greedy algorithm are output as the scaffolds of the assembly.
Genome Sequencer FLX System Workflow:
Genome Sequencer FLX System Software Manual. General Overview and Data File Formats. The data analysis phase offers a choice of …