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Topics in Blog web:
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Changed: now 15:45 GMT
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Changed by:
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ArchivedNotesAndComments
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19 Nov 2008 - 12:26 - r1.8
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TWikiGuest
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rolroracal // Rambaud Drummond Pybus coolness HIV substitution rate predicts disease Main.IanHolmes 16 Feb 2007 06:18:40 // Stephen Salzberg on genome wikis Main.IanHolmes 13 Feb 2007 21:07:15 // Indelign: ML inference of evolutionary indel histories for a given multiple alignment Main.IanHolmes 12 Feb 2007 04:35:41 // Challenges in Engineering Microbes for Biofuel Production (Science sustainable energy issue) Main.IanHolmes 09 Feb 2007 10:13:35 // A ...
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BiologicalWarfare
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26 Nov 2007 - 13:56 - r1.11
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IanHolmes
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As well as being a tool for medicine and biotechnology, molecular biology has functioned as a weapon. // Here are a few random links about molecular biological warfare in ancient and modern times, // in honor of the 25th anniversary of computer viruses. // Anthrax // First used by the Japanese cult Wikipedia:Aum Shinrikyo // More recently the Wikipedia:2001 anthrax attacks // http://www.defencejournal.com/dec98/anthrax.htm // The 1978 assassination of Wikipedia ...
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BombesAndBombBees
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16 Apr 2007 - 18:32 - r1.25
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TWikiGuest
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// Bioinformatics: "Gene Wiki" (at the proposal stage) // Lamb et al's "Connectivity Map" defined by RNA levels and chemical perturbation // Human-Accelerated Regions: fast-evolving ncRNAs found with Main.PhyloGrammars // the gene in question is HAR1F, and it's enriched in Cajal-Retzius neurons // here's on the human-accelerated regions from the Haussler group // Geekdom: dangerously seductive Ajax DNS registration // 200-line webserver; Google Code Search exploits ...
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BooksBoundInHumanSkin
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10 Jan 2006 - 22:26 - r1.24
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IanHolmes
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// Main.WebCritic on 10 Jan 2006: Blog.BooksBoundInHumanSkin (post comment) // Yi Xing reviews how selection at the RNA level may distort measurements of Ka/Ks // BMC Bioinformatics roundup: // SuperMimic is a peptidomimetic docking program. Can't critique v well as I'm no chemist, but looks fun // ZCURVE V is a proke/viral genefinder, billed as a Main.GeneMark replacement // And an update announcement for EcoCyc // More therapeutic RNAi excitement from Nature ...
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BritishCensors
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01 Sep 2007 - 21:17 - r1.7
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IanHolmes
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// Rejecting a work is a very serious action and one which we do not take lightly. Where possible we try to consider cuts or, in the case of games, modifications which remove the material which contravenes the Board's published Guidelines. In the case of "Manhunt 2" this has not been possible. "Manhunt 2" is distinguishable from recent high-end video games by its unremitting bleakness and callousness of tone in an overall game context which constantly encourages ...
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BurgessTypeBiota
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22 Nov 2008 - 20:21 - r1.6
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IanHolmes
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Wikipedia:Burgess shale type biota // Reconstructions of half-billion-year-old Cambrian animals from the Burgess Shale in Yoho National Park, BC (via Boing Boing) . // As Gould says: the Old Ones... // They vaguely remind me of Drawings of Balinese Sorcery. // (Images all at wikimedia.org) // Main.IanHolmes 23 Nov 2008 //
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ChromatinsCodeAndCarlsonCurves
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12 Nov 2006 - 14:07 - r1.9
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IanHolmes
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// Moore's Law vs Carlson's Curves: DNA read/write tech accelerates faster than transistor density // William Gibson on mirror implants, the playa; Rudy Rucker at Biohackery // Brain-computer interfaces and neuroprosthetic software (N V, Making the Paper; more links via Boing Boing) // Ross Anderson's book "Security Engineering" is available free online // Biology: The Chromatin Code; stochastic cellular automata and microbial game theory // More stochasticity ...
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CyberpunkRealism
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10 Oct 2007 - 03:50 - r1.15
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IanHolmes
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Rudy coined the word "Transrealism" for the process of creating sci-fi by taking vignettes from your own autobiography and performing stylistic transformations on the key elements like transplantation to a futuristic setting, or substitution of teen alienation with alien abduction . // William, acknowledging that sci-fi is always truly set in the author's subjective present (which, he says, is trapped at least ten years in the past), has insisted on moving backwards ...
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DeletionMaps
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18 Jan 2006 - 21:52 - r1.10
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IanHolmes
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// Main.WebCritic on 19 Jan 2006: Blog.DeletionMaps (post comment) // Journals (mainly Nature group; sadly no Journal of Imaginary Genomics) // Mol Sys Biol reviews stochastic physics approaches to the noise in gene circuits // Rice tiling arrays... GO-annotated yeast mutant images... human genome epidemiology // Chemical ecology of maize... miRNAs on the brain... structural variation in the human genome // Evan Eichler comments on deletion maps, common polymorphisms ...
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EvolvingSocialNetworks
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12 Jan 2006 - 13:18 - r1.26
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IanHolmes
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// Main.WebCritic on 11 Jan 2006: Blog.EvolvingSocialNetworks (post comment) // BBC Radio Five programme on Declan Butler's avian flu maps // Structured blogging for laboratory journals; // Protein dynamics: modulate vibrations; determines folding // Local protein structure prediction using discriminative models // Insects and mammals share common fat-building pathway // Science: NIH budget shrinkage and peer review process // Virginity testing shudder ... govt ...
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ExploringOrigins
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17 Oct 2008 - 11:01 - r1.2
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IanHolmes
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Via Main.LarsBarquist: // 2008 NSF Science Engineering Visualization Winners: // http://www.nsf.gov/news/special reports/scivis/index.jsp?id win2008 // The honorable mention for interactive media is a site "Exploring Life's Origins" about the RNA World hypothesis, looks pretty neat. // http://www.exploringorigins.org/ // Main.IanHolmes 17 Oct 2008 //
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FightingAndroids
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09 Feb 2006 - 01:40 - r1.13
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IanHolmes
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// Main.WebCritic on 09 Feb 2006: Blog.FightingAndroids (view comments) // Transposon deserts in mammals... gypsy insulators... LINEs and alpha satellites // Protein design: loop grafting... redesigning catalysis... custom zinc fingers in fruitflies // High-throughput DNA methylation profiling... folding viroids and other circular RNAs // RNA genefinding: genome-wide survey in C.elegans ... experimental verification // "Where next for genome sequencing" metagenomics ...
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FuturistCookbook
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21 Nov 2008 - 12:45 - r1.36
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IanHolmes
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The Futurist Cookbook // “…and the diners were given materials of different textures such as velvet and sandpaper to stroke with their left hand. Sweet was combined with savoury to produce startling effects, and bitter and sour tastes were given their place: sardines with pineapple, mortadella with nougat, cooked salami with coffee and cologne. An aphrodisiac cocktail was devised, consisting of pineapple juice, eggs, cocoa, caviar, red peppers, nutmeg, and cloves ...
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GeneDesignSoftware
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29 Aug 2008 - 22:01 - r1.2
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IanHolmes
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Clotho // http://2008.igem.org/Team:UC Berkeley Tools // APE: A Plasmid Editor. // http://www.biology.utah.edu/jorgensen/wayned/ape/ // Code Monkey video on the youtubes // Gene Designer. // // http://www.dna20.com/tools.php // Main.IanHolmes 14 Mar 2008 //
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GuardLlamas
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28 Jan 2006 - 15:53 - r1.8
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IanHolmes
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// Main.WebCritic on 27 Jan 2006: Blog.GuardLlamas (view comments) // Two phylo-footprinting papers, using indels and CpG's // Chromosomal organisation of bacterial genomes... protein computing... kinase database // Molecular clocks in chimps... dog SINEs... PNA reporters // Pseudogene fossils... in vitro selection of HDV ribozyme // Engineered RNase P guide sequences... fluorescent cytidine for RNA probes // Yeast machines... microbiology video podcasts... ...
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GuideToCloudComputing
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25 Sep 2008 - 15:31 - NEW
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IanHolmes
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Information Week's Guide to Cloud Computing: // http://www.informationweek.com/news/services/hosted apps/showArticle.jhtml?articleID 208700713 // From June 2008. // Main.IanHolmes 25 Sep 2008 //
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HappyBecauseTheyEatLard
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28 Sep 2006 - 22:41 - r1.10
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TWikiGuest
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... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... // Main.WebCritic on 18 Jan 2006: Blog.HappyBecauseTheyEatLard (post comment) // Antiviral yoghurt... hemichordate evo-devo... compbio salaries... art in the genetic age... // Swicki adaptive search... Nature Biotech on ontologies... they're happy because they eat lard // Evolution of protein ...
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HelloBioBlogosphere
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13 Aug 2006 - 20:06 - r1.24
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TWikiGuest
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... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... Main.WebCritic on 06 Jan 2006: Blog.HelloBioBlogosphere // Tobias Sing on clinical decision support in HIV therapy // Neil Saunders cheerleads amateur bioinformatics // Declan Butler details a nifty avian flu hack for Google Maps // The 2006 NAR database issue with hat tip to Spitshine // After ...
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HoneywellKitchenComputer
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29 Aug 2008 - 21:58 - r1.7
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IanHolmes
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The Wikipedia:Honeywell 316 // Marketing line: "If only she could cook as well as Honeywell can compute". // Ewwww. So Mad Men. // Via Kevin Kelly // and this Dr Dobbs article. // Current bioinformatics link: OpenQuestions2008 // So Wikipedia:Mad Men ... //
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ImagingGeneMyers
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23 Oct 2008 - 11:31 - r1.4
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IanHolmes
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GeneMyers on imaging informatics. // http://www.bio-itworld.com/pb/2008/10/23/eugene-myers-imaging-informatics.html // Fun quotable statistic: mouse brain imaging will generate 4.2 trillion voxels/week // Main.IanHolmes 23 Oct 2008 //
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ImmuneActivation
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21 Feb 2007 - 04:45 - r1.62
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IanHolmes
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// Rate of HIV evolution predicts onset of AIDS // 1985: Li and Wu's molecular clock paper: // substitution rate varies in mammals // some (chimps, humans) evolve slow // some (mice, rats) evolve faster // this causes distortions // away from the "molecular clock" // away from "ultrametric" trees // somewhat asymmetric behavior. // A simple explanation fits the data: // fast evolutionary rate, short generation time // fast evolutionary rate, fast replication ...
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InsectCyborgs
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07 Nov 2006 - 20:51 - r1.25
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IanHolmes
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// Main.WebCritic on 19 Mar 2006: Blog.InsectCyborgs (view comments) // General news: // Prototype AJAX interface to GBrowse at genome.biowiki.org // Conflicting agents in the brain tell Bob Arctor // Social engineering and Cal basketball. Sneaky... and very funny // Katamari-like Flash minigame if (like me) you still haven't played the original // Slime mold and insect cyborgs: Adama had it easy // Disease genomics: // Extended series of papers on pathogen ...
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InventiveTransposons
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16 Jan 2006 - 18:18 - r1.18
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IanHolmes
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// Main.WebCritic on 17 Jan 2006: Blog.InventiveTransposons (post comment) // Gene circuits: state space models and other Bayesian approaches // GUUGle search for RNA; antisense transcripts; alt-splicing and operon arrays; TATA box flanking sequences // Fast metagenomics; soil bacteria communities; various approaches to prokaryotic gene prediction; 128 bacterial species in human guts // Magnetosomes; biocombinatorial synthesis of nonribosomal peptides; minimal ...
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JasonStajich065103062405
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07 Jan 2006 - 21:30 - r1.5
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IanHolmes
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Main.JasonStajich on June 24 2005 @ 6:51am BOSCBlog // http://www.affymetrix.com/support/developer/tools/download igb.affx // GregHelt 's talk at BOSC, about DAS/2 // New spec to deal with more explicit models // DAS/2 complete within a year // Runs off of the Main.GenericGenomeBrowser //
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JasonStajich072622062405
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07 Jan 2006 - 21:30 - r1.10
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IanHolmes
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Main.JasonStajich on June 24 2005 @ 7:26am // AaronDarling's mpiBLAST talk // Parallel BLAST, parallel allows it to scale the aggregate cluster memory // Superlinear speedup in terms of performance // 0.9 version // Accuracy was limited // poor fault tolerance // 1.0 // Accuracy is still limited // better useability and output formats // Scalability is actually reduced! // 1.2.1 // "distributed biosequence lookup" // packages // Improved scalability // Bad accuracy ...
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JasonStajich110427060905
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08 Jun 2005 - 11:11 - r1.2
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JasonStajich
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GMOD Progress. The links to the presentations from their May meeting are here // There is a new Architecture discussion group to hash out the ways to make the tools interoperate better. Hopefully these efforts will establish some standards and leadership for project coordination. // Main.JasonStajich 08 Jun 2005 //
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JasonStajich110944060905
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08 Jun 2005 - 11:10 - NEW
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JasonStajich
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Testing molecular clock in PAML. // Basically this code for doing an en-masse comparison. This is as per MBL MolEvo Course slides // # $type would be either 'clock' or 'noclock' depending on which file you are reading. // # so you'd want this type of loop to run over all the result files from PAML // # in my case I've numbered all the gene clusters and that number is stored in $num // # designed to parse PAML mlc files from codeml // while() { // if( /lnL\( ...
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JasonStajich111931060905
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08 Jun 2005 - 11:20 - NEW
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JasonStajich
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Almost finished setting up my new data site for fungal genomes. http://fungal.genome.duke.edu // This site has a BLAST interface which uses my Bio::SearchIO parser and Writer (Main.BioPerl) to re-write the report with links in to Main.GenericGenomeBrowser. // There is also gene retrieval CGI direct from Bio::DB::GFF which I think is pretty cool. // Main.JasonStajich 03 Jun 2005 //
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JasonStajich120841062405
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08 Jan 2006 - 10:40 - r1.6
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IanHolmes
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Main.JasonStajich on June 24 2005 @ 12:08pm BOSC Blog, Lightning Talk // Main.AlanChristoffels !Bio.Mambo // Bioinformatics portal. http://www.tll.org.sg http://www.tll.org.sg/res/alan pub.asp // Parallel data distribution // Cluster management // Main.VectorNTI integration with BioPerl // Development environment within windows environment // Main.VectorNTI API, allow use of the Main.VectorNTI framework, COM based... // Main.VectorNTI is commited to making ...
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JasonStajich182009061205
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23 Jun 2005 - 07:25 - r1.2
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JasonStajich
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Main.JasonStajich on 11 Jun 2005 // New page for looking at pairwise orthologs // To Do: Improve pairwise alignment viewer to show gene structure snapshot as FTstring text and then as Main.GenericGenomeBrowser image need to make it a very small image though. // Write homolog browser to display summary results and links //
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JasonStajichLinks
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23 Jun 2005 - 12:34 - r1.13
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JasonStajich
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Jason Stajich 123136062405 // JasonStajich120841062405 // JasonStajich120629062405 // JasonStajich072622062405 // JasonStajich065103062405 // JasonStajich182009061205 // JasonStajich114057060905 // JasonStajich114057060905 // JasonStajich111931060905 // JasonStajich110944060905 // JasonStajich110427060905 // JasonStajich105713060905 // JasonStajich105226060905 //
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JavascriptIPhone
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30 Aug 2008 - 02:21 - NEW
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IanHolmes
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Writing Javascript for Safari on the iPhone: // http://www.evotech.net/blog/2007/07/web-development-for-the-iphone/ // Nice code snippet for getting the viewport orientation 8-) // Main.IanHolmes 30 Aug 2008 //
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JeffMinter
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05 Mar 2007 - 21:22 - r1.8
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IanHolmes
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I just met Jeff Minter at the GDC. // Jeff founded LlamaSoft and wrote colourspace, an early light synth, as well as a bunch of cult psychedelic 8-bit shoot-em-ups featuring llamas, camels and yaks. // I missed his talk but saw him in the program, so when I bumped into the yak-like figure at the top of the elevator, I said hello. // What a guru. I am so star-struck. // I also met some machinima people (one from Melbourne) // and met one of those passionate laptop ...
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MakerFaire
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04 Jun 2007 - 14:54 - r1.3
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IanHolmes
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Maker Faire 2007 was fun. // Sorta like "Why Don't You" meets Burning Man. // Laughing Squid has photos. // Main.IanHolmes 04 Jun 2007 // dorkbotSF looks fun too... //
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MalwarePhylogeny
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30 Aug 2007 - 00:13 - r1.10
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IanHolmes
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Data Rescue?'s IDA disassembler applied to computer virus phylogeny (PDF). // The tree includes Wikipedia:Netsky, Wikipedia:Mydoom, Bagle, Sasser and other variants. // Related pages on biowiki: TeachingVirusProgramming, ViralRiboswitches. //
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NotesAndComments
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19 Nov 2008 - 12:23 - r1.472
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TWikiGuest
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delliolo // and Comments // Origin and evolution of human microRNAs from transposable elements // This Spells DNA in your face RIAA/SoundExchange // Side-channel optimality of genetic code Main.IanHolmes 10 Apr 2007 04:56:26 // Human amplicons Main.IanHolmes 10 Apr 2007 04:55:35 // History of human DNA transposons Feschotte et al Main.IanHolmes 10 Apr 2007 04:53:57 // bio::blogs #9 Main.IanHolmes 07 Apr 2007 02:49:50 // Nature Medicine news article ...
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OlderPosts
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16 Apr 2006 - 18:59 - r1.4
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IanHolmes
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Here are some of the older, bizarrely named blog posts from our baroque attempt at a TWiki blog plugin. // WebCritic114051122205 // WebCritic222110121505 // WebCritic222110121505 // WebCritic025057112605 // WebCritic191423111005 // WebCritic144051101905 // WebCritic143723100905 // WebCritic114935100505 // WebCritic114935100505 // WebCritic231501092205 // WebCritic145146082405 // WebCritic183748072205 // WebCritic093600071605 // WebCritic160620062405 // WebCritic143204061405 ...
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OpenQuestions2008
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28 Feb 2008 - 18:49 - r1.10
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IanHolmes
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Open questions (moving into) 2008 // Indel processes // Consider all approximations: // gaps as extra substitution character // closed-form approximations: TKF91, TKF92 // xrate: gap-model; gaps as characters; with context... // discrete-time transducers // Statistical alignment MCMC // The definitive sampler? // Simultaneous alignment gene prediction // Best way to build Main.ReadingFrameConservation into a generative model? // Measurement of indel rates / ...
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PageRank
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15 Oct 2008 - 06:54 - r1.3
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IanHolmes
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The Wikipedia:PageRank for http://biowiki.org/ is up a point, to 5/10 perhaps indicating a recovery from the spam attacks of yesteryear? // Or just that we're getting more links? // Not that I take this all that seriously we could do a lot of things to improve PageRank if we really cared, like minimizing the number of outgoing links per page (see especially the left bar) but it's nice to be nudging up in the Google rankings... // Now, if only the Dow Jones ...
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PaleoVirology
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19 Dec 2007 - 09:54 - r1.6
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IanHolmes
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Paleovirology in the New Yorker. // Mentions Heidmann et al reconstructing the human endogenous retroviral ancestor, "Phoenix". // Thanks to steady advances in computing power and DNA technology, a talented undergraduate with a decent laptop and access to any university biology lab can assemble a virus with ease. // via Bruce Sterling // Main.IanHolmes 19 Dec 2007 //
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ParanoiaRPG
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04 Jun 2007 - 15:08 - r1.22
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IanHolmes
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// The computer is your friend // I was sad enough to be into several RPG's as a teen geek in the 80's. // Maelstrom, D D, Traveller... my favorite, however, was the classic "Paranoia". // Wikipedia page // http://en.wikipedia.org/wiki/Paranoia (role-playing game) // The Rules // 1st edition (1984) ISBN:0874310253 // 2nd edition (1989) ISBN:0874310180 // (Avoid the substandard 5th edition, or so they say) // Paranoia XP (2004) ISBN:1904854265 // Paranoid ...
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ProceduralRhetoric
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03 Sep 2008 - 11:41 - r1.3
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IanHolmes
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Logic applied to automated game design // Described in this book: // http://www.bogost.com/books/persuasive games.shtml // Recommended by MichaelMateas // Main.IanHolmes 03 Sep 2008 //
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RaphKoster
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09 Mar 2007 - 21:02 - r1.18
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IanHolmes
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UPDATE: Raph's comment below indicates that I did, in fact, misinterpret his reaction to "Bioengineering". // I now feel like a complete tool... ah well... I do enjoy a good rant! // // Warning: this post is a bit of a rant... // Back at the Game Developers' Conference today. // On Wednesday I met Raph Koster, who worked as a designer on Ultima Online, Star Wars Galaxies and a bunch of MUDs in the early 90's. // I went up and introduced myself after his panel ...
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RiboWiki
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01 Sep 2007 - 21:16 - r1.12
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IanHolmes
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y'know. wikipedia has a lot of cool stuff. // Wikipedia:RNA world hypothesis // Wikipedia:RNA structure lots of algorithms // Wikipedia:Ribosomal RNA // Wikipedia:Ribozyme // Wikipedia:Aptamer // Wikipedia:Riboswitch // Wikipedia:Hammerhead ribozyme ... I mean, I could go on ... // Wikipedia:RNA // Wikipedia:Non-coding RNA // Wikipedia:WikiProject RNA aims to cultivate articles on each noncoding RNA family // This is a mini-class in RNA right here 8-) // Main ...
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SharBlog120402033105
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30 Mar 2005 - 12:36 - r1.7
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TWikiGuest
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// Added tgcheck.c and tgcheck.h to Main.TeleGraph in Dart. These tgcheck comprises functions to determine whether the grammar is in Chomsky Normal form or RNA Normal form. // Main.SharonChao 30 Mar 2005 // //
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SharBlog151527061805
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17 Jun 2005 - 15:15 - NEW
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TWikiGuest
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// Main.SharonChao 3 Jun 2005 // June 3, Morning // tgexpression.h // has the tg expr structure, which encapsulates the operation and operands // Also has a vector, tg expression vec, that holds all these structures // Depending on the type of the operands, what the operation is, we choose one // of the functions from tgdefs.c to call // tgdefs.c // tg make prob expr makes a binary expression using the grammar, the prob of // type tg prob , and the tg vec ...
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SharBlog151552061805
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17 Jun 2005 - 15:16 - NEW
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TWikiGuest
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// Main.SharonChao 7 Jun 2005 // June 7, 2005 Afternoon // Today, wrote tg alloc prob score table, which takes a tg grammar and mallocs // enough space for all of the declared probabilities. For example, // prob paramZero 5 , paramOne DNA , paramTwo DNA DNA 3 // would allocate 5 sizeof(tg score) for paramZero, four sizeof(tg score) for paramOne, // and 4 4 3 sizeof(tg score) for paramTwo. // Each spot in the tg prob score tab corresponds to each probability ...
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SharBlog151659061805
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17 Jun 2005 - 15:18 - r1.2
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TWikiGuest
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-- Main.SharonChao 8 Jun 2005 // June 8, 2005 Morning // (from parse.tg) // token DNA { A C G T }; // term DNA1 DNA , DNA2 DNA ; // nonterm start, match, insert, delete; // prob subst DNA DNA , gapOpen, gapExtend; // ... // / the "script" / // gapOpen .5; // gapExtend .3; // subst A C 1.3; // So when we declare subst DNA DNA , we are just allocating space for the probability // substitution matrix. But then when we make the assignment of gapOpen 0.5, we // fill ...
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SharBlog151832061805
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17 Jun 2005 - 15:18 - NEW
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TWikiGuest
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// Main.SharonChao 9 Jun 2005 // June 9, Afternoon // Wrote the tg ProbAssign part for eval expr, which now should be writing to the prob score // table. // Changed the prob score table to be a vector of vectors or tg scores. // //
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SharBlog151852061805
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17 Jun 2005 - 15:19 - NEW
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TWikiGuest
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// Main.SharonChao 10 Jun 2005 // une 10, Morning // Changed the free prob score table so that it uses the vector delete fn instead of a direct free. // The loop that was calling eval expr was not executing cuz tg- expr was empty then. // So used something similar to the call to write expr in tg write grammar, which // cycles through the assign vector of tg. Infinite looping. hmmm // Afternoon // Need to make sure the writing is correct. Looks like its not ...
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SharBlog151920061805
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17 Jun 2005 - 15:19 - NEW
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TWikiGuest
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// Main.SharonChao 13 Jun 2005 // June 13, Morning // Something strange--the printf output would be fine on the terminal but when it was to a file, it woulndt output all the // entries in the prob score table. It turns out it was a problem with the freeing of the non-matrix probabilities like gapOpen, // and the freeing of the probscoretable. Will get back to this later, but I think this is automatically freed. Looks like // everything is working fine now ...
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SharBlog151942061805
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03 Apr 2006 - 04:49 - r1.2
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TWikiGuest
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// Main.SharonChao 14 Jun 2005 // June 14, Morning // CVS, here are some notes // setenv CVSROOT :ext:schao@128.32.184.7:/home/schao/MYCVS // setenv CVS RSH ssh // get in SharonsCVS directory // cvs import SharonsCVS schao alpha // in vi, type i to write, esc to stop, :wq to quit // cvs d:pserver:drpotamuss@cvs.sourceforge.net:/cvsroot/dart login // hit return when asked for password // cvs z3 d:pserver:drpotamuss@cvs.sourceforge.net:/cvsroot/dart co dart ...
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SharBlog152015061805
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17 Jun 2005 - 15:20 - NEW
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TWikiGuest
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// Main.SharonChao 15 Jun 2005 // June 15, Morning // Questions updated: // 1. So score is the log2 integer form of probability? What do we want to return when evaluating rule expressions? Right now, we're // making const expressions out of the scores. // 2. Freeing correctly? // 3. possible to mix dollar subscripts with non-dollar subscripts in a subscript vec? // 4. Does dollar binding get filled out during runtime? Or do we just want to bind $1 to something ...
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SharBlog152106061805
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17 Jun 2005 - 15:21 - NEW
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TWikiGuest
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// Main.SharonChao 17 Jun 2005 // June 16 // Expanding the grammar to allow for list probability assignments. Saved in list assignment temp. // Changed in gram.y // ln 47 type subscript list fixed subscript list dim list prob list // (added prob list) // where to put prob list element? // AND... // list assignment: // PROBID EQUALS BITS prob list ';' // { tg list assign prob(tg, $1, $3); } // ; // prob list: // prob list ',' prob list element { $$ tg vec append ...
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SharBlog152141061805
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17 Jun 2005 - 15:22 - NEW
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TWikiGuest
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// Main.SharonChao 17 Jun 2005 // June 17 // It looks like we fixed the binding problem. We were originally calling eval rules AFTEr freeing the prob score table. // Here is a sample of the output. Note: dollar binding is just a vector of 0's. // gapOpen .5; // gapExtend .3; // subst A A 0.1; // subst C A 0.2; // subst C G 0.3; // subst T C 0.4; // probby A C A 0.1; // probby A C T 0.2; // probby C A A 0.3; // probby C A C 0.4; // probby C T G 0.5; // probby ...
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SharBlog162102062805
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27 Jun 2005 - 16:23 - NEW
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TWikiGuest
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// Main.SharonChao 27 Jun 2005 // June 21 // 3D is ok. But the problem with this algorithm is that it won't work like this for n dimensions. // Prob Score Table // prob tab 0 3321 0 0 0 2321 0 1736 0 0 0 0 0 0 1321 0 0 // prob tab 1 0 0 0 0 3321 0 0 2321 0 0 0 0 0 0 0 0 1736 1321 0 0 0 0 0 0 0 0 0 0 0 0 999 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 736 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 // prob tab 2 137 263 485 584 // prob tab 3 3321 2321 1736 1321 999 736 514 321 152 ...
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SharBlog172705063105
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30 Jun 2005 - 17:28 - NEW
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// Main.SharonChao 30 Jun 2005 // { // June 28 // Where we left off, tg iterate draft 1 written, but doesnt totally work yet. it looks like its getting stuck around the updating positions part. // Cleaned up tgcompiler.c so it calls separate functions, now in tgtest.c that check the grammar, test the prob score table, test the iteration etc... // { // June 29 // Its producing semi-right answers right now, but we're having a little trouble on the recursive ...
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SharBlog172812063105
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30 Jun 2005 - 17:36 - NEW
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TWikiGuest
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// Main.SharonChao 30 Jun 2005 // Cool iterate works with n 1. We just need to test this out with multidimensional solutions. Maybe try with the case of n 2, y (3,2), m 3 // Do we want the function to be called on a generic M N matrix of integers, or is it okay as it is now, being called on a "solvec", which is a vector // of intvecvecs, a vector of intvecs. It makes it easier this way to carry around the size of each level, but it requires dereferencing the ...
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SharBlog175022062805
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27 Jun 2005 - 17:50 - NEW
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TWikiGuest
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// Main.SharonChao 27 Jun 2005 // How do we associate the probability with a parse. // We need some sort of traceback variable? // Need to use a stack to parse bottom up? // Do we wanna have one parse tree per sequence? // For folding, we want to find the max parse for the sequence, but for alignment, we want to look for matches across sequences // Input: a vector of sequences. // Starting with tg iterate // We can probably use this generic algo to iterate ...
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SharBlog175648062105
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20 Jun 2005 - 17:59 - NEW
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TWikiGuest
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// Main.SharonChao 20 Jun 2005 // Fixed compile errors related to the list assignment extension. // Runtime: need to fix--we might only be assigning the last of the list assignment // YEAH! we fixed that...the problem was not reinitializing a new subscript vec for each assignment // had a little problem with prob assignments without subscript vectors like gapOpen 0.5 // This was a shift/reduce error, and they are now getting read as list assignments, but it ...
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SharBlogLinks
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30 Jun 2005 - 17:36 - r1.24
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TWikiGuest
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Shar Blog 172812063105 // SharBlog172705063105 // SharBlog175022062805 // SharBlog162102062805 // SharBlog175648062105 // SharBlog152141061805 // SharBlog152106061805 // SharBlog152015061805 // SharBlog151942061805 // SharBlog151920061805 // SharBlog151852061805 // SharBlog151832061805 // SharBlog151659061805 // SharBlog151552061805 // SharBlog151527061805 // SharBlog130001060305 // SharBlog120133050505 // SharBlog120402033105 // SharBlog1 // SharBlog101944031705 ...
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SharRotationBlog145504021406
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13 Feb 2006 - 17:48 - NEW
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SharonChao
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Notes on Bergman paper // conservation across 8 genomic regions from 4 different drosophila species // covers ~500 kb of D. melanogaster // All D melanogaster genes showed functional constraints // Rates of a.a. substitution // Conserved non-coding sequences (CNCSs) //
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SharRotationBlog153642021806
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17 Feb 2006 - 16:17 - r1.4
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SharonChao
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// 2/17/06 // Met with Ian today to talk about the projects. // BOINC: I need to talk to Yuri at some point about applying BOINC to the project he worked on for his summer rotation. // Blog: Looks at Scoop, Slashcode, and maybe Wordpress. We need something that's easy to install and multiuser. // A link to possible blog software // Protein-Coding Gene Training Set: Lior Pactor has an 8 fly and 9 fly database of alignments, the genomes for each, and a file that ...
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SharRotationBlog160331021106
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10 Feb 2006 - 16:19 - r1.4
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SharonChao
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Rotation Project Ideas // Friday 2/11/06 // After meeting with Ian today, I've got a few rotation project to work on this semester. // 1. Working on protein coding models for xgram and the genome browser. // This involves aligning known protein coding genes with the fruitfly genome to come up with a training dataset. // 2. Distributive computation using BOINK. // Divide the xgram batches into small jobs running as an awesome screensaver. // 3. Finding a suitable ...
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SharRotationBlog173531021606
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17 Feb 2006 - 15:59 - r1.2
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SharonChao
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// 2/16/06 // Downloaded Rhodopsin 1 data, which was used in the Bergman paper. This might be a good starting point, although the paper was written in 2002 when there were only 4 species. Also downloaded the drosophila chromosome arm files from Release 4. I got these off of the Berkeley Drosophila Genome Project. // 2/15/06 // Built dart, had a little trouble with getting binutils and coreutils for the mac. Rob suggested downloading Xcode's legacy, which had ...
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SharRotationBlogProjIdeas
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10 Feb 2006 - 16:22 - NEW
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SharonChao
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Rotation Project Ideas // Friday 2/11/06 // After meeting with Ian today, I've got a few rotation project to work on this semester. // 1. Working on protein coding models for xgram and the genome browser. // This involves aligning known protein coding genes with the fruitfly genome to come up with a training dataset. // 2. Distributive computation using BOINK. // Divide the xgram batches into small jobs running as an awesome screensaver. // 3. Finding a suitable ...
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SingleSpeciesEcosystem
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10 Oct 2008 - 10:47 - r1.3
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IanHolmes
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Metagenomics reveals anoxic, single-bacterium ecosystem in a gold mine: // http://newscenter.lbl.gov/press-releases/2008/10/09/bold-traveler’s-journey-toward-the-center-of-the-earth/ // via http://news.bbc.co.uk/2/hi/in depth/7663927.stm // Can't find the Science paper yet but here is an anticipatory methods review article with Main.AdamArkin as co-author: // Main.IanHolmes 10 Oct 2008 //
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SocialProlog
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02 Apr 2007 - 10:38 - r1.23
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IanHolmes
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Game Dev // So I had this idea for a game that was a sort of blend of social networking and Prolog 8-) // Sounds weird, I know. // More later (maybe). // In the meantime, here are some links I've been scoping out as background research. // Main.IanHolmes 02 Apr 2007 // Open Source Social Networking Software // Social networking engines // http://elgg.org/ seems quite funky; PHP, "educationally" targeted, has !MediaWiki plugins... // http://peopleaggregator ...
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SpookCountry
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23 Aug 2007 - 22:58 - r1.15
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IanHolmes
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// William Gibson's new book Spook Country has almost nothing in common with the original proposal, reproduced below. // Publishers Note: In around July 2005 (according to his blog) William // Gibson began writing the novel that became Spook Country and // delivered it 18months later to his publishers. Reproduced below is // William Gibson’s original proposal for this novel // Proposal for a novel by William Gibson // “Warchalker” is one of the more obscure ...
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StormWorm
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24 Oct 2007 - 13:43 - r1.5
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IanHolmes
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From Bruce Schneier: // Peer-to-peer, stealthy, for-profit malware. // Although it's most commonly called a worm, Storm is really more: a worm, a Trojan horse and a bot all rolled into one. It's also the most successful example we have of a new breed of worm, and I've seen estimates that between 1 million and 50 million computers have been infected worldwide. // Old style worms Sasser, Slammer, Nimda were written by hackers looking for fame. They spread as ...
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SummerOfCode
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23 Mar 2007 - 22:47 - r1.31
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IanHolmes
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// Google SummerOfCode 2007: project submissions due March 26th // Our Entries: Ajax Phylo-Informatics, Automated Pipeline Tools // NESCENT has a page up about Google's 2007 summer of code. // Here's my contribution so far (excerpted from the NESCENT phyloinformatics wiki): // Evolve Unix phyloinformatics tools into Ajax applications // Rationale // Many powerful new tools for phylogenetic stochastic grammar analysis of multiple alignments, such as xrate or ...
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SwearAtTheMachine
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12 Nov 2006 - 14:07 - r1.15
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IanHolmes
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// Toys: Backstreet magnetic fingertip implants via Boing Boing // ...whose David Pescovitz also writes Berkeley Lab Notes // Sfold, Sribo: synthetic biology tools for RNA folding and rational design // http://www.picotux.com/ .. it's a computer that's the size of a RJ45 socket (tm ottaky) // Counterculture: Steal This Book wiki Abbie Hoffman's survival manual goes live // Ethical hacking course at University of Abertay // British Goth spot-fined eighty quid ...
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SyntheticBioFiction
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09 Jun 2007 - 00:40 - r1.51
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IanHolmes
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// Rewatching Wikipedia:Farscape, whose biomechanoid Leviathans I love, I was reminded of the cheesily-titled but good "The Helix and the Sword" by John !McCloughlin (reviews, random blog comment, ISBN:0812545567). // Massive zooloads of engineered posthuman species ("synes"), including living ships... a post-apocalyptic exile of humanity into the solar plate... and the "Sisterhood of the Nucleotides", a secretive order of genetic engineers to pit against Dune ...
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TeachingVirusProgramming
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23 Aug 2007 - 23:04 - r1.42
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IanHolmes
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// Bruce Schneier has a post up on Teaching Virus and Worm Programming. // I allude to the A-life qualities of computer viruses and worms in my introductory computational biology class. // Seems fair game to me. // I'm not at Michal Zalewski's level, but dreaming's free... // Who's Michal Zalewski, you ask? Only the coollest virus designer ever (outside of SpookCountry, I guess...) // Sebastian authored a virus that could... perform cross-platform infections ...
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TheRealWire
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28 Aug 2007 - 16:38 - r1.20
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IanHolmes
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Source material for HBO's The Wire. // (William Gibson likes this show too.) // This bulletin maintains that the gang violence under review in Baltimore is a symptom of the powerful influence of gang leaders. These gang leaders, though small in number, are largely responsible for the fear that touches Baltimore's citizens. Head gangsters are vulnerable, however, because the violence they command is revulsive to others, and law enforcement can direct that revulsion ...
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