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Changed: now 16:07 GMT
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WebStatistics
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21 Aug 2008 - 08:23 - r1.173
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TWikiGuest
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// Statistics for Web // Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: // // Aug 2008 12358 1 0 1813 1062 WebHome 793 741 WebSearch 303 294 WebStatistics 211 174 SummerOfCode 146 128 VideoGameWorkout 127 EvolutionAndMedicine 1 Main.TWikiGuest // Jul 2008 11346 2 0 2972 640 WebHome 343 336 WebStatistics 310 222 WebSearch 200 171 SummerOfCode 156 126 GeneDesignSoftware 118 XMLandScheme 2 Main ...
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EvolutionAndMedicine
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30 Jul 2008 - 18:46 - r1.2
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IanHolmes
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// http://www.evolutionandmedicine.org/ "a resource for scientists and medical professionals working at the interface of evolutionary biology and medicine" // Includes the 2006 Science editorial Why Medicine Needs Evolution (PDF). // via this post on evolgen. // Main.IanHolmes 31 Jul 2008 //
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GeneDesignSoftware
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13 Mar 2008 - 18:01 - NEW
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IanHolmes
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// 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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XMLandScheme
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28 Feb 2008 - 19:18 - r1.6
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IanHolmes
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// XML as a dialect of Scheme: // http://classes.eclab.byu.edu/330/wiki/index.cgi?XMLandScheme // http://okmij.org/ftp/Scheme/xml.html // Main.IanHolmes 29 Feb 2008 //
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HoneywellKitchenComputer
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28 Feb 2008 - 18:54 - r1.6
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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 //
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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 //
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UrgeMechanics
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27 Feb 2008 - 11:22 - r1.10
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IanHolmes
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// "Urge Mechanics" is my new sexy name for "Ergonomics". // The old word is so stuffily work-oriented: // ergonomics // "scientific study of the efficiency of people in the workplace," coined 1950 from Gk. ergon "work" (see urge (v.)) (ec)onomics . // The Swedish TCO Congress (English page) were recommended to me as having tougher ergonomic emission standards than anyone else. // My friend who recommended them said: // "Unfortunately they only certified one ...
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VideoGameWorkout
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26 Feb 2008 - 23:13 - r1.14
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IanHolmes
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// Games like // Prop Cycle, // Dance Dance Revolution and // Mocap Boxing // herald a new era of digital arcade entertainment where physical fitness is a byproduct of play. // Products like // Toysight // (for Apple Mac's iSight webcam), // along with fitness-oriented game controllers like // Kilowatt Sport from Powergrid Fitness, // have brought exercise games from the arcade to the desktop. // Is this the future? // Glen Raphael at videogameworkout.com thinks ...
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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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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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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 ...
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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 ...
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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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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 //
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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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// DataRescue'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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ViralRiboswitches
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28 Aug 2007 - 16:52 - r1.5
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IanHolmes
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// Following my earlier post on TeachingVirusProgramming ... // Here's a nice application of aptamers that highlights some of the potential a theophylline-triggered riboswitch implanted in tomato bushy stunt virus: // http://www.f1000biology.com/article/id/1087232 // A systems biology paper from the same F1000 issue, on how noise determines B.subtilis fates: // http://www.f1000biology.com/article/id/1087316 // Main.IanHolmes 24 Jun 2007 // // From the syntheticbiology ...
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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 ...
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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...) //
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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 //
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WebHome
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18 Jun 2007 - 23:33 - r1.25
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IanHolmes
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// URLPARAM{"search" default ". " } " web "INCLUDINGWEB " } " regex "on" nosearch "on" order "created" reverse "on" limit "" } // // OK, I've stopped trying to bend the wiki into being a blog and am now using this subweb as, uh, a wiki for random one-off observations. // Images are often reposted at biowiki.org home. // Here are the 25 most recent new pages. Main.IanHolmes 04 Jun 2007 // //
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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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NotesAndComments
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05 May 2007 - 09:44 - r1.471
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IanHolmes
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// 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 on wikis ...
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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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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 ...
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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" //
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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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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. (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/immune "infectogenomics ...
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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. (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 topology... RPM blogs ...
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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: . // 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 the fall of NCBI ...
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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. (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? (plankton ...
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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. (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... guard llamas ...
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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. (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 and ...
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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. (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 bacteria; fluorescent ...
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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. (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 cryptozoology: Werner ...
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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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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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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 //
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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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Number of topics: 50
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