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Topics in Blog web:
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Changed: now 20:51 GMT
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Changed by:
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WebStatistics
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16 Mar 2010 - 22:30 - r1.520
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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: // // Mar 2010 9128 0 0 1939 1445 WebRss 1077 371 WebCritic 187 146 WebIndex 140 117 TeachingVirusProgramming 101 82 NotesAndComments 74 SummerOfCode // Feb 2010 20386 2 0 2528 2330 WebStatistics 1827 632 WebCritic 374 331 ExploringOrigins 320 302 TeachingVirusProgramming 289 282 EvolutionOfMalware 184 XMLandScheme 2 ...
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WebHome
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15 Feb 2010 - 13:04 - r1.27
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TWikiGuest
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// For a more comprehensive and frequently-update feed please go to !FriendFeed: // http://friendfeed.com/ianholmes // 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 ...
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GeneDesignSoftware
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05 Nov 2009 - 16:34 - r1.3
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TWikiGuest
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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. // // https: //www.dna20.com/tools/genedesigner.php // Main.IanHolmes 14 Mar 2008 //
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WolframAlphaSucks
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26 May 2009 - 19:38 - r1.2
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IanHolmes
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// Reposted from a Boing Boing comment on a Main.RudyRucker post: // Why do technology evangelizers give Wolfram Alpha a free pass? It is quite clearly orders of magnitude less useful than Google. I have not yet seen the problem it solves. Everyone I know personally who's used it says it sucks. For even the simple computations it boasts that it can do well, it sucks awfully because its knowledge model is just not up to the job, and never will be. (I typed "murders ...
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PrimordialSoup
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14 May 2009 - 17:21 - NEW
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IanHolmes
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// More evidence supporting the RNA World hypothesis: // "Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions." Powner, Gerland Sutherland, Nature 2009 // http://www.nature.com/nature/journal/v459/n7244/full/nature08013.html // http://www.nytimes.com/2009/05/14/science/14rna.html? r 1 em // Main.IanHolmes 15 May 2009 //
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NumbersStations
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14 May 2009 - 13:50 - NEW
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IanHolmes
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// Wikipedia:Numbers stations robot voices reading cryptic numbers over shortwave radio may be good fodder for bioinformatics Teaching.CryptanalysisExercises. // The Atención station played a central role in the federal case against the Wikipedia:Wasp Network, aka the Wikipedia:Cuban Five. // "prioritize and continue to strengthen friendship with Joe and Dennis" 68 characters // "Under no circumstances should agents German nor Castor fly with BTTR or another ...
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WikipediaRNA
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01 May 2009 - 15:41 - NEW
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IanHolmes
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// Wikipedia and RFAM // The first Wikipedia paper in RNA Biology, from the Eddy lab's "secret agent man", Tom Jones. // // http://www.nature.com/news/2008/081216/full/news.2008.1312.html // http://selab.janelia.org/people/eddys/blog/?p 24 // Main.IanHolmes 01 May 2009 //
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MissionToEarthsCore
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16 Apr 2009 - 00:09 - r1.4
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IanHolmes
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// Stevenson, David J. Mission to Earth’s Core A Modest Proposal. Nature , 423 , 239-240, 2003. // ... // Earth’s interior is // opaque to electromagnetic signals with // periods less than the mission timescale, // and neutrinos are difficult to use, so // acoustic communication is best. // ... //
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EvolutionOfMalware
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31 Mar 2009 - 22:48 - r1.3
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IanHolmes
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// Evolution of viruses and worms // On the eve of Conficker's new payload activation period, I found this article from 2004, detailing four main "waves" in the evolution of viruses and worms: // http://vx.netlux.org/lib/atc01.html // From the book "Statistical Methods in Computer Security" // (ISBN:0824759397, Google search) // A bit out-of-date now, since it's pre-Storm and pre-Conficker, but interesting historically. // Here's a little sumpn-sumpn on Conficker ...
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AdaLovelaceDay
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23 Mar 2009 - 17:39 - r1.26
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IanHolmes
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// Ada Lovelace Day // March 24 2009 is Ada Lovelace Day, on which we recognize female role models in science and technology. // http://ada.pint.org.uk/list.php // http://twitter.com/findingada // Amongst the women whom I admire most in science engineering history are pioneers in // computer programming: Wikipedia:Ada Lovelace // electronic music: Wikipedia:Delia Derbyshire // structural biology: Wikipedia:Rosalind Franklin // genetics: Barbara McClintock (Wikipedia ...
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BodySwap
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03 Dec 2008 - 13:16 - r1.3
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IanHolmes
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// Body swap research shows that self is a trick of the mind // "If I Were You: Perceptual Illusion of Body Swapping" (PLoS ONE) // http://www.boingboing.net/2008/12/03/experiment-provides.html // Brain scientists have succeeded in fooling people into thinking they are inside the body of another person or a plastic dummy. // The out-of-body experience which is surprisingly easy to induce will help researchers to understand how the human brain constructs a ...
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BiowikiPageRank
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27 Nov 2008 - 08:52 - r1.7
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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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ProceduralRhetoric
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27 Nov 2008 - 08:51 - r1.4
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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 Main.MichaelMateas // Main.IanHolmes 03 Sep 2008 //
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GeneImagery
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27 Nov 2008 - 08:49 - r1.5
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IanHolmes
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// Main.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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TonyBennsMagneticMap
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27 Nov 2008 - 08:47 - r1.5
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IanHolmes
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// Parking in his local area was so bad that Benn made this magnetic map so he and his wife, who died in 2000, could locate the their far-flung vehicles in the morning. // http://news.bbc.co.uk/today/hi/today/newsid 7550000/7550123.stm // http://www.boingboing.net/2008/11/27/tony-benns-invention.html // Main.IanHolmes 27 Nov 2008 //
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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. //
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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 ...
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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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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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WebPreferences
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29 Aug 2008 - 21:45 - r1.17
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IanHolmes
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// Web Preferences // The following settings are web preferences of the web. These preferences overwrite the site-level preferences in ., and can be overwritten by user preferences (your personal topic, eg: .TWikiGuest in the web). // Preferences: // Koala skin: // Set SKIN koala // Set NAVBARH // Set NAVBARF // Set NOWEBSBAR // Set WIKILOGOIMG http://biowiki.org/twiki/pub/TWiki/TWikiLogos/BioWikiLogo.png // List of topics of the . web: //
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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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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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ArchivedNotesAndComments
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05 May 2007 - 09:42 - NEW
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IanHolmes
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// 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 post by Raph ...
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WikiGangsign
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25 Mar 2007 - 16:14 - r1.68
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TWikiGuest
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// LTR Struc (PubMed): de novo annotation of LTR retrotransposons // Random links: fake eggs... script.aculo.us demos... the wiki gangsign // RNA logic (Breaker et al ); binding site evolution (Laessig et al ) // #CommentsSection // Comments // ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... no changes ... // Main.TWikiGuest 09 Jul 2006 14:57:47 // .. ...
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SummerOfCode
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23 Mar 2007 - 23:47 - 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): //
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WebCriticLinks
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17 Feb 2007 - 22:56 - r1.79
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IanHolmes
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// ImmuneActivation // WikisForSpooks // WarGamesAndHoneyBees // BombesAndBombBees // ChromatinsCodeAndCarlsonCurves // SwearAtTheMachine // WikiGangsign // InsectCyborgs // WhereInTheWorldIsPhilipKDick // TheThirdWay // FightingAndroids // GuardLlamas // TrackingDollarBills // DeletionMaps //
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WikisForSpooks
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03 Feb 2007 - 02:31 - r1.48
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TWikiGuest
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// Games, scifi, fun // Working jetpack! (more like paragliding than the classic Speccy game, though) // More retro game walkthrus on Youtube: Skool Daze (yet more here) // A history of computer RPGs; Mark Hurst's list of free games // Video game workout links: exercise bike workstation; Tetris weightlifting // Rudy Rucker's Flurb zine; wasting the Prince of Darkness at Microsoft // Christmas: the time of year for pardoning witches and praying to hacker gods ...
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WhereInTheWorldIsPhilipKDick
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16 Dec 2006 - 02:18 - r1.24
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TWikiGuest
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// Main.WebCritic on 17 Feb 2006: Blog. (view comments) // Prizes: Michael Ashburner wins Ben Franklin... GE essay on molecular motors // Gene circuits: evolution of body plans... negative feedback and spectral shifts... comparing networks // RNA: programmed recoding and degradation... modifications and folding... IRESes in L1 elements // Sequence analysis and the human meta-genome (aka gut flora...) // Mammalian evolution: Z-DNA and deletions... duplicate genes ...
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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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WebCritic222110121505
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14 Dec 2005 - 22:35 - r1.3
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IanHolmes
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// Main.WebCritic on 15 Dec 2005 // The dog genome: recently published in Nature, discussed in Genome Research // Linux on the Treo 650 wow. Too bad the new Treo uses Windows. But Motorola's linux efforts are promising // Via Science magazine's Netwatch: Phosphosite is a clickable database of protein phosphorylation sites // Also from Science: signaling models and DNA self-assembly //
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WebCritic231501092205
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26 Sep 2005 - 18:41 - r1.15
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IanHolmes
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// Main.WebCritic on 22 Sep 2005 // Ranganathan et al describe, in Nature, how modeling covariation is necessary in order to mimic folds in protein design... // ...but is their Statistical Coupling Analysis just another take on mutual information? // Perhaps something like Bill Bruno's Corind could work just as well? Or some kind of Markov random field? // That said, David Baker's group has designed proteins without modeling covariation, using Rosetta... hmmmm ...
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WebCritic224224042505
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26 Apr 2005 - 08:55 - r1.5
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TWikiGuest
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// Main.WebCritic on 25 Apr 2005 // STEM: Spatiotemporal Epidemiological Modeler // Environmental genomic tags: eco-fingerprinting // Pharmacognostic text-mining for ethnobotany // More MRI mind-reading (but, "you could use it to detect peoples' prejudices" ? Please...) //
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WebCriticFirstEntry
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04 Mar 2005 - 15:56 - r1.6
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TWikiGuest
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// Main.WebCritic on 25 Feb 2005 // Ewan Birney wins 2005 Ben Franklin award // so expect kite-flying lightning talk at BOSC 2005 // Liked the argument sketch at 2005 OpenEye CUP // c2.com's InformalHistoryOfProgrammingIdeas //
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Number of topics: 50
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