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Topics in Main web:
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Changed: now 21:14 GMT
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Changed by:
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AluinoRuzicka
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17 Mar 2010 - 10:03 - NEW
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TWikiGuest
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// Name: Aluino Ruzicka // Email: 1@02f.info // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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TWikiUsers
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17 Mar 2010 - 10:03 - r1.215
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TWikiGuest
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// List of users // Please take the time and add yourself to the list. To do that fill out the form in .TWikiRegistration. This will create an account for you which allows you to edit topics. // #ListStart // A B C D E F G H I J K L M N O P Q R S T U V W X Y Z // A // AdemBrown 25 Jan 2010 // AhmedHimel 07 Dec 2005 // AidanRoberts 24 Jan 2010 // AlannaConnell 15 Sep 2009 // AlbertVilella 04 Apr 2006 // AleoMok 01 Sep 2009 //
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JassyBroot
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17 Mar 2010 - 01:52 - NEW
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TWikiGuest
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// Name: JassyBroot // Email: jassy665@yahoo.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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PattinGodish
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16 Mar 2010 - 13:55 - NEW
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TWikiGuest
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// Name: Pattin Godish // Email: ioi8jwkko@gawab.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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TiffanieEcocafe
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16 Mar 2010 - 13:38 - NEW
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TWikiGuest
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// Name: Tiffanie Ecocafe // Email: b072dc723ac4@9f6c2430520d.anonbox.net // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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WebStatistics
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15 Mar 2010 - 17:48 - r1.877
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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 66989 28 0 6565 2877 RecentChanges 2351 2257 BioWiki 1318 1269 MercatorTutorial 786 718 WebChanges 596 531 IanHolmes 512 HolmesLab 15 Main.IanHolmes 13 Main.TWikiGuest // Feb 2010 117183 27 0 10771 4334 RecentChanges 4199 2714 BioWiki 2197 1764 WebSearch 1763 1068 WebChanges 947 878 ClusterNFSBenchmarks ...
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MarioPlummer
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13 Mar 2010 - 11:11 - NEW
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TWikiGuest
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// Name: Mario Plummer // Email: allhail@lavabit.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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ZooGas
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11 Mar 2010 - 09:01 - r1.33
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IanHolmes
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// Z00 Gas // Zoo Gas is a game that attempts to pose a familiar question in computational ecology how are complex food webs stabilized? as a real-time Wikipedia:game mechanic. // Formally, Zoo Gas is an entropy-maximizing game of population-balancing and (highly simplified) natural selection, set on a cellular automaton model of the Wikipedia:Lotka-Volterra equation. // The underlying engine is a general-purpose, peer-to-peer reaction-diffusion simulator ...
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HolmesLab
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10 Mar 2010 - 17:42 - r1.156
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IanHolmes
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// HolmesLab // Address: 381 StanleyHall, University of California, Berkeley, CA 94720-3220. // Phone: (510) 666 2791. // Events // Lab members // lab members // Undergrad rotation students: AlanWang, DavidTam, ArthurYu //
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GatesYount
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09 Mar 2010 - 10:01 - NEW
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TWikiGuest
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// Name: Gates Yount // Email: fairdeal@lavabit.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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CorrySevern
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07 Mar 2010 - 09:20 - NEW
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TWikiGuest
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// Name: Corry Severn // Email: elevated@lavabit.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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JamieMurnaghan
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06 Mar 2010 - 04:04 - NEW
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TWikiGuest
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// Name: Jamie Murnaghan // Email: dabeat@lavabit.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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DART
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05 Mar 2010 - 13:43 - r1.255
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IanHolmes
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// The Dart Library: XRate, Handel, Stemloc, EvolDeeds more... // For instructions on how to get dart, go to this page: dart. // What it is? // The DART library includes a number of bioinformatics programs, including: stemloc for RNA alignment; xrate for phylo-grammars; phylocomposer and other alignment programs in the package; and more. //
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DownloadingDart
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05 Mar 2010 - 13:41 - r1.47
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IanHolmes
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// Downloading DART // The latest version of dart can be downloaded as a tarball or zipfile from http://github.com/ihh/dart/archives/master // Download the tarball (this will be named something like ihh-dart-abc0123.tar.gz ), then extract it and rename the top-level directory from ihh-dart-abc0123 to dart . // You can also browse the source code at http://github.com/ihh/dart/tree/master // If you have the git source code revision management tool installed, you ...
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XrateFormat
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05 Mar 2010 - 11:24 - r1.183
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IanHolmes
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// xrate file format // Introduction // The Participle, with an Article before it, and the Preposition of after it, becomes a Substantive, expressing the action itself which the Verb signifies: as, "These are the Rules of Grammar, by the observing of which you may avoid mistakes." // Bishop Robert Lowth, A Short Introduction to English Grammar, 1775. // This document describes the grammar file format for the xrate phylo-grammar alignment analysis package. ...
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EvolutionarySoftwareFoundation
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02 Mar 2010 - 12:46 - r1.21
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IanHolmes
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// Evolutionary Software Foundation // The Evolutionary Software Foundation (ESF) is a 501(c)(3) nonprofit corporation dedicated to promoting // scientific research into and public understanding of the theory of evolution and its implications, through development and maintenance of software (including but not limited to research tools, educational software and evolution-themed computer games), publications, websites, animations, lectures or otherwise. // Software ...
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MoriaDavidovich
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02 Mar 2010 - 11:33 - NEW
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TWikiGuest
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// Name: Moria Davidovich // Email: deepdeep@lavabit.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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JagrutibahenJoshi
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24 Feb 2010 - 13:22 - NEW
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TWikiGuest
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// Name: Jagrutibahen Joshi // Email: joshi.jagu@yahoo.in // Comment: welcome... // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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PicornaIRES
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19 Feb 2010 - 15:33 - r1.9
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TWikiGuest
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// Some papers discussing the function/structure/evolution of IRES elements, particularly in picornaviruses // Structure/function // // // // // // // // // Origin/Evolution //
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XRumerTest
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16 Feb 2010 - 12:24 - NEW
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TWikiGuest
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// Name: XRumerTest // Email: yourmail@gmail.com // Comment: Hello. And Bye. // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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ShaniaGray
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15 Feb 2010 - 13:02 - NEW
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TWikiGuest
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// Name: Shania Gray // Email: othothislove@aol.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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JackSuresh
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10 Feb 2010 - 23:21 - NEW
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TWikiGuest
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// Name: Jack Suresh // Email: jacksuresh54@yahoo.in // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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XrateMacros
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10 Feb 2010 - 17:18 - r1.15
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IanHolmes
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// Documentation of the macro language that forms part of the xrate format. // For the longer complete description of the format, including the grammar description as well as these macros, please see the format page. // The xrate macro preprocessor // Several kinds of macro are automatically expanded by xrate before any training or alignment takes place. // Macro expansion is a one-off, irreversible event: // if the grammar file is saved after macro substitution ...
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IndieGram
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10 Feb 2010 - 13:56 - r1.33
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IanHolmes
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// IndieGram // TreeTransducers , finite-state machines which can mutate parse trees, // provide a framework for modeling the evolution of structured RNAs along a phylogenetic tree. // Our software Indiegram implements a tree-transducer-based model of the evolution // of three structured RNAs. The Structure Tree model is provided with the software, // but users can create their own models using the provided Perl code-generation // scripts. Given a model, the ...
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FastaFormat
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05 Feb 2010 - 14:56 - r1.6
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IanHolmes
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// FASTA // FASTA is a bare-bones flat-file format for DNA, RNA and protein sequence data. // It's the most widely used understood format for unannotated sequence, probably due in large part to its simplicity. // It can also be used to represent multiple alignments (see FASTA format). // For details see e.g. // Wikipedia:Fasta format // http://www.ebi.ac.uk/help/formats frame.html //
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NewMat
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25 Jan 2010 - 16:20 - r1.2
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IanHolmes
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// Newmat // Newmat is a linear algebra library by RobertDavies. It is used by the DART library. // Here is the page for Newmat: // http://www.robertnz.net/nm intro.htm //
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AdemBrown
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25 Jan 2010 - 04:22 - NEW
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TWikiGuest
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// Name: Adem Brown // Email: us.drugstore@yahoo.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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AidanRoberts
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24 Jan 2010 - 11:59 - NEW
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TWikiGuest
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// Name: Aidan Roberts // Email: us.drugstore@yahoo.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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MoliLop
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19 Jan 2010 - 08:12 - NEW
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TWikiGuest
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// Name: moli lop // Email: moli@trash2009.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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WendyDawson
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04 Jan 2010 - 12:29 - NEW
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TWikiGuest
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// Name: Wendy Dawson // Email: wendydawson91@gmail.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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JayBowden
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01 Jan 2010 - 12:12 - r1.3
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JayBowden
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// Name: Jay Bowden // Email: reviews@topacaiberry.org // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me // top3acaiberry.org // paraslimforweightloss.blogspot.com // flushexcessweight.blogspot.com // acai-berry-actives.blogspot.com // flushexcessweight.com //
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KandrapeduDorairaju
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25 Dec 2009 - 22:36 - NEW
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TWikiGuest
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// Name: kandrapedu dorairaju // Email: dorairajusvu@gmail.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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JeremySalomon
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21 Dec 2009 - 15:55 - NEW
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TWikiGuest
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// Name: Jeremy Salomon // Email: bunny.hops.south@hotmail.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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MartinChardy
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21 Dec 2009 - 15:51 - NEW
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TWikiGuest
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// Name: Martin Chardy // Email: siestainbed25@hotmail.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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BuildingDart
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16 Dec 2009 - 18:28 - r1.32
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IanHolmes
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// Building DART // 1 Download (or checkout) the source distribution: see DownloadingDart // 1 You will need GNU tools including gcc (v4.0 or later), make , binutils and coreutils // See the INSTALL file in the top-level directory for more info (or type more dart/INSTALL ) // These tools come with many linux distributions, but gcc in particular, though stable in the last couple of years, has evolved by leaps bounds in the past and may be out of date if you have ...
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RfamRiboswitches
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10 Dec 2009 - 07:51 - r1.3
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IanHolmes
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// For a list of riboswitches in RFAM, use the "search by type" feature: // http://rfam.sanger.ac.uk/search/type#tabview tab4 // You could also try this keyword search (a bit less robust...) // http://www.sanger.ac.uk/cgi-bin/Rfam/queryrfam.pl?terms riboswitch //
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IanHolmes
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09 Dec 2009 - 19:12 - r1.604
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IanHolmes
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// Ian Holmes // Contact details // Email: ihh $\begin{picture}(10,10)\put(5,5){\circle{10}}\put(2,3){$\alpha$}\end{picture}$ berkeley $\circ$ edu // Skype: ianholmes // AIM/iChat: dartcoder@mac.com // Office address: 374C StanleyHall, UC Berkeley, CA 94720-3220 // Office phone: (510) 666 2790 //
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KatieSimer
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06 Dec 2009 - 23:09 - NEW
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TWikiGuest
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// Name: Katie Simer // Email: sheenflock@gmail.com // Comment: kostenlose Kontaktborse // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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KukuTena
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06 Dec 2009 - 03:24 - NEW
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TWikiGuest
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// Name: kuku tena // Email: kuku.tena@yahoo.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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SisayT
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06 Dec 2009 - 03:20 - NEW
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TWikiGuest
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// Name: SisayT // Email: sisefe@yahoo.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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BioinformaticsWorkflows
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24 Nov 2009 - 14:16 - r1.43
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IanHolmes
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// Bioinformatics workflows // Bioinformatics workflows can be approached in several ways. // Unix hackers often resort to make, // while computer scientists dream of more elegant approaches. // Meanwhile, projects like Taverna offer the beginnings of GUI-designed grid workflows. // Taverna // TomOinn leads development on // Taverna // (recently covered by Hublog, // Propeller Twist // and // Flags and Lollipops). //
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HowToAdministerSunGridEngine
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24 Nov 2009 - 08:50 - r1.53
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TWikiGuest
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// // How to Administer Sun Grid Engine // This is the page for how to administer Sun Grid Engine jobs, hosts, queues, users, policies, etc. on the BabylonCluster. For other info on SGE, visit: // SunGridEngine (installation guide and some notes on our setup) // HowToUseSunGridEngine (basic usage guide) // some How To pages from the SGE project site, with useful stuff, particularly: // Basic Usage of Grid Engine //
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PhyloGrammars
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15 Nov 2009 - 16:23 - r1.14
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IanHolmes
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// PhyloGrammars // A "phylo-grammar" is a stochastic grammar whose emissions (i.e. terminals) // are alignment columns, typically generated by evolving a continuous-time Markov process // on a phylogenetic tree. // As a class of models, phylo-grammars include all simple point substitution models // (including e.g. codon substitution, conditional approximations to context-dependent substitution, etc). // They also include HMM- and SCFG-like models for co-ordinated ...
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TafDearce
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13 Nov 2009 - 21:19 - NEW
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TWikiGuest
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// Name: TafDearce // Login Name: TafDearce // Email: rob@wep6.com // Phone: 123456 // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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Number of topics: 50
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