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Topics in Main web:
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Changed: now 15:37 GMT
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Changed by:
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WebStatistics
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03 Jul 2009 - 22:56 - r1.707
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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: // // Jul 2009 18357 4 1 2172 1445 BioWiki 985 885 WebSearch 211 157 ClusterNFSBenchmarks 153 98 LabMeeting 82 80 HolmesLab 75 TwelveFlyScreenResults 3 Main.IanHolmes 2 Main.TWikiGuest // Jun 2009 143103 20 1 14726 8235 WebRss 5213 3661 WebSearch 2566 1099 RecentChanges 807 800 IanHolmes 772 693 HolmesLab 692 MobileDNA ...
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IanHolmes
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02 Jul 2009 - 14:24 - r1.589
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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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BellaBorovsky
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01 Jul 2009 - 04:43 - NEW
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TWikiGuest
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// Name: Bella Borovsky // Email: bella.borovsky@sial.com // 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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01 Jul 2009 - 04:43 - r1.176
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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 // AhmedHimel 07 Dec 2005 // AlbertVilella 04 Apr 2006 // AlexA 08 Feb 2007 // AlexBroot 13 Oct 2006 // AlexPhan 11 Nov 2006 // AlexisAvitia 04 Nov 2005 //
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PosteriorDecoding
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15 Jun 2009 - 00:04 - r1.3
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IanHolmes
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// Posterior decoding is an application of DecisionTheory to find maximally-scoring alignment paths or parse trees in HiddenMarkovModels and StochasticGrammars. // // See also // PairwisePosteriorDecoding // SequenceAnnealing // Main.IanHolmes 03 Oct 2007 //
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PaperArchive
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06 Jun 2009 - 12:11 - r1.69
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IanHolmes
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// Paper archive for the Holmes Lab, Berkeley // Journals and conference proceedings // 1 (pdf) // 1 // 1 (pdf) // 1 (pdf) // 1 (pdf) // 1 (pdf) // 1 (pdf) // 1 (pdf) (errata) // 1 (pdf) // 1 (pdf) //
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DART
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01 Jun 2009 - 12:10 - r1.252
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TWikiGuest
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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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MakeComparison
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01 Jun 2009 - 12:00 - r1.8
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IanHolmes
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// Quick comparison of automated build tools related frameworks // Changelog: // Moved here from MakefileLabMeeting. Main.IanHolmes 03 Dec 2007 // Added Ruffus stub Main.IanHolmes 01 Jun 2009 // Tool Language Declarative MD5 triggers SQL hooks Extensible Parallelism SGE compatible Implemented Thriving Concise Practical GNU-compatible Tried it? // make C Y no no no (threads) no Y Y Y Y Y Y // omake C Y Y no no ? no Y Y Y Y Y no // distmake C Y no no no Y ...
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HIVRecombinationMechanisms
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29 May 2009 - 11:57 - r1.4
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TWikiGuest
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// Reviews / general info // // Review of hypothesized mechanisms for recombination/strand switch in HIV. Outlines breakage, pause sites, RNA structure, etc // // Selection/protein viability // // Using a cell culture system, recombinants are generated, then these are tested for viability of the env protein, and these distributions are compared to each other as well as the global breakpoint distribution. Main conclusion: protein viability accounts for quite ...
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OscarWestesson
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27 May 2009 - 23:23 - r1.189
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TWikiGuest
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// Name: Oscar Westesson // Email: oscar.westesson $\begin{picture}(10,10)\put(5,5){\circle{10}}\put(2,3){$\alpha$}\end{picture}$ gmail dottt com // Berkeley Office: 381D StanleyHall // UCSF: I can usually be found in the Andino wet lab or the Derisi computational room, both at UCSFMissionBay // About Oscar // I am a first-year bioengineering graduate student interested in computational sequence analysis. I studied mathematics at Univeristy of Rochester and ...
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AcronymList
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27 May 2009 - 23:06 - r1.4
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TWikiGuest
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// This is intended to serve as a reservoir of acronyms for general use. // Established but uncommon acronyms // BPC before politically correct. From a Montanan truck driver, after describing the progression of generations. // Note: gourmet magazine circa 1990 is definitely BPC. "Aruba: our only business is your vacation" // TCB taking care of business. Possibly originated by Cosmo Kramer // DUMBO down under the manhattan bridge overpass. brooklyn-ers, what ...
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HowToAdministerSunGridEngine
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27 May 2009 - 17:41 - r1.52
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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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LabMeeting
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26 May 2009 - 14:28 - r1.222
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IanHolmes
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// LabMeeting // Lab meetings are held on Wednesdays, from 1-2pm, in 482 StanleyHall . (With some exceptions.) // Calendar // (Also shows club) // Edit this list to add date, meeting and topic: // 28 Jan Soeren Biolog: Probabilistic Logic Programming for Bioinformatics // 4 Feb Ian recent enhancements to phylocomposer/handalign //
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RudyRucker
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26 May 2009 - 14:18 - NEW
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IanHolmes
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// Rudy Rucker: mathematician, CS lecturer, cyberpunk sci-fi author... // http://www.rudyrucker.com/ // http://www.cs.sjsu.edu/faculty/rucker/ //
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SherinderBhinder
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23 May 2009 - 05:34 - NEW
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TWikiGuest
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// Name: Sherinder Bhinder // Email: gstudent8@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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SurendraK
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21 May 2009 - 06:26 - NEW
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TWikiGuest
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// Name: Surendra Kumar // Email: skdhanraj@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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BarbaraKryvko
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15 May 2009 - 09:33 - NEW
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TWikiGuest
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// Name: Barbara Kryvko // Email: barbara.kryvko@wellsfargoadvisors.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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MarkHudson
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11 May 2009 - 10:53 - r1.4
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MarkHudson
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// Name: Mark Hudson // Email: mark.biowikiNOSPAM@mhudson.net // Comment: like wiki and GraphViz aka TWiki.DirectedGraphPlugin // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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TWikiGuest
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06 May 2009 - 12:55 - r1.10
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IanHolmes
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// TWikiGuest signifies an anonymous guest of this TWiki web, not unlike yourself. // You can leave your trace behind you, instead of remaining anonymous. // Just add your name in .TWikiRegistration and create your own page. //
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AmazonMachineImageIDs
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01 May 2009 - 13:54 - r1.32
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LarsBarquist
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// AMI changelog // Amazon machine images published by the Holmes lab. // Strikeouts indicate obsolete images which have been deleted or overwritten. // 32-bit images // ami-7c6c8b15 (based on 4/2/09 image; installed emacs, increased java heapsize for hmmoc, pulled latest dart/jbrowse rebuilt, added /etc/profile.d/dart.sh script to set env vars, cleaned up; 4/3/09) // ami-f3ac4a9a (handalign image; 4/15/09 image with s3curl.pl; 5/01/09) // ami-4340a72a (handalign ...
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GeneWiki
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29 Apr 2009 - 20:25 - r1.2
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IanHolmes
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// Gene wikis // "Gene wiki" is a somewhat ambiguous phrase that is typically understood to mean a wiki-fied version of a gene database. // This could be a wiki whose pages discussed genes in an individual genome (c.f. the Main.FlyBase gene pages) // or entries in a database (such as Pfam families, or Main.GeneOntology terms). // For example: // Zebrafish genome wiki // contributions to Wikipedia // The Gene Wiki Portal () // WikiProject RNA (RFAM et al) // ...
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GenomeWiki
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29 Apr 2009 - 20:24 - r1.91
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IanHolmes
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// Genome wiki // The idea of a genome wiki was articulated by // Here, it's meant in the sense of a web-based genome browser to which annotation tracks can be uploaded, persistently, so that they can be shared with other users. // This page presents a single point of view on what a "genome wiki" should be, acknowledging that the term is ambiguous and the concept somewhat flexible. // Ideal properties // A wiki would allow the community of experts to work out ...
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BioWiki
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29 Apr 2009 - 20:23 - r1.144
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IanHolmes
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// About Biowiki.org // biowiki.org is a server hosting various wikis, including // A lab notebook for the lab at the University of California, Berkeley; // A weblog for the Holmes lab; // A developers' wiki for JBrowse, the AJAX interface to the genome browser; // A teaching wiki for classes in the Department of Bioengineering at UC Berkeley. // Content of this site //
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StringTransducers
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22 Apr 2009 - 06:00 - r1.70
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TWikiGuest
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// transducers // Introduction // String transducers a.k.a. sequence transducers are finite-state machines (that is to say, automata) with an input tape $X$ and an output tape $Y$ (in the case of a two-tape transducer), or an input tape $X$ and multiple output tapes $Y 1 \ldots Y N$ (in the general, 1-input N-output case). // A two-tape transducer, with one input and one output, is similar to a Pair HMM; // the major difference is that the probabilistic weights ...
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DownloadingDart
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19 Apr 2009 - 23:05 - r1.41
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IanHolmes
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// Downloading DART // The latest version of dart is available from http://github.com/ihh/dart/tree/master. // If you don't have the git source code revision management tool installed, you can download a tarball or zipfile from github.com (click on the "Download" tab). // If you do have git installed, you can git clone the repository and stay up-to-date with the latest version, like this: // git clone git://github.com/ihh/dart.git // You can also browse the ...
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CharlesKey
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15 Apr 2009 - 08:36 - NEW
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TWikiGuest
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// Name: Charles Key // Email: chazkey@aol.com // Comment: Travel Jobs with MyTravelJob.com a Travel Job. // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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IndiegramExamples
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10 Apr 2009 - 17:00 - r1.16
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IanHolmes
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// Indiegram examples // Some examples of three-way reconstructions of ancestral RNA structures. // The tRNA and nanos examples are somewhat obvious, because some of the branch lengths are very short, so that the inferred ancestral structure is almost identical to one of the extant descendants. // However, this does at least illustrate the output of the programs. // Alignment ancestral structure reconstructed by IndieGram; sequences reconstructed by XRATE. ...
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IndieGram
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10 Apr 2009 - 13:13 - r1.27
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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 easily create their own models using the provided Perl code-generation // scripts. Given a model ...
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AllisonBerke
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10 Apr 2009 - 12:41 - r1.5
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IanHolmes
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// Name: Allison Berke // Email: berke@berkeley.edu // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
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HolmesLab
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10 Apr 2009 - 12:40 - r1.154
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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: PatrickHarrigan, VedranPogacnik //
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LarsNotes
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09 Apr 2009 - 16:25 - r1.9
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LarsBarquist
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// Limiting number of slots on cluster // The best solution I've come up with to limiting the number of slots assigned to long-running jobs on the cluster is denying access to nodes for the project involved. So, as of now, handalign is denied access on half the cluster nodes. Is there a better way to do this with share policies? It seems there's a better (or at least less confusing) option in SGE 6.1, 'Flexible Resource Quotas', but unfortunately we're running ...
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BoozeForBugs
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07 Apr 2009 - 15:41 - r1.11
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TWikiGuest
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// Booze for bugs // As an incentive to report bugs in DART, I offer a biannual "booze prize" for the nastiest, gnarliest, seamiest bugs that you're able to dig out from dart's dark underbelly. // This tradition was inspired by EwanBirney, who used to promise champagne for reporting segfaults with GeneWise. // (Of course, Ewan doles out champagne on the drop of a hat, as is well known) // There are very few segfaults in DART but plenty of opportunities to find ...
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EvolDeeds
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07 Apr 2009 - 10:28 - r1.24
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IanHolmes
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// Evol Deeds // The EvolDeeds package simulates the evolution of RNA structure both forwards and backwards in time, by probabilistic means. // It includes the following packages: // EvolSayer, a forward-time simulator // EvolDoer (formerly 'tkfstalign') , a pairwise aligner // IndieGram, a code-generating three-way aligner ancestral reconstructor // Related programs in the DART package include // StemLoc, a heuristic but extremely accurate RNA multiple alignment ...
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EvolSayer
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07 Apr 2009 - 10:28 - r1.10
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IanHolmes
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// EvolSayer // A simulator for RNA structure evolution using the Structure Tree model. // Part of the EvolDeeds package. // How to get it: DownloadingDart // Browse CVS: DartPerl:evolsayer.pl // Example tree files in DartSrcDir:evoldoer/t // Misc notes: // Output looks better piped through Main.ColorStock // EvolSayer also works as a plugin to Main.SimGenome // See also // TreeTransducers, EvolDoer, EvolDeeds, IndieGram //
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TKFStructureTree
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07 Apr 2009 - 10:28 - r1.7
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IanHolmes
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// The TKF Structure Tree // The TKF Structure Tree (TKFST) is a continuous-time Markov chain model for evolution of RNA structure, with loops, stems, insertions and deletions, that is based on mutually nested instances of the model. // That is, it is a recursively-nested birth-death process for the evolution of foldback secondary structure in nucleic acid sequences. // TKFST is described in the following open-access paper: // // Implementations // The TKFST ...
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TreeTransducers
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07 Apr 2009 - 10:28 - r1.25
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IanHolmes
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// transducers // Introduction // Tree transducers are extensions of transducers. // Rather than locally mutating strings, tree transducers locally mutate parse trees. // Formal rules for intersection and composition of tree transducers make them amenable to alignment and in particular RNA alignment. // Tree transducers can be used to perform structural alignment of multiple RNAs or even reconstruct possible ancestral RNA structures. // Our programs, EvolDoer ...
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MouseExperiment
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06 Apr 2009 - 20:12 - NEW
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TWikiGuest
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// To come: // Schedules for infection, feces collection, etc // Data organization // A paper on this topic, long before the days of UHTS: // Main.TWikiGuest 07 Apr 2009 //
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AmazonEC2
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03 Apr 2009 - 15:53 - r1.21
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IanHolmes
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// Amazon Elastic Compute Cloud (EC2) // Resources: // Getting Started Guide // Developer Guide // S3 Getting Started Guide // Centos Bundle Script link courtesy of MitchSkinner... modify this to install DART? hmmm... // OS X S3 browser unpolished but useful proof-of-concept-type app. // Holmes lab AMIs: // Machine Image IDs // The following construct can be used to seed the random number generator with a hostname-specific value (useful e.g. for running several ...
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MercatorPerl
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03 Apr 2009 - 13:13 - r1.37
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IanHolmes
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// MercatorPerl // Step-by-step instructions for extracting "training alignments" from // MERCATOR/MAVID output using Flybase annotations on the cluster at /mnt/nfs... // See MercatorTutorial for a tutorial on how to use Mercator and MAVID. // 8-) Install DART // See DownloadingDart and BuildingDart. // Note especially the section in BuildingDart concerning the dart perl modules: // you need to add something like the following to your .cshrc //
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Number of topics: 50
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