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Topics in Main web:
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Changed: now 01:24 GMT
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Changed by:
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ClusterSoftware
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19 Aug 2008 - 14:48 - r1.55
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LarsBarquist
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// Software on the BabylonCluster // List of packages installed on the HolmesLab cluster NFS. // In /nfs/src // AMAP // Protein multiple alignment by sequence annealing. See the AMAP page. //
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OscarWestesson
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19 Aug 2008 - 12:49 - r1.146
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OscarWestesson
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// Name: Oscar Westesson // Email: breadbaron at gmail // About Oscar: // I am a maths undergraduate working in the Holmes lab. I came from Malmö, Sweden and grew on the East Coast, in scenic upstate New York. (This has confused many californians; new york is a city as well as a state). As an undergrad I studied at University of Rochester for 1.5 years before coming to Berkeley. Besides computational biology I like climbing, bicycling, harassing my lab-mates ...
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EvolutionarySoftwareFoundation
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19 Aug 2008 - 09:41 - NEW
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IanHolmes
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// Evolutionary Software Foundation // The Evolutionary Software Foundation (ESF) is a nonprofit organization 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 projects ...
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StockholmTools
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18 Aug 2008 - 11:36 - r1.30
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IanHolmes
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// StockholmFormat-related tools in DART // N.B. these lists include general-purpose StockholmFormat utilities and not the heavyweight probabilistic modeling tools in DART, many of which use Stockholm as their native alignment format (see in particular PhyloGram.pm and xgram). // Standalone Perl scripts: // colorstock.pl color alignment columns by stem in a Stockholm alignment of RNA secondary structures, using ANSI terminal color // fasta2stockholm.pl convert ...
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WebHome
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18 Aug 2008 - 10:11 - r1.273
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IanHolmes
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// BioWiki // Welcome to biowiki.org. // This site hosts wikis for various computational biology projects. // Right now you're in the Main web, used mostly as an online lab notebook by the lab at UC Berkeley. // Anyone can edit almost any page, so please feel free to contribute content. // You may have come here for //
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WebStatistics
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17 Aug 2008 - 19:36 - r1.526
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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 148488 94 8 11921 8542 PaperArchive 8481 8372 PhyloFilm 7645 3843 WebRss 2352 1894 BioWiki 1799 1413 WebStatistics 741 RecentChanges 74 Main.IanHolmes 10 Main.RobertBradley 10 Main.TWikiGuest 8 Main.LarsBarquist // Jul 2008 143855 78 0 10138 9399 WebRss 4375 4359 WebChanges 4245 4221 FreeSoftware 4214 4153 ...
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DART
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16 Aug 2008 - 08:16 - r1.238
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IanHolmes
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// The Dart Library: XRate, Handel, Stemloc 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. // The programs use statistical algorithms (MCMC, EM) //
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WebPreferences
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15 Aug 2008 - 12:36 - r1.47
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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: // Top buttons // Set TOPBUTTONS // Koala skin: // Set SKIN koala // Set NAVBARH // Set NAVBARF // Set NOWEBSBAR //
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ClusterInstallPolicy
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15 Aug 2008 - 11:16 - r1.3
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LarsBarquist
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// Cluster Install Policies // This is an effort to demystify and standardize our software installation process on the cluster for current and future lab members, so as to (hopefully) make it clear where packages should be installed and stop duplicating efforts. Note that in a few cases software is currently in non-standard locations (for instance Sun Java in /nfs/src) this should be corrected eventually. // This is very much a work in progress please feel ...
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XrateSoftware
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15 Aug 2008 - 06:53 - r1.103
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IanHolmes
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// XRATE: // A page about xrate and the derived programs xgram , xprot xfold . // Introduction // xrate is an interpreter for phylo-grammars. // Together with the derived programs xfold , xprot and xgram , // it allows the following //
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RnaModels
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14 Aug 2008 - 15:11 - r1.51
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IanHolmes
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// PFold vs. RFAM-trained parameters // Below are bubbleplots of the covariant RNA basepair model from PFOLD, and similar models that were re-estimated using XRATE from various structure-annotated RNA alignment datasets: // Original Pfold parameters RFAM-trained parameters rRNA-trained parameters // // The rRNA-trained parameters (right) were estimated from the CONSAN mix80 dataset, derived by Dowell Eddy from the European rRNA database. // References: // / ...
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RnaModelDiscussion
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14 Aug 2008 - 14:41 - NEW
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IanHolmes
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// RNA models // See RnaModels. // Suggestions of improvement // From former ticket #71 ("Estimate basepair substitution rates from high-quality ncRNA alignments") by Ian, which is along the same lines: // retrain the PFOLD rates on a subset of RFAM and possibly other ncRNA alignments... // not ALL the published structures (as we did before), but the ones that have high-quality basepairs... // e.g. rRNA, tRNA (NB not all rRNA is in RFAM) //
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RobertBradleyNotes
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14 Aug 2008 - 11:07 - r1.5
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RobertBradley
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// Network traffic // 1 To capture network traffic, wave your hands and type '/usr/sbin/tcpdump c 3000 i eth1 dst port 2049 cut d' ' f3 sort uniq c'. // LaTex // 1 If using the macports tetex installation, put style files in /opt/local/share/texmf-dist/tex/latex/. Run 'mktexlsr' to re-build the directory listing after putting it there. // Leopard // 1 Leopard's X11 installation is reportedly problematic (I've had problems!). See http://lists.apple.com/archives ...
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SimGenome
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13 Aug 2008 - 18:54 - r1.10
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IanHolmes
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// SimGenome // SimGenome is a simulator for syntenic genomic blocks, built using SIMGRAM and // GSIMULATOR. // Installation // Installation instructions: // 1 Install DART (see DART). // 1 Install GSIMULATOR. // Once installed, run the script dart/perl/simgenome.pl // You can also browse the underlying grammar: dart/grammar/simgenome.eg //
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GSIMULATOR
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13 Aug 2008 - 18:53 - r1.14
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IanHolmes
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// GSimulator // GSIMULATOR is a program that uses context-dependent transducers to simulate genome evolution. // Installation // With CVS installed, check out the source code from the CVS repository // by typing the following from a terminal prompt: // cvs d:ext:anonymous@cvs.biowiki.org:/usr/local/cvs co gsimulator // The source code may also be browsed here: // BiowikiCvsDir:gsimulator //
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SimGram
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13 Aug 2008 - 18:52 - r1.11
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IanHolmes
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// SimGram // SimGram is a simulator for the XRATE program. It generates randomized sample alignments from a grammar. // Installation // SimGram is included with the DART package. See DART for installation instructions. // Example usage // Example usage with the three-state protein secondary structure phylo-HMM of : // Input tree file: simgram-tree.newick (NewickFormat) // Input grammar file: prot3.eg (XrateFormat) // Output alignment file: simgram-output.stock ...
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HowToUseSunGridEngine
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12 Aug 2008 - 10:18 - r1.56
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LarsBarquist
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// How to Use Sun Grid Engine // This is the page for how to use Sun Grid Engine to run jobs on the BabylonCluster. // Other resources // SunGridEngineExamples (actual examples of how to make SGE do the stuff described below you should READ THIS BEFORE LAUNCHING SGE JOBS , because examples are very often more useful than reading the manual) // some How To pages from the SGE project site, with useful stuff, particularly: // Basic Usage of Grid Engine // Common ...
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StringTransducers
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07 Aug 2008 - 22:31 - r1.69
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IanHolmes
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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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IndiegramSoftware
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07 Aug 2008 - 17:38 - r1.17
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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 TKF 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 ...
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TKFStructureTree
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07 Aug 2008 - 17:24 - NEW
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IanHolmes
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// The TKF Structure Tree // The TKF Structure Tree is a model for evolution of RNA structure that is implemented by the following programs: // Main.EvolDoer // Main.IndieGram // Main.IanHolmes 08 Aug 2008 //
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TreeTransducers
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07 Aug 2008 - 15:58 - r1.12
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RobertBradley
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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 software Indiegram ...
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DownloadingDart
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06 Aug 2008 - 10:22 - r1.29
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IanHolmes
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// Downloading DART // The latest version of dart is available by anonymous CVS (or by authenticated CVS over ssh, if you are a dart developer). // If you have never heard of CVS, or are unsure whether you have it installed, try one of the following links: // Wikipedia:Concurrent Versions System // http://www.nongnu.org/cvs/ (CVS home page; description of what CVS actually does is more technical/terse than wikipedia's) // With CVS installed, check out the source ...
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TwelveFlyScreenPredictions
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05 Aug 2008 - 10:36 - r1.117
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LarsBarquist
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// Structured RNA predictions for Drosophila melanogaster // Brief description of methodology // The following page contains links to our predictions of conserved structured RNA features in Drosophila . // The predictions were made by sliding a window across multiple sequence alignments of the twelve Drosophila genomes discussed e.g. by (2007). // Our methodology was as follows. // We used multiple alignments built with the PECAN program. // We then used the ...
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TwelveFlyIntergenicCliques15
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05 Aug 2008 - 10:34 - NEW
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LarsBarquist
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// graph 55 { // 0 1 fontsize 10, URL "http://biowiki.org/results/ncRNA predictions/12fly/clustering 15 clique//0.html", label 18.472 ; // 0 2 fontsize 10, URL "http://biowiki.org/results/ncRNA predictions/12fly/clustering 15 clique//1.html", label 19.939 ; // 0 3 fontsize 10, URL "http://biowiki.org/results/ncRNA predictions/12fly/clustering 15 clique//2.html", label 17.461 ; // 1 2 fontsize 10, URL "http://biowiki.org/results/ncRNA predictions/12fly/clustering ...
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TwelveFlyIntergenicComponents20
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05 Aug 2008 - 10:20 - NEW
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LarsBarquist
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// graph 17 { // 0 1 fontsize 10, URL "http://biowiki.org/results/ncRNA predictions/12fly/clustering 20 comp/0.html", label 20.264 ; // 1 2 fontsize 10, URL "http://biowiki.org/results/ncRNA predictions/12fly/clustering 20 comp/1.html", label 25.354 ; // 1 shape box, fontsize 10, label "3L:15635683..15635766\n1307 135779 135862 ", URL "http://flybase.org/cgi-bin/gbrowse/dmel/?name 3L:15635183..15636266 h region 3L:15635683..15635766" ; // 2 shape box, fontsize ...
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TwelveFlyIntergenicCliques20
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05 Aug 2008 - 10:12 - r1.4
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LarsBarquist
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// graph 11 { // 0 1 fontsize 10, URL "http://biowiki.org/results/ncRNA predictions/12fly/clustering 20 clique/0.html", label 20.649 ; // 1 shape box, fontsize 10, label "3R:23366077..23366126\n751 81748 81799 ", URL "http://flybase.org/cgi-bin/gbrowse/dmel/?name 3R:23365577..23366626 h region 3R:23366077..23366126" ; // 0 shape box, fontsize 10, label "2L:15966331..15966396\n2038 452626 452692 ", URL "http://flybase.org/cgi-bin/gbrowse/dmel/?name 2L:15965831 ...
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TwelveFlyIntergenicCliques25
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05 Aug 2008 - 10:08 - r1.4
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LarsBarquist
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// graph 1 { // 0 1 fontsize 10, URL "http://biowiki.org/results/ncRNA predictions/12fly/clustering 25 cliques/0.html", label 28.189 ; // 0 shape box, fontsize 10, label "3R:9302710..9302823\n327 191833 191946 ", URL "http://flybase.org/cgi-bin/gbrowse/dmel/?name 3R:9302210..9303323 h region 3R:9302710..9302823" ; // 1 shape box, fontsize 10, label "2R:10950092..10950165\n3607 159156 159230 ", URL "http://flybase.org/cgi-bin/gbrowse/dmel/?name 2R:10949592. ...
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IanHolmes
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03 Aug 2008 - 07:29 - r1.466
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IanHolmes
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// IanHolmes // 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 // Fax2email: (866) 486 7316 // Office address: 374C StanleyHall, UC Berkeley, CA 94720-3220 // Office phone: (510) 666 2790 // Department: Bioengineering //
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WebLowerLeftBar
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03 Aug 2008 - 07:25 - r1.24
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IanHolmes
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// misc bio links // bio projects // wikis, blogs // Meetings, journals // // off-site links // Rfam / Pfam // GMOD/GBrowse // UCSC, Ensembl // Bioperl wiki // AAA fly wiki // ISCB; RNA society // //
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StemlocTutorial
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02 Aug 2008 - 12:48 - r1.110
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IanHolmes
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// X : This tutorial was originally written in 2004. The stemloc grammar has changed // slightly since then. The tutorial has been updated through Section 3, but log-likelihood scores, // alignments, etc. from tutorial examples in the other sections // may be slightly different from what you obtain now. Please contact IanHolmes or // RobertBradley if you notice any discrepancies between the tutorial and the behavior you experience. // Contents // 1. Introduction ...
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HolmesLab
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01 Aug 2008 - 12:21 - r1.129
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IanHolmes
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// HolmesLab // Address: 381 StanleyHall, University of California, Berkeley, CA 94720-3220. // Phone: (510) 666 2791. // Group members // HolmesLab Members // Graduate students: Main.RobertBradley // Specialists: Main.LarsBarquist, Main.OscarWestesson // Programmers: Main.MitchSkinner // PI: Main.IanHolmes //
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AllisonBerke
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31 Jul 2008 - 13:05 - NEW
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TWikiGuest
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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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TWikiUsers
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31 Jul 2008 - 13:05 - r1.161
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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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BlogRoll
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31 Jul 2008 - 08:23 - r1.52
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IanHolmes
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// Here is an OPML file of blog subscriptions. // And here is a list: // bioinformatics blogs // Life Scientists room // Neil Saunders // Roland Krause // Pedro Beltrao // Jason Stajich // Euan Adie // Lars Jensen //
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RnaStructurePredictionResources
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29 Jul 2008 - 16:45 - r1.34
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IanHolmes
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// RNA structure prediction resources // How in the world can this be organized? // Hmm, what questions can be asked about a structure prediction method? // Maybe I can use them to make a decision tree/flowchart, or maybe each question could be a table column. // What structure are you predicting? // Secondary or 3-D // Pseudoknots? // Base pair triples other tertiary interactions? (no method currently does this stuff, but maybe someday...) // How are you incorporating ...
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XreiProgram
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29 Jul 2008 - 16:45 - r1.30
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IanHolmes
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// xREI // xREI ( pron. "X-ray") is an AJAX web interface and visualization server for xrate and its grammar files. // Along with xrate's annotation and training functionality, it provides web access to grammar state diagrams and substitution matrix bubbleplots. // A decent run down of it's features can be found in the usage notes. // Demonstration version // http://harmony.biowiki.org/xrei/ //
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MakefileManifesto
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29 Jul 2008 - 16:45 - r1.72
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IanHolmes
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// // The cons of using make for job control // Like others, our lab uses Makefiles for bioinformatics pipeline development. // After all, a pipeline is basically an organized way of converting data from one form to another, right? // Is this not what Makefiles were designed to do except for the specific purpose of converting source code to object code? // Can we not hack the make system to do our bidding? // Why focus on the cons? // Because they are technical ...
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ClusterMaintenanceLog
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29 Jul 2008 - 15:35 - r1.7
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LarsBarquist
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// I'm planning for this to serve as a centralized location to log problems with the cluster and their solutions, as well as any general maintenance issues. Feel free to post entries for cluster-related issues. The idea is that eventually if we're having a problem with a node, we can search through this page and get a rough history, see if anything like this has occurred in the past, etc. // // 6/19/2008 // Mitch and I went down to the colo. 5 nodes were down ...
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Number of topics: 50
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