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Topics in Main web:
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Changed: now 02:52 GMT
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WebStatistics
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05 Jul 2008 - 17:16 - r1.482
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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 2008 16562 5 0 1573 837 WebHome 569 255 WebChanges 206 175 RecentChanges 175 161 RnaModels 144 144 XrateSoftware 130 ClusterNFSBenchmarks 3 Main.IanHolmes 2 Main.TWikiGuest // Jun 2008 106946 240 3 10340 5682 WebHome 1667 1102 FlyNcRna 1054 897 CompbioConferences 882 823 RecentPages 790 696 JournalFeeds 668 ...
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IanHolmes
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02 Jul 2008 - 12:41 - r1.462
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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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HolmesLab
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02 Jul 2008 - 12:38 - r1.128
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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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XreiProgram
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26 Jun 2008 - 16:55 - r1.29
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TWikiGuest
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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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RnaStructurePredictionResources
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26 Jun 2008 - 12:52 - r1.33
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TWikiGuest
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// 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 structural context into your ...
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BuildingDart
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26 Jun 2008 - 06:26 - r1.31
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TWikiGuest
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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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XrateSoftware
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25 Jun 2008 - 02:28 - r1.94
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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 // fast EM-based parameterisation of evolutionary grammars for annotation of multiple sequence alignments. //
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StemLoc
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25 Jun 2008 - 00:48 - r1.45
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IanHolmes
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// loc // stemloc is a program included in the Main.DART package for doing Main.MultipleRNAAlignment // with trainable Main.StochasticContextFreeGrammars (SCFGs). // The main innovation of stemloc was to use "alignment envelopes" and "fold envelopes" to simultaneously constrain both the alignment and the secondary structures of the sequences being compared. // This makes the Sankoff algorithm tractable. // See Stemloc-AMA for a description of our implementation ...
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TwelveFlyRocCurveEstimation
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24 Jun 2008 - 19:20 - r1.19
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TWikiGuest
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// ROC curves for RNA gene prediction in Drosophila // This page is a work in progress // A ROC curve is a plot of sensitivity versus specificity for a score-based classification tool. // The following page describes the common procedures for generating such ROC curves that were used for the following experiments: // 1 Comparison of RNA gene prediction grammars (TwelveFlyScreenPredictions); // For this experiment, multiple different xrate-format grammars were ...
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OscarWestesson
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23 Jun 2008 - 22:05 - r1.145
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TWikiGuest
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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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LarsBarquist
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23 Jun 2008 - 16:35 - r1.24
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TWikiGuest
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// Name: Lars Barquist // Email: lbarquist@gmail.com // Projects // xREI, an ajax web interface and visualization server for xrate. // CASA, consensus alignments using a stripped down version of AMAP. // Other Biowiki Pages // Cluster Maint Log: heylookitmeblagrilly. // Random Notes // Publications //
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TwelveFlyScreenPredictions
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20 Jun 2008 - 12:46 - r1.106
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IanHolmes
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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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SimulationTools
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20 Jun 2008 - 11:38 - r1.9
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IanHolmes
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// Simulation tools // This is the page linked in our genome simulation paper. // It is the primary point of access for the three tools described in that paper: // GSIMULATOR: transducer-based simulation of neutral DNA // SIMGRAM: simulation from generic phylo-grammars // SIMGENOME: simulations of structured genomic DNA // Related links: // simgenome.eg: the underlying grammar of simgenome. Edit to add your own features // format: the page documentating the ...
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ClusterMaintenanceLog
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20 Jun 2008 - 11:04 - r1.3
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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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TomPeat
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18 Jun 2008 - 14:20 - NEW
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IanHolmes
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// Tom Peat works at theBio21 Collaborative Crystallisation Centre, Melbourne, Australia: // http://www.csiro.au/c3/facility/c3 centre.htm //
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WebLowerLeftBar
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18 Jun 2008 - 14:18 - r1.19
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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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ClusterInstallPolicy
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18 Jun 2008 - 12:26 - r1.2
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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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PaperArchive
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17 Jun 2008 - 11:51 - r1.48
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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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KrishnaReddy
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11 Jun 2008 - 19:26 - NEW
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TWikiGuest
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// Name: Krishna Reddy // Email: krishna p reddy@medinews.com // Comment: Visted lab page // 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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11 Jun 2008 - 19:26 - r1.160
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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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CompbioConferences
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11 Jun 2008 - 04:18 - r1.80
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IanHolmes
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// Computational biology conferences for abstract or poster submission // NOTE: all dates are in the MM-DD or YYYY-MM-DD format (makes sorting easier, click on table header to sort). // ...in 2008 // Start date End date Registraton due date Title Location Other info Other due dates // 2008-03-30 2008-04-02 2008-02-20 (early registration) RECOMB 2008 National University of Singapore 2008-01-14: Poster Submission Deadline // 2008-05-06 2008-05-10 Biology of Genomes ...
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StringTransducers
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06 Jun 2008 - 15:29 - r1.68
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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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TransducerComposition
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03 Jun 2008 - 09:50 - r1.55
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OscarWestesson
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// Transducer Composition // StringTransducers can be "composed" to yield multi-sequence transducers and HMMs. // This page contains references and examples of transducer composition. // Descriptions of Transducer Composition // A colloquial introduction to transducer composition algorithms notation can be found on this wiki page: // Main.PhyloComposer user's guide to the phylocomposer program, which implements the algorithm for biological sequence inference ...
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MercatorProgram
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02 Jun 2008 - 12:15 - r1.24
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OscarWestesson
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// Mercator: a program to construct multiple whole-genome orthology maps using exon anchors. // Available as part of ColinDewey's source code distribution: // http://www.biostat.wisc.edu/~cdewey/software.html // See MercatorTutorial for a tutorial on how to use Mercator and MAVID. // See MercatorPerl for a tutorial on related Perl scripts. //
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MakefileLabMeeting
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02 Jun 2008 - 12:12 - r1.118
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OscarWestesson
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// Makefile lab meeting // 12 noon, Wednesday 4/4, 2007, 425 Hearst Mining Building (see LabMeetings) // The topic of this meeting was the use of automated build tools for bioinformatics pipelines. // (See, for example, this intro on nodalpoint.org, // or .) // Conclusions // The conclusions of the meeting are summarized on the MakeComparison page. // Miscellaneous notes //
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RobertBradley
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27 May 2008 - 15:22 - r1.111
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RobertBradley
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// Robert K. Bradley // I'm a !PhD student working in the Holmes lab at UC Berkeley. I primarily study non-coding RNAs but occasionally work on other projects. // Here's my contact info: // Email: rbradley@no.spam.berkeley.edu (remove the 'no.spam.') // Lab: 381 Stanley Hall, UC Berkeley, CA // Lab phone: (510) 666 2791 //
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MultipleRNAAlignment
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26 May 2008 - 08:43 - r1.22
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RobertBradley
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// Multiple alignment of RNA sequences and structures // Problem: identify shared motifs (potentially cis regulatory) in RNA sequences // ZipCodes, RiboSwitches, SplicingSignals, ViralPackagingSignals ... // viruses, eukaryotes, bacteria // HolmesLab approaches: Stemloc-AMA, StemLoc , EvolDoer // // // // PhyloGrammars (NB these are mainly used to annotate existing alignments, but can be used in likelihood functions for alignment sampling) // KnudsenHein algorithm ...
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ClusterSoftware
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22 May 2008 - 16:00 - r1.54
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OscarWestesson
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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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StemLocAMA
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22 May 2008 - 15:17 - r1.13
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TWikiGuest
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// Stemloc-AMA // Stemloc-AMA is a multiple alignment mode included as part of stemloc. Stemloc-AMA uses sequence annealing, a technique introduced by Schwartz and Pachter in the AMAP program for protein multiple alignment, to search the space of multiple alignments. Sequence annealing avoids many of the well-known shortcomings of naive progressive alignment, including its inability to correct mistakes and poor handling of indels. // Stemloc-AMA uses the pairwise ...
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BubblePlots
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21 May 2008 - 13:59 - r1.44
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RobertBradley
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// This sketch of a page is intended to help people understand and use the script visualizeRates.pl to make nice bubbleplots of Markov chain rate matrices. It was used to e.g. produce many of the figures in the Xrate paper, a description of our generic PhyloGrammar engine. // (A bubbleplot, as shown above, is a visualization of the rate matrix corresponding to a Wikipedia:substitution model. // The circle in the i'th row j'th column is scaled such that its area ...
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MakefileManifesto
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19 May 2008 - 13:17 - r1.70
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AndrewUzilov
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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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LarsNotes
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12 May 2008 - 17:03 - r1.7
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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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MitchSkinner
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08 May 2008 - 19:54 - r1.15
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MitchSkinner
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// Mitch Skinner // I'm a staff member in the HolmesLab at UC Berkeley. I work on our Genome Browser and some of our sequence analysis projects. // Email: mitch skinner at berkeley dot edu // Rants // FileFormatDesign // Random Notes // PerlOneLiners //
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FileFormatDesign
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08 May 2008 - 13:19 - r1.3
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MitchSkinner
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// The laws of bioinformatics file format design // I'm not bitter // 1. Make up a new format. Clearly, you are so brilliant that no-one has dealt with this kind of data before. The only time you should stick to an existing format is when it obeys the guidelines below. Alternatively, take an existing format and bend it to your needs. The more subtle the difference is, the better. Some people won't have to change their software at all! And other people will just ...
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LabNews
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05 May 2008 - 10:46 - r1.48
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LarsBarquist
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// news // Welcome two new lab members: Avinash Varadarajan (!PhD) and Mitch Skinner (GBrowse.WebHome)! // "Bioinformatics 2.0"? (nodalpoint.org) // First fall LabMeeting, Friday 9/8/2006 // Berkeley Lab Notes // // UC Berkeley fall classes start Monday 8/28/2006... // This week Benasque. Next month Fortaleza (7/13/2006) // Um, thanks Varig :-( //
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Number of topics: 50
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