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Topics in Main web:
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Changed: now 13:48 GMT
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Changed by:
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DanielOrtizBarrientos
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22 Nov 2008 - 15:55 - r1.5
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TWikiGuest
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// Name: Daniel Ortiz-Barrientos // Email: d.ortizbarrientos@uq.edu.au // Address: The University of Queensland, School of Biological Sciences, St. Lucia QLD 4072 Australia // Web: profiles.bacs.uq.edu.au/Daniel.Ortiz-Barrientos.html // BIOGRAPHY // Daniel arrived to Australia in October 2007 after finishing postdoctoral studies with Prof. Loren Rieseberg, and PhD studies with Prof. Mohamed Noor. His lab (OB lab) studies the genetics and ecology of speciation ...
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OscarWestesson
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21 Nov 2008 - 11:34 - r1.160
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TWikiGuest
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// Name: Oscar Westesson // Email: breadbaron at gmail // About Oscar: // I am a bioengineering graduate student working in the Holmes lab. My office is at 381C Stanley Hall. Besides computational biology I like climbing, bicycling, harassing my lab-mates, recovering bread (see email address), and drinking tea. // Projects/Work: // Last fall I began working on a phylo-HMM to detect recombination events in multiple alignments. This paper has been submitted but ...
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JournalClub
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21 Nov 2008 - 10:46 - r1.170
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MitchSkinner
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// JournalClub // Journal club is on Fridays from 11-12 in 521 StanleyHall, // starting October 17th (excluding November 7th). // Organizer: SorenMork. // Calendar // (Also shows meeting) // Edit this list to add date, name and paper: //
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WebLeftBar
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21 Nov 2008 - 10:04 - r1.250
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IanHolmes
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// Classes // BioE131/231 // BioE241 // // Research // Software // Papers // Movies // People // Lab Meeting // Journal Club // // Site tools // About // Changes //
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YuriBendana
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20 Nov 2008 - 11:30 - r1.115
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YuriBendana
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// Contact Info // Name: Yuri Bendana // Email: ybendana at gmail com // About Me // After starting out as a control systems and software engineer, I enrolled in the UC Berkeley/UCSF Joint Graduate Group in Bioengineering in 2004. I was a member of the Main.HolmesLab from February 2006 to June 2007. // My research interests are broadly in computational biology, more specifically in applying statistical machine learning methods to biological data, especially ...
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WebStatistics
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20 Nov 2008 - 06:46 - r1.586
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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: // // Nov 2008 58227 24 0 6269 4565 WebRss 916 606 WebStatistics 587 497 IanHolmes 426 395 RecentPages 392 378 HolmesLab 363 XrateSoftware 16 Main.IanHolmes 5 Main.TWikiGuest 1 Main.AllisonBerke 1 Main.OscarWestesson 1 Main.MitchSkinner // Oct 2008 99368 306 4 11025 7984 WebRss 1242 1007 WebStatistics 857 819 WebChanges ...
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IanHolmes
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18 Nov 2008 - 21:12 - r1.565
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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 // Office address: 374C StanleyHall, UC Berkeley, CA 94720-3220 // Office phone: (510) 666 2790 // Department: Bioengineering // Office hours: Wednesdays (11am-noon) Fridays (1-2pm) //
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WindowEater
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17 Nov 2008 - 21:47 - r1.12
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IanHolmes
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// windoweater.pl // A layer between windowlicker.pl and xrate in our pipeline; throws out windows below some threshold of conservation. // Located in: // /nfs/projects/pipeline/perl/windoweater.pl // BiowikiCvs:pipeline/perl/windoweater.pl // windoweater.pl is part of the pipeline CVS project; // see http://biowiki.org/HowToRunPipeline#Check out the project // the Point //
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AllisonBerke
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16 Nov 2008 - 20:34 - r1.4
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AllisonBerke
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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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FileFormatDesign
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13 Nov 2008 - 16:14 - r1.4
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IanHolmes
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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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TwelveFlyScreenPredictions
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13 Nov 2008 - 16:09 - r1.121
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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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LabMeeting
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13 Nov 2008 - 14:18 - r1.194
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TWikiGuest
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// LabMeeting // Lab meetings are held on Thursdays, from 1-3pm, in 421 StanleyHall starting on October 9th. // Organizer: LarsBarquist. // Calendar // (Also shows club) // Edit this list to add date, meeting and topic: //
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XreiProgram
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12 Nov 2008 - 08:25 - r1.31
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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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XrateSoftware
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12 Nov 2008 - 08:20 - r1.104
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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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XrateFormat
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12 Nov 2008 - 08:11 - r1.133
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IanHolmes
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// Introduction // xrate file format // 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. //
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RebeccaPoon
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10 Nov 2008 - 16:20 - NEW
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TWikiGuest
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// Name: Rebecca poon // Email: rebecca.poon@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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10 Nov 2008 - 16:20 - r1.166
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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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ReconstructionTargets
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31 Oct 2008 - 12:26 - r1.25
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OscarWestesson
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// Broad classification of targets for ancestral sequence reconstruction // See also papers on JournalClub page. // Ancient genes // Transcriptional machinery // e.g. RNA polymerase // // Translational machinery // e.g. the ribosome // // Widely-conserved genes //
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WebLowerLeftBar
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31 Oct 2008 - 08:44 - r1.25
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IanHolmes
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// misc bio links // bio projects // wikis, blogs // Meetings, journals // ISI web of knowledge // // off-site links // Rfam / Pfam // GMOD/GBrowse // UCSC, Ensembl // Bioperl wiki // AAA fly wiki // ISCB; RNA society // //
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PROLOG
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27 Oct 2008 - 14:25 - r1.2
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IanHolmes
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// Prolog // Prolog: a logic programming language. // Wikipedia:Prolog // Related pages: // Blog.SocialProlog in the Blog web // Main.PrologAdventures in the Main web // Main.PrologLanguage in the Main web // Main.PRISM in the Main web // Main.IanHolmes 27 Oct 2008 //
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PRISM
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27 Oct 2008 - 14:24 - NEW
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IanHolmes
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// PRISM // PRISM: Programming In Statistical Modeling. // An extension of PROLOG to probabilistic models, PRISM implements sum-product algorithm on PROLOG parse trees. // http://sato-www.cs.titech.ac.jp/prism/ //
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MichaelHoffman
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24 Oct 2008 - 09:00 - NEW
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TWikiGuest
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// Name: Michael Hoffman // Email: mdhoffman@berkeley.edu // Comment: Mathematics Undergraduate // 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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23 Oct 2008 - 09:58 - r1.151
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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: Main.MichaelHoffman, Main.PatrickHarrigan //
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AnatCaspi
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23 Oct 2008 - 09:23 - r1.4
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IanHolmes
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// AnatCaspi // Teaching.AnatCaspiRepetitiveElementSegmentationUsingConditionalRandomFieldsGraduateProject // Teaching.AnatCaspiHomologyAssignmentUsingConditionalRandomFieldsGraduateProject //
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GeneFamilyEvolutionLabMeeting
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23 Oct 2008 - 09:23 - r1.11
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IanHolmes
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// Evolution of paralogous families // 4/18/07, noon, 425 HMMB. See LabMeeting // This is a follow-up to the GeneSpeciesTreeReconciliationLabMeeting. // Roderic Page // // (article in PDF on BMC) // GP Karev, EV Koonin Birth/Death models and Power Laws to model gene family evolution // Simple, linear Birth-Death-Innovation Models (BDIM): // // Unrealistic time to formation of largest families via simple BDIMs; advocacy of nonlinear BDIMs: // //
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GenomeAssemblyLabMeeting
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23 Oct 2008 - 09:23 - r1.27
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IanHolmes
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// Wednesday 6/13/2007, noon, 425 HMMB // (see LabMeeting) // Salzberg et al review (Mitch): // Genome Sequence Assembly Algorithms and Issues. http://lcbb1.epfl.ch/compbio07/sequencing.pdf // Batzoglou/Arachne (Rob): // // Myers (Avinash): // // //
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HIVFitnessLandscapeLabMeeting
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23 Oct 2008 - 09:23 - r1.34
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IanHolmes
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// General topic: probabilistic models of the fitness (particularly as regards drug resistance) mutation/recombination landscapes for the HIV virus genome. // For date/time see LabMeeting. // MitchSkinner: pairwise amino acid correlations via $K a/K s$ ratios // // http://www.bioinformatics.ucla.edu/HIV // AndrewUzilov: "mutagenic tree" graphical models for correlated amino acid mutations; mixtures of same // // AvinashVaradarajan: mutagenic-tree models that ...
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MetagenomicsClusteringLabMeeting
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23 Oct 2008 - 09:23 - r1.23
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IanHolmes
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// Wednesday 5/23/2007, noon, 425 Hearst Mining Building. // See LabMeeting. // Review of phylogenetic taxonomic approaches to metagenomics datasets. // Pachter et al review (Avinash) // Focus on the section titled "Phylogeny and Community Diversity" // // Sorcerer (Andrew) // Focus on the section titled "Taxonomic Diversity" // // Edwards et al : Prediction of physiology, metabolism, and ecology from metagenomes (Rob) //
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OntologyModelingLabMeeting
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23 Oct 2008 - 09:23 - r1.18
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IanHolmes
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// Probabilistic Models on Bioinformatics Ontologies // Date/time/place: 5/2/2007, noon, 425 HMMB. See LabMeeting. // Bayesian networks (graphical models) and related methods for modeling and predicting relationships in structured ontologies, // particularly the GeneOntology. // One goal of this study could be the development of models for predicting GO terms associated with metagenomics samples. // Main assignments (15 minutes each) // Models for ontology associations ...
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OrthologyResolutionLabMeeting
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23 Oct 2008 - 09:23 - r1.20
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IanHolmes
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// Reconstruction of orthology/paralogy relationships // It looks like material for at least two lab meetings is developing here... e.g. one on basic algorithms (reconciliation of gene/species trees, MCMC approaches...) and another on how these algorithms are being used to develop ortholog databases. Although, perhaps we can consider if this is not the optimal split, since Jason would like to compare !OrthoMCL to !InParanoid. Evolution of gene families may be ...
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PathwayEvolutionLabMeeting
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23 Oct 2008 - 09:23 - r1.7
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IanHolmes
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// Modeling pathway evolution, and selected informatics applications. // For example: // detecting pathways by looking at grouping patterns of gene gain loss; // phylogeny based on pathways. // Barker Pagel // // Marcotte et al // // Wu et al // //
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ProjectMeetings
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23 Oct 2008 - 09:23 - r1.13
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IanHolmes
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// Project meetings // ATTENTION: During the fall semester, project meetings are rolled into the main LabMeeting. // All meetings in 425 Hearst Mining Memorial Building unless otherwise stated. // Meeting (click to edit) Co-ordinator Usual day Usual time Other info, e.g. date of next meeting // Lab Ian Wednesday Noon See separate LabMeeting page //
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AndrewUzilovLinks
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23 Oct 2008 - 09:23 - r1.12
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IanHolmes
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// // Useful Links // This is mostly an attempt to keep track of !BioWiki stuff to which I contributed. // Also see: silly notes to self. // TODOs // Fix AndrewUzilovTopicMap (see Directed Graph Web Map Plugin for info) // Put a "comments" section in every page below, in case someone stumbles on it and wants to add a note, but is afraid to use the wiki edit function. //
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MakefileLabMeeting
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23 Oct 2008 - 09:23 - r1.144
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IanHolmes
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// Makefile lab meeting // 12 noon, Wednesday 4/4, 2007, 425 Hearst Mining Building (see LabMeeting) // 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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OldLabMeetingInfo
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23 Oct 2008 - 09:23 - r1.2
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IanHolmes
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// Past lab meetings // Spring 2007 lab meetings are held on alternate Wednesdays, from 12-1:30pm, in 381 StanleyHall. // Each lab meeting will focus on a particular topic in bioinformatics algorithms or software. // One goal of this format is to work out ideas for new projects. // Prior to the meeting, one or two related papers will be assigned to each group member. // Each person will present a quick summary of their assigned paper(s) and will then lead a ...
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ClusterInstallPolicy
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22 Oct 2008 - 14:49 - r1.4
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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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PanditDatabase
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18 Oct 2008 - 10:57 - r1.4
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IanHolmes
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// PANDIT is a database of DNA-level alignments of protein-coding sequences, derived from Pfam, // maintained by NickGoldman's group. // See http://www.ebi.ac.uk/goldman-srv/pandit/ // The flatfile format is described here. // // Main.IanHolmes 10 Jan 2006 //
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StanleyHall
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18 Oct 2008 - 10:44 - r1.22
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IanHolmes
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// Stanley Hall // Stanley Hall on the UC Berkeley campus is the home to both the Department of Bioengineering and to the QB3 California Institute for Quantitative Biosciences. // It's also the location of the HolmesLab. // Bioengineering Dept's Stanley Hall page // Facilities Services Stanley Hall page // Location on campus map (right-hand edge of map square B5, bordering on Gayley Road University Drive) // Parking: you're driving into Berkeley? Seriously ...
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Number of topics: 50
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