|
| The following is a list of recent changes. See also Recent Pages for new pages
|
Topics in Main web:
|
Changed: now 13:10 GMT
|
Changed by:
|
|
WebStatistics
|
08 Feb 2010 - 22:29 - r1.859
|
TWikiGuest
|
|
// Statistics for Web // Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: // // Feb 2010 34982 6 0 3415 1302 WebRss 1147 828 BioWiki 637 636 WebStatistics 610 481 ClusterNFSBenchmarks 269 239 RecentPages 230 IanHolmes 4 Main.TWikiGuest 2 Main.IanHolmes // Jan 2010 166554 20 0 19073 7304 BioWiki 5391 4726 WebSearch 2186 1965 WebStatistics 1518 925 HolmesLab 884 870 IanHolmes 858 XrateSoftware ...
|
|
|
PicornaIRES
|
08 Feb 2010 - 18:40 - r1.7
|
TWikiGuest
|
|
// Some papers discussing the function/structure/evolution of IRES elements, particularly in picornaviruses // Structure/function // // // // // // // // //
|
|
|
FastaFormat
|
05 Feb 2010 - 14:56 - r1.6
|
IanHolmes
|
|
// FASTA // FASTA is a bare-bones flat-file format for DNA, RNA and protein sequence data. // It's the most widely used understood format for unannotated sequence, probably due in large part to its simplicity. // It can also be used to represent multiple alignments (see FASTA format). // For details see e.g. // Wikipedia:Fasta format // http://www.ebi.ac.uk/help/formats frame.html //
|
|
|
DownloadingDart
|
25 Jan 2010 - 18:35 - r1.45
|
IanHolmes
|
|
// Downloading DART // The latest version of dart can be downloaded as a tarball or zipfile from http://github.com/ihh/dart/archives/master // You can also browse the source code at http://github.com/ihh/dart/tree/master // If you have the git source code revision management tool installed, you can git clone the repository and stay up-to-date with the latest version, like this: // git clone git://github.com/ihh/dart.git // This is the preferred way to get dart ...
|
|
|
NewMat
|
25 Jan 2010 - 16:20 - r1.2
|
IanHolmes
|
|
// Newmat // Newmat is a linear algebra library by RobertDavies. It is used by the DART library. // Here is the page for Newmat: // http://www.robertnz.net/nm intro.htm //
|
|
|
AdemBrown
|
25 Jan 2010 - 04:22 - NEW
|
TWikiGuest
|
|
// Name: Adem Brown // Email: us.drugstore@yahoo.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
TWikiUsers
|
25 Jan 2010 - 04:22 - r1.201
|
TWikiGuest
|
|
// List of users // Please take the time and add yourself to the list. To do that fill out the form in .TWikiRegistration. This will create an account for you which allows you to edit topics. // #ListStart // A B C D E F G H I J K L M N O P Q R S T U V W X Y Z // A // AdemBrown 25 Jan 2010 // AhmedHimel 07 Dec 2005 // AidanRoberts 24 Jan 2010 // AlannaConnell 15 Sep 2009 // AlbertVilella 04 Apr 2006 // AleoMok 01 Sep 2009 //
|
|
|
AidanRoberts
|
24 Jan 2010 - 11:59 - NEW
|
TWikiGuest
|
|
// Name: Aidan Roberts // Email: us.drugstore@yahoo.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
HolmesLab
|
20 Jan 2010 - 16:53 - r1.155
|
TWikiGuest
|
|
// 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 //
|
|
|
MoliLop
|
19 Jan 2010 - 08:12 - NEW
|
TWikiGuest
|
|
// Name: moli lop // Email: moli@trash2009.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
WendyDawson
|
04 Jan 2010 - 12:29 - NEW
|
TWikiGuest
|
|
// Name: Wendy Dawson // Email: wendydawson91@gmail.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
JayBowden
|
01 Jan 2010 - 12:12 - r1.3
|
JayBowden
|
|
// Name: Jay Bowden // Email: reviews@topacaiberry.org // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me // top3acaiberry.org // paraslimforweightloss.blogspot.com // flushexcessweight.blogspot.com // acai-berry-actives.blogspot.com // flushexcessweight.com //
|
|
|
LoraZepam
|
26 Dec 2009 - 00:43 - r1.2
|
TWikiGuest
|
|
// Reducing the dose gradually under medical supervision can help prevent or decrease these withdrawal symptoms. People who have a history of addiction or substance use problems should discuss the risks and benefits of taking this medication. // There may be an interaction between lorazepam and any of the following: // alcohol // anticonvulsants (e.g., carbamazepine, phenytoin, valproic acid) // antidepressants (e.g., fluoxetine, paroxetine, venlafaxine) // ...
|
|
|
KandrapeduDorairaju
|
25 Dec 2009 - 22:36 - NEW
|
TWikiGuest
|
|
// Name: kandrapedu dorairaju // Email: dorairajusvu@gmail.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
JeremySalomon
|
21 Dec 2009 - 15:55 - NEW
|
TWikiGuest
|
|
// Name: Jeremy Salomon // Email: bunny.hops.south@hotmail.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
MartinChardy
|
21 Dec 2009 - 15:51 - NEW
|
TWikiGuest
|
|
// Name: Martin Chardy // Email: siestainbed25@hotmail.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
BuildingDart
|
16 Dec 2009 - 18:28 - r1.32
|
IanHolmes
|
|
// 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 ...
|
|
|
RfamRiboswitches
|
10 Dec 2009 - 07:51 - r1.3
|
IanHolmes
|
|
// For a list of riboswitches in RFAM, use the "search by type" feature: // http://rfam.sanger.ac.uk/search/type#tabview tab4 // You could also try this keyword search (a bit less robust...) // http://www.sanger.ac.uk/cgi-bin/Rfam/queryrfam.pl?terms riboswitch //
|
|
|
IanHolmes
|
09 Dec 2009 - 19:12 - r1.604
|
IanHolmes
|
|
// 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 //
|
|
|
KatieSimer
|
06 Dec 2009 - 23:09 - NEW
|
TWikiGuest
|
|
// Name: Katie Simer // Email: sheenflock@gmail.com // Comment: kostenlose Kontaktborse // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
KukuTena
|
06 Dec 2009 - 03:24 - NEW
|
TWikiGuest
|
|
// Name: kuku tena // Email: kuku.tena@yahoo.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
SisayT
|
06 Dec 2009 - 03:20 - NEW
|
TWikiGuest
|
|
// Name: SisayT // Email: sisefe@yahoo.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
XrateFormat
|
24 Nov 2009 - 14:25 - r1.181
|
IanHolmes
|
|
// xrate file format // Introduction // The Participle, with an Article before it, and the Preposition of after it, becomes a Substantive, expressing the action itself which the Verb signifies: as, "These are the Rules of Grammar, by the observing of which you may avoid mistakes." // Bishop Robert Lowth, A Short Introduction to English Grammar, 1775. // This document describes the grammar file format for the xrate phylo-grammar alignment analysis package. ...
|
|
|
BioinformaticsWorkflows
|
24 Nov 2009 - 14:16 - r1.43
|
IanHolmes
|
|
// Bioinformatics workflows // Bioinformatics workflows can be approached in several ways. // Unix hackers often resort to make, // while computer scientists dream of more elegant approaches. // Meanwhile, projects like Taverna offer the beginnings of GUI-designed grid workflows. // Taverna // TomOinn leads development on // Taverna // (recently covered by Hublog, // Propeller Twist // and // Flags and Lollipops). //
|
|
|
HowToAdministerSunGridEngine
|
24 Nov 2009 - 08:50 - r1.53
|
TWikiGuest
|
|
// // 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 //
|
|
|
PhyloGrammars
|
15 Nov 2009 - 16:23 - r1.14
|
IanHolmes
|
|
// PhyloGrammars // A "phylo-grammar" is a stochastic grammar whose emissions (i.e. terminals) // are alignment columns, typically generated by evolving a continuous-time Markov process // on a phylogenetic tree. // As a class of models, phylo-grammars include all simple point substitution models // (including e.g. codon substitution, conditional approximations to context-dependent substitution, etc). // They also include HMM- and SCFG-like models for co-ordinated ...
|
|
|
TafDearce
|
13 Nov 2009 - 21:19 - NEW
|
TWikiGuest
|
|
// Name: TafDearce // Login Name: TafDearce // Email: rob@wep6.com // Phone: 123456 // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
XrateSoftware
|
10 Nov 2009 - 17:59 - r1.116
|
TWikiGuest
|
|
// XRATE // A page about the phylo-grammar alignment-analysis package, xrate. // Table of contents // Introduction // xrate is an interpreter for phylo-grammars. // It allows the following // fast EM-based parameterisation of evolutionary grammars for annotation of multiple sequence alignments. // maximum-likelihood analysis of multiple alignments and phylogenies using phylo-grammars. //
|
|
|
ZooGas
|
09 Nov 2009 - 11:09 - r1.31
|
IanHolmes
|
|
// Z00 Gas // Zoo Gas is an Wikipedia:educational game that attempts to pose a familiar question in computational ecology how are complex food webs stabilized? as a real-time Wikipedia:game mechanic. // At the moment it is an experimental prototype, probably playable by no-one. // But feel free to try it out. // Formally, Zoo Gas is an entropy-maximizing game of population-balancing and (highly simplified) natural selection, set on a cellular automaton model ...
|
|
|
LabMeeting
|
31 Oct 2009 - 12:37 - r1.228
|
IanHolmes
|
|
// LabMeeting // Lab meetings are held on Thursdays, from 1-2pm, in 421 StanleyHall . (With some exceptions.) // Calendar // (Also shows club) // Edit this list to add date, meeting and topic: // 17 Sep joint BBOP/HL meeting 381 Stanley // 29 Oct Le Petit Cheval //
|
|
|
IncreasePlays
|
28 Oct 2009 - 01:45 - NEW
|
TWikiGuest
|
|
// Name: Increase Plays // Email: alexbutlerderfkl@gmail.com // Comment: Download MySpace MP3 Plays Increaser, increase MySpace MP3 plays. // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
JonathanSmith
|
28 Oct 2009 - 00:10 - r1.2
|
TWikiGuest
|
|
// Name: jonathan smith // Email: jonathansmith@imails.info // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
CladeStructureGrammar
|
23 Oct 2009 - 12:23 - r1.16
|
OscarWestesson
|
|
// Clade-specific structure grammar // Motivation // Detecting species-specific structured elements, particularly in viruses // Estimating rate/frequency of these events, as well as their 'location' on species tree // Relevant Papers // // // // // // Examples // S are structural states, whereas N are non-structural. This example leads me to believe that the hybrid-chains are not working correctly, since the mutations in A,B //
|
|
|
EvolutionarySoftwareFoundation
|
19 Oct 2009 - 22:45 - r1.14
|
IanHolmes
|
|
// Evolutionary Software Foundation // The Evolutionary Software Foundation (ESF) is a 501(c)(3) nonprofit corporation dedicated to promoting // scientific research into and public understanding of the theory of evolution and its implications, through development and maintenance of software (including but not limited to research tools, educational software and evolution-themed computer games), publications, websites, animations, lectures or otherwise. // Software ...
|
|
|
XrateMacros
|
12 Oct 2009 - 00:36 - r1.13
|
IanHolmes
|
|
// Documentation of the macro language that forms part of the xrate format. // For the longer complete description of the format, including the grammar description as well as these macros, please see the format page. // The xrate macro preprocessor // Several kinds of macro are automatically expanded by xrate before any training or alignment takes place. // Macro expansion is a one-off, irreversible event: // if the grammar file is saved after macro substitution ...
|
|
|
AcronymList
|
06 Oct 2009 - 23:20 - r1.7
|
TWikiGuest
|
|
// 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 ...
|
|
|
OscarWestesson
|
01 Oct 2009 - 11:32 - r1.195
|
OscarWestesson
|
|
// 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 second-year bioengineering graduate student interested in computational sequence analysis. I studied mathematics at Univeristy of Rochester and ...
|
|
|
SubramanianAjay
|
24 Sep 2009 - 07:34 - NEW
|
TWikiGuest
|
|
// Name: Subramanian Ajay // Email: shankar.ajay@gmail.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
CigarFormat
|
23 Sep 2009 - 14:20 - r1.6
|
IanHolmes
|
|
// CigarFormat // "Cigar" (Compact Idiosyncratic Gapped Alignment Report) format // is a compressed (run-length encoded) pairwise alignment format. // It is useful for representing long (e.g. genomic) pairwise alignments. // Manpage for exonerate // Ensembl glossary // As in Treefam, and here. //
|
|
|
AlannaConnell
|
14 Sep 2009 - 21:00 - NEW
|
TWikiGuest
|
|
// Name: Alanna Connell // Email: Alannersugarface@yahoo.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
ZainAbidin
|
14 Sep 2009 - 20:57 - NEW
|
TWikiGuest
|
|
// Name: Zain Abidin // Email: zabidin901@gmail.com // Comment: // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me //
|
|
|
AleoMok
|
11 Sep 2009 - 17:23 - r1.21
|
AleoMok
|
|
// Name: Aleo Mok // Email: aleo.mok@gmail.com // Comment: website for BioE 131 // (unable to attach a picture because of website restriction) // A Few Things About Myself // Hi, my name is Aleo Mok. I am currently a sophomore at UC Berkeley with a Bioengineering Major with computational emphasis. (I am also considering doubling/tripling in EECS, but that's another story). I was actually born in Berkeley, but I moved away when I was just a wee little kid...and ...
|
|
Number of topics: 50
|
