Difference: WebIndex ( vs. 1)

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Results from BETA web retrieved at 08:52 (GMT)

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Meeting May 9, 2007: Action items are marked with introduction Bioinformatics reading group time, set to Tuesdays 1:00 2:00 Every once a while, this meeting...
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MINUTES OF SEPTEMBER 13, 2007 MEETING PRESENT: Dave Tompkins, Dave Brent, David Kirkpatrick, Irmtraud Meyer, Sohrab Shah, Baharak Rastegari, Hosna Jabbari, Chris...
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Back to MeetingMinutes BETA Meeting: 2008.01.07 Printer . David Kirkpatrick will ask Dave Brent about the status of the new printer purchase....
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VoteAbstractsJan2006 RNA Journal (suggested by Holger) H1 selection is not required to explain universal compositional patterns in rRNA secondary structure categories...
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Every account needs to be sponsored by a full BETA faculty member. Until the department keeps track of this information, it will be maintained on this page. Please...
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On this page you can find a library of benchmark problems for algorithm configuration. ChrisFawcett 09 Sep 2009
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This page is meant to serve as a central location for all of the algorithm configuration work occurring in BETA. Research in progress can be documented on sub pages...
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Just made... AndrewCarbonetto 27 Mar 2008
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The Arrow cluster and our 22 CPLEX licenses were funded under a CFI grant. This grant requires us to complete annual reports explaining how this infrastructure is...
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This page lists software we need installed on arrow to run our experiments. If you need something else, please add it to the list and put your name in parentheses...
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BETA Web Pages Add comments on the BETA web pages, ideas for changes, errors, links to revised pages, etc. HolgerHoos 20 May 2005 Here are links to first drafts...
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Benchmarking for AC on the Cloud Goals We wish to perform algorithm configuration in a cloud setting. To do this effectively, we need to be able to deal with some...
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Bioinformatics Reading Group Summer Schedule, 2009 Please sign up! May 12: Anne Condon May 19: June 9: June 16: Rosalia Aguirre Hernandez...
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VoteAbstractsJan2006 AbstractsJan2006 MeetingOct3 MinutesSep19 VoteAbstracts BioinfRGSummer09
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The BETA Lab Library Policies Try not to remove books from the lab Try not to `hog` a book at your desk / terminal for too long If you are going to...
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To create an external build (i.e. executables compile in a directory different from source): 1. navigate to the directory where you would like your build to be...
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CPSC 101 Course Development Goals and activities: Surveys (design, deploy, analyse results) This includes entrance, mid term and exit surveys, as...
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Who could possibly teach CPSC 445 in 2010W2 (or 2010W1)? Mirela Andronescu (HH: IMO clearly qualified, have to check baby situation) Sohrab Shah (HH: probably...
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Using CVS This page is part of the EmpiricalAlgorithmics web. Permissions Here`s something from Sean Godel: If the CVS client is configured to go through okanagan...
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BETA Lab Christmas Party, Wed Dec 20, 2006, at 3:30pm, in room X530. The BETA Lab Christmas Party is getting close, and all of us will surely enjoy it, because we...
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BETA Christmas Party 2007 Date: Friday, December 14th, 2007 Proposed start time: 4:00pm Location: Room X530 (Beta Lab) Type: Potluck It`s time...
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Note: a hardware freeze policy has not yet been determined for the Beta lab. We will review the list of Freeze periods entered on this page at the next Beta lab meeting...
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I don`t know what rules there are about how much a student can consult, but I`d imagine that the granting agencies have rules that go along with their scholarships...
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Using CPLEX This page is part of the EmpiricalAlgorithmics web. ILOG CPLEX: Linear, Integer and Quadratic Programming Software Here`s the email explaining CPLEX usage...
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Here`s an updated list of speeds of our aligner vs other aligners: All run on skorpios from the /tmp/ directory, timed with time , using the 2622382 reads file...
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04/01/10 The basic working bacterial aligner is complete, next up: Include quality information i.e. fill in a meaningful mapping quality value in the...
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02/01/10 Made FastqEntry in a class (it was a struct ), which required the addition of a lot of accessor methods. More importantly, it now has a new MutateBelowThreshold...
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Daniel`s January 2010 Research Journal 01/20/10 Spent afternoon familiarizing self with BETA Lab workstation leros and the following NGS aligners (and tool) currently...
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07/01/10 Traced bowtie in maq like quality aware alignments The maq like part with seeds and 4 phases confuses me and the results seem inconsistent compared...
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06/01/10 Meeting with Jay and Chris, up next: Create a simple minimal locate function Modify the aforementioned function to make a single mismatch locate...
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03/01/10 Well, I was planning on doing another large self expository entry for Vigna`s select9 , but due to certain circumstances (including but not limited to the...
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05/03/10 Meeting with Chris, some things to do and their status: vectorized SW (assigned to Jay) testing and integration readaligner index integration...
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Well... it feels more journal than research... but I guess it gets the job done. 2010 Archive 2010 Archive 2010 Archive 2010 Archive 2010 Archive 2010 Archive...
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Draft Agenda for the next Lab Meeting Time: TBA, see http://doodle.com/2feam2wavsq536i3 Place: X5 Meeting Room next to the lab summer students (implications...
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Amazon`s Elastic Compute Cloud (EC2) Introduction Amazon`s Elastic Compute Cloud is a service which allows users to purchase computing resources by the hour in the...
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Empirical Algorithmics in BETA One of the BETA research areas is Empirical Algorithmics. Of course many computer scientists rely on empirical methods for testing and...
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Notes on the BETA Facilities ( X5 Meeting Room and Kitchen) (Put information, deficiencies, etc. here; it would be great if someone could post a few pictures!)...
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We can share files under /ubc/cs/research/condon/people/ or /ubc/cs/research/condon/share/projects/ . You must follow a couple of steps to ensure the group has...
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Git We have set up a common remote location for git repositories. These repositories are located on the netapp filesystem at /ubc/cs/project/arrow/git . Note that...
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Assuming you`ve up a working git repository, the typical work flow is as follows: 1. In your private repo, move to the branch you wish you branch off of,...
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Feature Milestones HAL 1.0 target: September, 2010 Web UI Features Page to add new external target algorithms Page to add new parameter spaces for a...
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HAL 1.1 Projects Memory Efficiency redundant instantiation of immutable or largely immutable objects inefficient serialized representations of hierarchical...
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HAL Web Tutorial HAL WebUI Tutorial Starting HAL WebUI Start HAL by running HAL version .jar ( java jar HAL version .jar ) The WebUI is available...
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Using Mercurial with Git Repositories Git: the cool new kid on the block when it comes to revision management. Everyone`s using it. Only problem? Like many tools...
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The Holger H. Hoos Style Guide For writing academic papers with Holger H. Hoos Spelling Use British spelling: Colour, neighbourhood, behaviour......
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New stuff: CPSC 101 course development Old stuff: MetaAlgorithmics OMEUsePolicy
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How To Guides Using R Apr 6, 2011 Installing R and RServe Installing R see http://www.r project.org/ Installing packages Installing packages can be...
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07/01/10 Played around with multithreading some more. I tried making a light weight test file, where I just add a value a few billion (probably more) times, just to...
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06/01/10 Here are a few more times, this time with all bin and data files on the /tmp/ folder with times calculated from /usr/bin/time . Using commit 5a82392eeeb5653d1b75b7a8dd7c...
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05/06/10 I`m starting this journal 3 days late (whoops). Here`s a brief overview of what happened during my first three days: Read through a bunch of Daniel`s...
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2010 archive 2010 archive 2010 archive 07/30/10 Started to implement the new StaticDNASequence. The build process is going to get a little ugly, but the ranks...
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01/05/2011 Started reading more in depth into CUDA. Made some notes (I`ll post them later). Things to do: Finish up the local aligner changes and commit...
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LaTeX tips and tricks This page is part of the EmpiricalAlgorithmics web. Space squeezing %% add a line to a page \enlargethispage{\baselineskip} %% keep figures...
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BETA Lab Party LabTeaJan2009 Date: Tuesday, January 27, 2009 Time: 4:00pm 5:00pm Location: Beta Lab Please plan to attend and if you can volunteer...
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BETA Lab Seating / Facilities We have developed a policy that will hopefully avoid conflicts and problems allocating seats in the BETA lab. Before claiming a seat...
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Beta Lab Tea Date: Tuesday, January 27, 2009 Time: 4:00pm 5:00pm Location: Beta Lab Volunteers We need volunteers to help with the following:...
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This page is meant to serve as a central source for tracking the students and faculty currently responsible for various service positions in the Beta lab. Position...
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HosnaJabbari 10 May 2007 %% keep figures from going onto a page by themselves \renewcommand{\topfraction}{0.85} \renewcommand{\textfraction}{0.1} \renewcommand{\floatpagefraction...
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hello, world Main.xulin730 01 May 2008
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Using Matlab This page is part of the EmpiricalAlgorithmics web. Compiling Matlab Code modification: the `main` function is an m file (myFunction.m...
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Notes and minutes from BETA Lab meetings 2007.09.11 2007.05.09 2008.01.07 Template
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Metabolic Pathways Background (Rosalia) Paper (Sanja) Paper (Baharak)
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meta algorithmic design patterns: tuning/config: input: parametric algorithm A p ; set of benchmark instances I; performance measure m output...
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We quickly went over the abstracts each of us selected. (Holger`s selection will be on the page soon). For the next meetings, we`ll select a topic, and discuss papers...
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Useful SQL Getting information Get table information describe MY DB NAME; Get the column names from your table select COLUMN NAME from COLUMNS...
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Concerning Multimaps I sort of came to my conclusion about this already, but I`ll spam it here anyway for posterity. When faced when multimaps, there are three modes...
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Main page for NGS aligner project Quick facts project directory : /ubc/cs/research/condon/share/projects/ngs aligner blessed code repository : /ubc...
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Specifications File Formats Reads input as FASTQ Alignments output as SAM General Needs Works in letter space with RNA Seq data Works in colour...
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HolgerHoos 08 Feb 2006 Use of the ICICS Open Media Environment DRAFT, version 0.3 hh comments and suggestions welcome! See footnotes for explanations. Background...
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Goals Useful ideas Anne`s loop example a b c b c d e d e b a d ChrisThachuk 06 Oct 2010
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This page exists to give status reports and documentation of the Fall 2009 comparison between Iterated F RACE and ParamILS on various problem domains. These domains...
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Cheat sheet for Matlab user: vs. R Some useful R commands: # command line execution of R scripts: R CMD BATCH help (`write.table) # write data to file:...
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The Database (SQL) drop table if exists RUNS JMALT; create table RUNS JMALT ( i INT NOT NULL AUTO INCREMENT, job INT, run file VARCHAR(128), out file VARCHAR(128)...
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HolgerHoos 07 Feb 2006 RNA Tertiary Structure Prediction (Holger Anne) Other Research Topics (Anne Holger)
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Assume for all instances below that a single FASTA reference ref.fasta and a single FASTQ read file reads.fastq are in the same directory as the program executable...
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Project Goals SMAC in HAL Port SMAC to HAL through Java/MATLAB interface (January) Implement: ROAR as instantiation of SMBO framework (FH: 8h) Implement...
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Setting up a clean private repository: 0. have git installed on your system 1. navigate to the repository where your private ngsa suite repo directory will...
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Sun Grid Engine quick user guide This page is part of the EmpiricalAlgorithmics web. Introduction This page gives a quick overview of computational facilities...
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Sun Grid Engine Administration This page is part of the EmpiricalAlgorithmics web. For general information about using Sun Grid Engine, see SunGridEngine. Checking...
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Main.cchris13 2017 01 10 TORQUEViewer Viewer for monitoring TORQUE (installation guide) This page is part of the EmpiricalAlgorithmics web. Getting Started Running...
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Back to MeetingMinutes BETA Meeting: YYYY.MM.DD Item One . Discussion Person Name : Action Item A Person Name : Action Item B Item Two...
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ticgit is the issue tracker we`ll be using that`s integrated with git: Setting up RubyGems so gems are installed into your home directory (i.e. on the lab computers...
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Command: timerun time limit cmd 1 result file 2 time file Description: Run cmd for at most time limit and cmd outputs are in result file and runtime...
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Tips and Tricks Here are documents provided by Beta members for cool Tips and Tricks HolgerHoosStyleGuide The guide to writing papers with Holger H. Hoos...
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# read data from file: rtd median(rtd$V2) summary(rtd) V1 V2 V3 Min. :0.0010 Min. : 95 Min. :0....
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Valgrind is a software suite that includes many useful tools, like a memory checker and a cache profiler. Installation I`m not really sure how to install this on...
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Will you want to present a paper on October 3rd? If so, please add your name here (we need at least 3 names, the more the better): Mirela, Sanja, Baharak Please add...
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Please write your name next to the papers which are interesting to you. The abstracts are at AbstractsJan2006. H1 Mirela, Rosalia, Dan, Sanja, Baharak H2 H3...
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Beta Lab Water Cooler 2009 Update Note from Dave: So Canadian Direct FINALLY gave us (me) our money back for the water cooler and the deposits on all those bottles...
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TWiki`s BETA web The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise.
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Welcome to the home of BETA. This is a web based collaboration area for members of the BETA Lab. Lab related pages DraftAgenda for next lab meeting MeetingMinutes...
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Web Web Home Changes Index Search Webs
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This is a subscription service to be automatically notified by e mail when topics change in this BETA web. This is a convenient service, so you do not have to come...
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BETA Web Preferences The following settings are web preferences of the BETA web. These preferences overwrite the site level preferences in ., and can...
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/BETA The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise.
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Statistics for BETA Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top viewers: Top contributors...
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Top Menu of BETA Web This topic defines the menu structure of the BETA web, used by the TopMenuSkin. 1 Web` Create New Topic...
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WestGrid quick user guide This page is part of the EmpiricalAlgorithmics web. Introduction WestGrid operates high performance computing (HPC), collaboration and...
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WestGrid quick user guide This page is part of the EmpiricalAlgorithmics web. Introduction WestGrid operates high performance computing (HPC), collaboration and...
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This is how I create new wiki topics here... there may be a smarter way, but I haven`t figured it out: 1. type a WikiWord (multiple words in camel base), in...
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Number of topics: 106
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See also the faster WebTopicList

 
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