Results from BETA web retrieved at 10:14 (GMT)
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...
MINUTES OF SEPTEMBER 13, 2007 MEETING PRESENT: Dave Tompkins, Dave Brent, David Kirkpatrick, Irmtraud Meyer, Sohrab Shah, Baharak Rastegari, Hosna Jabbari, Chris...
Back to MeetingMinutes BETA Meeting: 2008.01.07 Printer . David Kirkpatrick will ask Dave Brent about the status of the new printer purchase....
VoteAbstractsJan2006 RNA Journal (suggested by Holger) H1 selection is not required to explain universal compositional patterns in rRNA secondary structure categories...
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...
On this page you can find a library of benchmark problems for algorithm configuration. ChrisFawcett 09 Sep 2009
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...
Just made... AndrewCarbonetto 27 Mar 2008
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...
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...
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...
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...
Bioinformatics Reading Group Summer Schedule, 2009 Please sign up! May 12: Anne Condon May 19: June 9: June 16: Rosalia Aguirre Hernandez...
VoteAbstractsJan2006 AbstractsJan2006 MeetingOct3 MinutesSep19 VoteAbstracts BioinfRGSummer09
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...
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...
CPSC 101 Course Development Goals and activities: Surveys (design, deploy, analyse results) This includes entrance, mid term and exit surveys, as...
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...
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...
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...
BETA Christmas Party 2007 Date: Friday, December 14th, 2007 Proposed start time: 4:00pm Location: Room X530 (Beta Lab) Type: Potluck It`s time...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
05/03/10 Meeting with Chris, some things to do and their status: vectorized SW (assigned to Jay) testing and integration readaligner index integration...
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...
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...
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...
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...
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!)...
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...
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...
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,...
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...
HAL 1.1 Projects Memory Efficiency redundant instantiation of immutable or largely immutable objects inefficient serialized representations of hierarchical...
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...
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...
The Holger H. Hoos Style Guide For writing academic papers with Holger H. Hoos Spelling Use British spelling: Colour, neighbourhood, behaviour......
New stuff: CPSC 101 course development Old stuff: MetaAlgorithmics OMEUsePolicy
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...
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...
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...
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...
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...
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...
LaTeX tips and tricks This page is part of the EmpiricalAlgorithmics web. Space squeezing %% add a line to a page \enlargethispage{\baselineskip} %% keep figures...
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...
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...
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:...
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...
HosnaJabbari 10 May 2007 %% keep figures from going onto a page by themselves \renewcommand{\topfraction}{0.85} \renewcommand{\textfraction}{0.1} \renewcommand{\floatpagefraction...
hello, world Main.xulin730 01 May 2008
Using Matlab This page is part of the EmpiricalAlgorithmics web. Compiling Matlab Code modification: the `main` function is an m file (myFunction.m...
Notes and minutes from BETA Lab meetings 2007.09.11 2007.05.09 2008.01.07 Template
Metabolic Pathways Background (Rosalia) Paper (Sanja) Paper (Baharak)
meta algorithmic design patterns: tuning/config: input: parametric algorithm A p ; set of benchmark instances I; performance measure m output...
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...
Useful SQL Getting information Get table information describe MY DB NAME; Get the column names from your table select COLUMN NAME from COLUMNS...
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...
Main page for NGS aligner project Quick facts project directory : /ubc/cs/research/condon/share/projects/ngs aligner blessed code repository : /ubc...
Specifications File Formats Reads input as FASTQ Alignments output as SAM General Needs Works in letter space with RNA Seq data Works in colour...
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...
Goals Useful ideas Anne`s loop example a b c b c d e d e b a d ChrisThachuk 06 Oct 2010
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...
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:...
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)...
HolgerHoos 07 Feb 2006 RNA Tertiary Structure Prediction (Holger Anne) Other Research Topics (Anne Holger)
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...
Project Goals SMAC in HAL Port SMAC to HAL through Java/MATLAB interface (January) Implement: ROAR as instantiation of SMBO framework (FH: 8h) Implement...
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...
Sun Grid Engine quick user guide This page is part of the EmpiricalAlgorithmics web. Introduction This page gives a quick overview of computational facilities...
Sun Grid Engine Administration This page is part of the EmpiricalAlgorithmics web. For general information about using Sun Grid Engine, see SunGridEngine. Checking...
Main.cchris13 2017 01 10 TORQUEViewer Viewer for monitoring TORQUE (installation guide) This page is part of the EmpiricalAlgorithmics web. Getting Started Running...
Back to MeetingMinutes BETA Meeting: YYYY.MM.DD Item One . Discussion Person Name : Action Item A Person Name : Action Item B Item Two...
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...
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...
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...
# read data from file: rtd median(rtd$V2) summary(rtd) V1 V2 V3 Min. :0.0010 Min. : 95 Min. :0....
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...
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...
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...
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...
TWiki`s BETA web The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise.
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...
Web Web Home Changes Index Search Webs
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...
BETA Web Preferences The following settings are web preferences of the BETA web. These preferences overwrite the site level preferences in ., and can...
/BETA The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise.
Statistics for BETA Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top viewers: Top contributors...
Top Menu of BETA Web This topic defines the menu structure of the BETA web, used by the TopMenuSkin. 1 Web` Create New Topic...
WestGrid quick user guide This page is part of the EmpiricalAlgorithmics web. Introduction WestGrid operates high performance computing (HPC), collaboration and...
WestGrid quick user guide This page is part of the EmpiricalAlgorithmics web. Introduction WestGrid operates high performance computing (HPC), collaboration and...
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...
Number of topics: 106
See also the faster WebTopicList 
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