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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...
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...
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...
WestGrid quick user guide This page is part of the EmpiricalAlgorithmics web. Introduction WestGrid operates high performance computing (HPC), collaboration and...
Sun Grid Engine quick user guide This page is part of the EmpiricalAlgorithmics web. Introduction This page gives a quick overview of computational facilities...
LaTeX tips and tricks This page is part of the EmpiricalAlgorithmics web. Space squeezing %% add a line to a page \enlargethispage{\baselineskip} %% keep figures...
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...
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...
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...
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...
Top Menu of BETA Web This topic defines the menu structure of the BETA web, used by the TopMenuSkin. 1 Web` Create New Topic...
HAL 1.1 Projects Memory Efficiency redundant instantiation of immutable or largely immutable objects inefficient serialized representations of hierarchical...
Project Goals SMAC in HAL Port SMAC to HAL through Java/MATLAB interface (January) Implement: ROAR as instantiation of SMBO framework (FH: 8h) Implement...
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...
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...
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...
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...
CPSC 101 Course Development Goals and activities: Surveys (design, deploy, analyse results) This includes entrance, mid term and exit surveys, as...
New stuff: CPSC 101 course development Old stuff: MetaAlgorithmics OMEUsePolicy
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...
Main page for NGS aligner project Quick facts project directory : /ubc/cs/research/condon/share/projects/ngs aligner blessed code repository : /ubc...
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...
Useful SQL Getting information Get table information describe MY DB NAME; Get the column names from your table select COLUMN NAME from COLUMNS...
Goals Useful ideas Anne`s loop example a b c b c d e d e b a d ChrisThachuk 06 Oct 2010
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...
Sun Grid Engine Administration This page is part of the EmpiricalAlgorithmics web. For general information about using Sun Grid Engine, see SunGridEngine. Checking...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
05/03/10 Meeting with Chris, some things to do and their status: vectorized SW (assigned to Jay) testing and integration readaligner index integration...
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...
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...
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...
Specifications File Formats Reads input as FASTQ Alignments output as SAM General Needs Works in letter space with RNA Seq data Works in colour...
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...
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...
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,...
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...
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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