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| > > | Recent Changes in BETA Web retrieved at 11:23 (GMT)<-- remove the format parameter to show absolute date instead if topic age --> <--/twikiTopRow--> Statistics for BETA Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top viewers: Top contributors... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Main.cchris13 2017 01 10 TORQUEViewer Viewer for monitoring TORQUE (installation guide) This page is part of the EmpiricalAlgorithmics web. Getting Started Running... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> WestGrid quick user guide This page is part of the EmpiricalAlgorithmics web. Introduction WestGrid operates high performance computing (HPC), collaboration and... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Sun Grid Engine quick user guide This page is part of the EmpiricalAlgorithmics web. Introduction This page gives a quick overview of computational facilities... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> LaTeX tips and tricks This page is part of the EmpiricalAlgorithmics web. Space squeezing %% add a line to a page \enlargethispage{\baselineskip} %% keep figures... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Top Menu of BETA Web This topic defines the menu structure of the BETA web, used by the TopMenuSkin. 1 Web` Create New Topic... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> HAL 1.1 Projects Memory Efficiency redundant instantiation of immutable or largely immutable objects inefficient serialized representations of hierarchical... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Project Goals SMAC in HAL Port SMAC to HAL through Java/MATLAB interface (January) Implement: ROAR as instantiation of SMBO framework (FH: 8h) Implement... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> CPSC 101 Course Development Goals and activities: Surveys (design, deploy, analyse results) This includes entrance, mid term and exit surveys, as... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> New stuff: CPSC 101 course development Old stuff: MetaAlgorithmics OMEUsePolicy <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Main page for NGS aligner project Quick facts project directory : /ubc/cs/research/condon/share/projects/ngs aligner blessed code repository : /ubc... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Useful SQL Getting information Get table information describe MY DB NAME; Get the column names from your table select COLUMN NAME from COLUMNS... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Goals Useful ideas Anne`s loop example a b c b c d e d e b a d ChrisThachuk 06 Oct 2010 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Sun Grid Engine Administration This page is part of the EmpiricalAlgorithmics web. For general information about using Sun Grid Engine, see SunGridEngine. Checking... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 05/03/10 Meeting with Chris, some things to do and their status: vectorized SW (assigned to Jay) testing and integration readaligner index integration... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Specifications File Formats Reads input as FASTQ Alignments output as SAM General Needs Works in letter space with RNA Seq data Works in colour... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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,... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult-->Show 10, 20, 50, 100, 500, 1000 results per page, or show all. Related topics:  RSS feed, ATOM feed, WebNotify, site changes, site map | |||||||
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