Research and Programming Resources

 

Collaboration

General Computing

Simulating Genomic Data

Computing with R

Computing with C/C++

Our group uses the GNU tools, such as the gcc C compiler and the g++ C++ compiler, for software development. How you access these tools depends on your operating system.

Linux

  • GNU tools come with any Linux distribution (Linux itself is GNU) and are available on the Department Linux servers such as queen.rcg.sfu.ca, oak.fas.sfu.ca, rcg-linux-ts1.rcg.sfu.ca and dumbcane.fas.sfu.ca

Windows

Windows users will have to install the tools themselves. Two options are MinGW and cygwin.

  • MinGW is a contraction of "minimalist GNU for Windows". Though not as full-featured a toolset as cygwin (see below) MinGW has the advantage that it is able to compile binary executable files that do not rely on any system-specific libraries, making these binary executables portable across systems.
    • Complete installation instructions from the MinGW website are available on their Getting Started page.
    • Some notes on the installation based on our experiences are given here.
  • Cygwin provides a complete Unix-like environment for Windows computers.   Binary executables compiled under cygwin rely on cygwin-specific libraries and hence can only be run by users with the same system as the one on which the binary file was compiled.
    • Full cygwin installation instructions are available at here.
    • Some notes on the installation based on our experiences are given here.

Mac

The development tools for Mac are part of a package called the "Xcode command line tools". Apple does not include this tool set by default.

  • The recommended way to install Command Line Tools is to type the following from a Terminal window:
    xcode-select --install
    
    If this installation method does not work for you, this thread on Stackexchange may be helpful for providing a work-around.

TeX/LaTeX

  • Templates for SFU Master's projects and PhD theses in LaTeX.
    •  LaTeX template from the SFU Library.
    • A BibTeX sytle file forwarded by Flora Qu: jasasty-ay.bst. The "ay" in the name appears to refer to "author-year" style references [e.g. Qu (2009)], rather than numeric citations in the text. Flora reports having had trouble with other bibtex style files, but that this one works. She notes: "When you use this bib style file, you need to add \usepackage{natbib} in the main tex file."
    • In addition to the LaTeX files, MSc students may be interested in looking at a few recent projects from the department to get sense of the scope and size of a typical MSc project: (i) Chenlu Shi, (ii)  Kunasekaran Nirmalkanna, (iii)  Rachel Lipson
  • LaTeX posters:
    • The package tizkposter is popular these days.
      • Download the LaTeX package zipfile,
      • use unzip to unpack it into its own directory,
      • change to this directory and run "latex tikzposter.ins" to generate the class files and examples.
      • The documentation file is tikzposter.pdf. An example poster is in the file tikzposter-example.tex. A template that you can use as a starting point for your own posters is in the file tizkposter-template.tex.
    • Another possibility is the beamerposter package, which you may prefer over tikzposter if you use beamer for presentations.
      • Downoad the LaTeX package zipfile,
      • use unzip to unpack it into its own directory and change to this directory.
      • The documentation is in the file beamerposter.pdf, and an example is in the file example.tex.
  • Information from Jean Shin (Dated Nov. 3, 2010) on poster printing places @ SFU and costs:
    • School of Resource and Environmental Management (REM) [updated by Elena Szefer, Apr. 2015]:
      • Regular paper only; $48 for an A0 poster.
      • If you send a pdf file to Laurence Lee (laurence_lee@sfu.ca) by 11AM, you can have the poster by 2 or 3PM in the same day
      • You can send the grant account number to be charged to Laurence. Sadika can provide the account number that is required. 
      • Before they release your poster to you, your supervisor needs to sign an invoice to agree to have their account charged.  You need to return this invoice to the REM office.  It's also possible to pick up a hard copy of the invoice before your poster is done printing to have signed by your supervisor.
      • I'm not sure which option is best, but it would be a good idea to ask about the invoice with Laurence when you place your order to make sure that you will be able to get your poster in time.
    • Cornerstone:
      • $3.99/ sq. ft (regular paper) and $5.99/ sq. ft (thicker glossy paper)
      • they need 1 business day
      • Bhagya Karunarathna (Apr. 2015) reports a cost of about $40 for an A0 poster on regular paper, but no invoicing.
    • IRMACS:
      • $6 per square-foot (white background) or $7 (dark background)
      • they need at least 24 hours
    A typical sized poster (4ft-by-3ft) costs $48 (REM), $48~$72 (cornerstone) and $72 ~ $84 (IRMACS).

Old Documents

 

  • Templates for LaTeX posters:
    • A template for a 2-column poster, courtesy of Kelly Burkett, is available as a gzipped tar file (for Unix -- unpack with with tar xzvf poster_2column.tar.gz) or as a zip file (for Windows). The archive includes a template .tex file and a complete poster.
    • A template for a 3-column poster, courtesy of Jean Shin, is available as a gzipped tar file (for Unix -- unpack with with tar xzvf poster_3column.tar.gz) or as a zip file (for Windows). The archive includes a template .tex file and a complete poster.
  • R Graphics using the Grid Package
    by Sigal Blay, January 2006.
    The grid package provides a low-level graphics system to produce reusable, editable graphical components.
    Formats: PowerPoint
                   Text file
  • How to Inspect R package documentation
    by Sigal Blay, 2005.

  • Using the 'snow' R package
    by Sigal Blay, January 2005.
    The 'snow' package provides a high-level interface for using a workstation cluster for parallel computations in R. snow Simplified is a friendly user guide.
    Formats: HTML
                   Text file

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