Todo List

From SimBio - A generic environment for bio-numerical simulations

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  • put link or copy of the current revision history of the svn repository
  • fill the page "Directory Structure"
  • fill the page "Coding Standard" (naming conventions etc.)
  • fill the page "File Formats"
  • make a MediaWiki template for code snippets (box, fixed width font, line break)
  • integrate contents from
  • Bug-Report system (e.g. MediaWiki Discussion Forum)


  • Matlab user interface design and implementation
  • grid class: revise the interface and information hiding
  • matrix class
    • revise the information hiding and functionality,
    • remove compiler dependent warnings
  • [Stephan] check in PSO
  • remove old, unused third-party packages
    • colsam (used in 1 function call)
    • libsol
  • make Fortran Code compliant to Fortran95 or Fortran2003,
    • Then the compilation problems disappear, because Fortran95+ is supported in gcc4.* and we don't need g77 and g2c any more.
  • Update copies of outdated third-party libraries
  • License tags and script to extract only the components with certain licenses
  • Switch for each external library to chose between SimBio copy and locally installed version (Linux)
  • Separation of the file I/O from the user interface into a separate component within the toolbox
  • Revision of the SVD code, which showed to be numerically instable in some studies
  • Performance optimization by reviewing code, not algorithms
  • Performance optimization by reviewing selected algorithms
  • Parallelization of basic operations to utilize multi-processor environments
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