The Tenth q-bio Summer School - New Mexico: Software

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Please install the following software to prepare for scheduled computer labs:

• AutoDock
• BioNetFit
• ML-Rules and SESSL
• COPASI
• MATLAB (MathWorks, Natick, MA) - license available courtesy of MathWorks if required (contact organizers for details)
• MCell and CellBlender
  • MCell is a spatial simulator based on Brownian dynamics and CellBlender is a Blendor-based interface to MCell.
  • A pre-release version of MCell/CellBlender can be downloaded here.
• BioNetGen
  • RuleBender is an Eclipse-based IDE for BioNetGen and NFsim, which provide deterministic and stochastic simulation capabilities appropriate in the well-mixed limit.
  • These tools are freely available and easy to install on most platforms (Mac OS, Windows, Linux). They enable rule-based modeling of cellular regulatory systems.
  • Download all the rule-based modeling software at http://bionetgen.org/index.php/Download
• Simmune
  • Download link for Simmune: Simmune Download
• StochSS

Please also familiarize yourself with BioModels Database.

• Data2Dynamics