Modeling living systems is not easy. It requires integrating skills from engineering and science fields from the disciplines of biology, chemistry, physics, mathematics, statistics and computation. We understand the challenges and are here to help. We offer both computational tools and access to a vibrant, welcoming community of other modelers using Biocellion.

Prerequisites

Basic proficiency with the Linux operating system and C++ programming are required. Familiarity with mathematical modeling concepts relevant to the particular system being modeled is assumed.

Tools

  • Modeling. A Biocellion Model is a user-created C++ library that is linked to the Biocellion Simulation Platform binary, resulting in an executable suitable for execution on an x86-based platform running Linux. Biocellion Models may be constructed by modifying examples shipped with the Biocellion Simulation Platform. 
     
  • Simulation. Download the Biocellion Simulation Platform free for non-commercial uses.
    Modelers employed by, or whose work is supported by, for-profit corporations must follow-up with Biocellion SPC to obtain a commercial license specific to their use.
    Modelers wishing access to the source code may have their organizations contact Biocellion SPC to apply to become an affiliate.
     
  • Visualization. Biocellion SPC has contracted with Kitware to make ParaView 5.2 and later versions compatible with Biocellion Simulation Platform output. ParaView is available free by download. 
    Biovision is a visualization product optimized for Biocellion output that is currently under development. Please contact us to request images or videos produced using Biovision for your publications or to join the waiting list.

Support

  • Tutorial. A community supported Wiki includes a tutorial here. This is the place to start.

  • Manual. Documentation for the Biocellion Simulation Platform is available here.

  • Wiki. In addition to the tutorial, the Wiki includes modeling examples and links to publications here.

  • Forum. A user forum where you can post your questions to the community is hosted here. Questions are encouraged: everyone recognizes the learning curve is steep and response time is usually under 24 hours.