Morpheus documentation

documentation:documentation

Anonymous (anonymous@undisclosed.example.com) — 2013-12-09T21:17:14+00:00

Documentation User Manual The user manual is the central resource for up-to-date information on: * graphical user interface and workflow tools * modeling formalisms and numerical implementation * model description language * model integration and simulation schedule

documentation:faq

Anonymous (anonymous@undisclosed.example.com) — 2021-08-17T14:14:15+00:00

Frequently asked questions General More details More information For more information, refer to the user manual. Modeling Random seed Random seed * Mersenne Twister from C\+\+ compiler (gcc version > 4.6) or Boost library when available. * Time $Latex$$Latex$

documentation:issues

Anonymous (anonymous@undisclosed.example.com) — 2021-08-17T14:50:34+00:00

Known Issues Installation Installation on Mac OSX Please see the page on troubleshooting for Mac. Simulation ''Function'' gives erroneous values Functions have been reported to generate erroneous values in the following situation: * Function is defined outside of

documentation:manual

Anonymous (anonymous@undisclosed.example.com) — 2015-01-07T09:49:15+00:00

User Manual Download user manual (pdf). The user manual is the main resource for information on: * graphical user interface and workflow tools * modeling formalisms and numerical implementation * model description language * model integration and simulation schedule

documentation:model_description_language

Anonymous (anonymous@undisclosed.example.com) — 2013-08-01T15:36:00+00:00

Model description language The Morpheus model description language (MDL) is a domain-specific extensible mark-up language (XML) for the specification of multiscale multicellular simulation models. It has been developed to separate the process of modeling from numerical implementation to allow users to specify simulation models in terms of familiar biological and mathematical concepts rather than in a general-purpose programming language (see sections [sub:Domain-specific-language] and [sec:Glos…

documentation:performance

Anonymous (anonymous@undisclosed.example.com) — 2014-02-18T20:25:40+00:00

Performance and scalability The performance and scalability of simulations in Morpheus heavily depend on the type of (multi-scale) model that is being simulated. It is therefore difficult to make general statements on the computational efficiency. However, we can test the performance on a set of $10^2$$20^2$$50^2$$100^2$$200^2$$500^2$$1000^2$$40^2$$100^2$$200^2$$400^2$$1000^2$

documentation:publications

Anonymous (anonymous@undisclosed.example.com) — 2021-08-17T14:47:44+00:00

Publications Research papers Meyer, K., Ostrenko, O., Bourantas, G., Morales-Navarrete, H., Porat-Shliom, N., Segovia-Miranda, F., Nonaka, H., Ghaemi, A., Verbavatz, J.M., Brusch, L. and Sbalzarini, I., Kalaidzidis, Y., Weigert, R., Zerial M. A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule. Cell Systems

documentation:tech_specs

Anonymous (anonymous@undisclosed.example.com) — 2013-08-02T22:02:42+00:00

Technical specification Solvers Ordinary differential equations (ODE) Morpheus implements explicit finite different solvers of numerical integration of ODEs: * Euler's method: 1st order * Heun's method (a.k.a. midpoint): 2nd order * Runge-Kutta's method: 4th order and stochastic differential equations (SDEs):$\delta t$$\boldsymbol{x}$$\sigma$$H=\sum_{\sigma > 0} \lambda_V (v_\sigma - V_t)^2 + \sum_{\sigma > 0} \lambda_P (p_\sigma - P_t)$$v_\sigma$$p_\sigma$$\sigma$$V_t$$P_t$$H$$\lambd…

documentation:work_flow_tools

Anonymous (anonymous@undisclosed.example.com) — 2021-08-18T18:34:46+00:00

Work flow tools Morpheus has a number of nifty tools to optimize your work flow from model development to high performance computing. Here, we present some use cases that use these features. Model development and testing Copy / paste between models