Berkeley Madonna

Berkeley Madonna
Original author(s) Robert Macey and George Oster
Stable release
Version 9.1.3 / 2018-05-10
Written in C, Java
Operating system Windows, MacOS
Platform PC, Macintosh
Type Mathematical software
License Proprietary
Website www.berkeleymadonna.com

Berkeley Madonna is a mathematical modelling software package, developed at the University of California at Berkeley by Robert Macey and George Oster. It numerically solves ordinary differential equations and difference equations, originally developed to execute STELLA programs.[1]

Berkeley Madonna is arguably the fastest differential equation solver, originally developed for modeling and visualization of chemical reactions.[2][3][4]

Its strength lies in a relatively simple syntax to define differential equations coupled with a simple yet powerful user interface. In particular, Berkeley Madonna provides the facility of putting parameters onto a slider that can in turn be moved by a user to change the value. Such visualizations enable quick assessments of whether or not a particular model class is suitable to describe the data to be analyzed and modeled, and, later, communicating models easily to other disciplines such as medical decision makers.

Uses

It has become a standard in the development and communication of pharmacometric models describing drug concentration and its effects in drug development ,[5] modeling of physiological processes.[6] A user community exists in the form of a LinkedIn user group[7] with currently more than 500 members.

The use of system dynamics modeling has expanded into other areas such as epidemiology,[8] environmental health,[9] and population ecology.[10]

Versions

There are two versions of Berkeley Madonna: a free version with slightly limited functionality and a licensed version that is registered to individuals.

References

  1. ↑ Macey, Robert; Oster. George; Zahnley, Tim (December 28, 2009). Berkeley Madonna User’s Guide University of California. Department of Molecular and Cellular Biology. Berkeley, California.
  2. ↑ Dunn, IJ; Heinzle, E; Ingham, J; Přenosil, JE (2000). Biological Reaction Engineering: Dynamic Modelling Fundamentals with Simulation Examples (2 ed.). Wiley-VCH Verlag GmbH & Co. KGaA. doi:10.1002/3527603050. ISBN 9783527307593.
  3. ↑ Robeva, RS; Kirkwood, JR; Davies, RL (2008). Laboratory Manual of Biomathematics. Academic Press. pp. 3–17. ISBN 9780123740229.
  4. ↑ Ingham, J; Dunn, IJ; Heinzle, E; Přenosil, JE (2008). Chemical Engineering Dynamics: Modelling with PC Simulation. John Wiley & Sons.
  5. ↑ Krause, A; Lowe, PJ (2014-05-28). "Visualization and Communication of Pharmacometric Models With Berkeley Madonna". CPT Pharmacometrics Syst. Pharmacol. 3: 113. doi:10.1038/psp.2014.13. pp. 1-20.
  6. ↑ Zhong, H.; Wade, S.M.; Woolf, P.J.; Linderman, J.J.; Traynor, J.R.; Neubig, R.R. (2003). "REGULATOR OF G PROTEIN SIGNALING (RGS) PROTEIN-MEDIATED KINETIC SCAFFOLDING". Journal of Biological Chemistry. 278 (9): 7278–7284. doi:10.1074/jbc.m208819200.
  7. ↑ "LinkedIn group Berkeley Madonna". LinkedIn.com. Retrieved November 17, 2015.
  8. ↑ Vinnycky, Emilia; White, Richard (2010-05-13). An introduction to infectious disease modelling. Oxford University Press. ISBN 978-0-19-856576-5.
  9. ↑ Robson, MG; Toscano, WA (2007). Risk Assessment for Environmental Health. John Wiley & Sons. ISBN 9780787988593.
  10. ↑ Weller, Florian; Sherley, Richard B.; Waller, Lauren J.; Ludynia, Katrin; Geldenhuys, Deon; Shannon, Lynne J.; Jarre, Astrid (2016). "System dynamics modelling of the Endangered African penguin populations on Dyer and Robben islands, South Africa". Ecological Modelling. 327: 44–56. doi:10.1016/j.ecolmodel.2016.01.011.

Further reading

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