BioMA

Biophysical Model Applications
BioMA is a public domain software framework for developing, parameterizing and running modelling solutions in the domains of agriculture and environment.
Model components and modelling solutions are reusable under different frameworks.
The software is developed using Microsoft C# of the .NET framework

Modelling frameworks are used in modelling and simulation and can consist of a software infrastructure to develop and run mathematical models. They have provided a substantial step forward in the area of biophysical modelling with respect to monolithic implementations.[1][2][3] The separation of algorithms from data, the reusability of I/O procedures and integration services, and the isolation of modelling solutions in discrete units has brought a solid advantage in the development of simulation systems. Modelling frameworks for agriculture have evolved over time, with different approaches and targets[4]

BioMA is a software framework developed focusing on platform-independent, re-usable components, including multi-model implementations at fine granularity.

BioMA - Biophysical Model Applications

BioMA (Biophysical Model Applications) is a public domain software framework designed and implemented for developing, parameterizing and running modelling solutions based on biophysical models in the domains of agriculture and environment.[5] It is based on discrete conceptual units codified in freely extensible software components .[6]

The goal of this framework is to rapidly bridge from prototypes to operational applications, enabling running and comparing different modelling solutions. A key aspect of the framework is the transparency which allows for quality evaluation of outputs in the various steps of the modelling workflow. The framework is based on framework-independent components, both for the modelling solutions and the graphical user's interfaces. The goal is not only to provide a framework for model development and operational use but also, and of no lesser importance, to provide a loose collection of objecst re-usable either standalone or in different frameworks. The software is developed using Microsoft C# language in the .NET framework.

The framework is a development of the work carried out under the APES [7] task of the 6th EU Framework Programm SEAMLESS project.

Deployments of the platform and its tools and components have been used to create weather datasets for biophysical simulation,[8] to estimate the impact on crop production in Europe,[9] and adaptation,[10][11] to simulate soil pathogens under climate change,[12][13] to simulate the survival of insects damaging maize under climate change [14] to estimate crop suitability to environment,[15] to perform modelling solutions comparison at sub-model level,[16] to develop a library of reusable models for crop development and growth,[17] to estimate the impact of climate change on crop production in Latin America,[18] to estimate fungal infections,[19][20][21] to estimate agro-meteorological variables,[22][23][24][25][26][27][28][29] to develop a library of functions to estimate soil hydraulic properties,[30] to estimate quality of agricultural products.[31]

BioMA applications and modelling solutions are the simulation tools used by the MARS unit of the European Commission to simulate agricultural production under scenarios of climate change. BioMA is also used in the EU FP7 project MODEXTREME.

The architecture

The simulation system is discretized in layers, each with its own features and requirements. Such layers are the Model Layer (ModL), where fine granularity models are implemented as discrete units,[32] the Composition Layer (CompL), where basic models are linked into more complex, aggregated models, and the Configuration Layer (ConfL), which allows providing context specific parameterization (in the software sense) for operational use. Applications can span from simple console applications to user-interacting applications based on the model-view-controller pattern, in the simplest cases linking either directly to either the ModL or the CompL, or accessing model ConfL. In all cases, the component oriented architecture allows implementing a set of functionalities which impact on the richness of functionality of the system and on its transparency. Layers implement no top-down dependency among them, hence facilitating the independent reuse of tools, utilities, and model components in different applications and frameworks.

Architectural layers of the BioMA simulation system
  • Model layer: fine grained/composite models implemented in components
  • Composition layer: modeling solutions from model components
  • Configuration layer: adapters for advanced functionalities in controllers
  • Applications: from console to advanced MVC implementations
  • Development Tools: tools mostly using code generation
  • Re-usable components implementing model libraries are composed into modelling solutions.
  • Modeling solutions are not specific to one modelling framework.
  • An adapter creates a version of the modelling solution specific to a framework application, such as BioMA.
  • The semantically explicit interfaces allow creating rich applications
From model components to modelling solutions, and to adapters

Applications

Model libraries used in BioMA to build modelling solutions

Advanced applications can be grouped under two categories:

Applications can be built based on the libraries as in the following figure. The libraries can be extended implementing new models, as shown in the software development kits, and new libraries can be added.

Availability

Model components and tools can be autonomously downloaded with the SDK at the components' portal. Same for modelling solutions (starting from 2016).

Applications must be requested by email, and, similarly to components, applications will be made available for free autonomous download during 2016.

Links

The BioMA Intellectual Property Rights model

Code of core components is available under the LGPL license, however, the reuse of binaries falls under the Creative Commons license as below, implying the no-commercial, share-alike clauses.[33]

Application and tools are available under the Creative Commons license as binaries, however code can be shared under specific agreements between parties. Model component developers may make code available, however, they must make binaries available for reuse.[34]

References

  1. ↑ Donatelli, M., J. Bolte, F. van Evert and W. Wang, 2003 Which software designs for evolution. In: van Ittersum M.K., Donatelli M. (Eds.), Modelling cropping systems: science, software and applications.European Journal of Agronomy 18, 193-195.
  2. ↑ Rizzoli A.E., G. Leavesley, J.C. Ascough II, R.M. Argent , I.N. Athanasiadis, V. Brilhante, F.H.A. Claeys, O. David, M. Donatelli i, P. Gijsbers, D. Havlik, A. Kassahun, P. Krause 2008 Environmental modelling, software and decision support - state of the art and new perspectives Elsevier 101-119
  3. ↑ Argent, R.M., 2004. An overview of model integration for environmental applicationsócomponents, frameworks and semantics, Environmental Modelling & Software, Volume 19, 3:219-234
  4. ↑ Holzworth D.P. , Snow V., Janssen S., Athanasiadis I.N., Donatelli M., Hoogenboom G., White J.W., Thorburn P., 2015. Agricultural production systems modelling and software: Current status and future prospects, Enrironmental Modelling and Software
  5. ↑ Donatelli M., Cerrani I., Fanchini D., Fumagalli. D., Rizzoli A. 2012. Enhancing Model Reuse via Component-Centered Modeling Frameworks: the Vision and Example Realizations. In: International Environmental Modelling and Software Society (iEMSs), 2012 International Congress on Environmental Modelling and Software, Managing Resources of a Limited Planet, Sixth Biennial Meeting, Leipzig, Germany, R. Seppelt, A.A. Voinov, S. Lange, D. Bankamp (Eds.) PDF
  6. ↑ Donatelli M., Rizzoli A. 2008 A design for framework-independent model components of biophysical systems International Congress onEnvironmental Modelling and Software iEMSs 2008 Proceedings of theiEMSs Fourth Biennial Meeting, Barcelona, Catalonia 7–10 July 2008: 727-734 PDF
  7. ↑ Donatellli M., G. Russell, A.E Rizzoli, et al. 2010 A component-based framework for simulating agricultural production and externalities. In: Environmental and agricultural modelling: Integrated approaches for policy impact assessment, F.Brouwer and M. van Ittersum editors, Springer, 63-108
  8. ↑ Donatelli M., Fumagalli D., Zucchini A., Duveiller G., Nelson R.L., Baruth B. 2012. A EU27 Database of Daily Weather Data Derived from Climate Change Scenarios for Use with Crop Simulation Models. In: International Environmental Modelling and Software Society (iEMSs), 2012 International Congress on Environmental Modelling and Software, Managing Resources of a Limited Planet, Sixth Biennial Meeting, Leipzig, Germany, R. Seppelt, A.A. Voinov, S. Lange, D. Bankamp (Eds.) PDF
  9. ↑ Donatelli M., Duveiller G., Fumagalli D., Srivastava A., Zucchini A., Angileri V., Fasbender D., Loudjani P., Kay S., Juskevicius V., Toth T., Haastrup P., Míbarek R., Espinosa M., Ciaian P., Niemeyer S. 2011 Assessing Agriculture Vulnerabilities for the design of Effective Measures for Adaption to Climate Change AVEMAC project. PDF
  10. ↑ Donatelli M., Srivastava A., Duveiller G., Niemeyer S. 2012. Estimating Impact Assessment and Adaptation Strategies under Climate Change Scenarios for Crops at EU27 Scale. In: International Environmental Modelling and Software Society (iEMSs), 2012 International Congress on Environmental Modelling and Software, Managing Resources of a Limited Planet, Sixth Biennial Meeting, Leipzig, Germany, R. Seppelt, A.A. Voinov, S. Lange, D. Bankamp (Eds.) PDF
  11. ↑ Donatelli M., Srivastava A.K., Duveiller G., Niemeyer S., Fumagalli D., 2015. Climate change impact and potential adaptation strategies under alternate realizations of climate scenarios for three major crops in Europe, Environ. Res. Lett. 10
  12. ↑ Manici L., Donatelli M., Fumagalli D., Lazzari A., Bregaglio S. 2012 Potential Response of Soil-Borne Fungal Pathogens Affecting Crops to a Scenario of Climate Change in Europe. In: International Environmental Modelling and Software Society (iEMSs), 2012 International Congress on Environmental Modelling and Software, Managing Resources of a Limited Planet, Sixth Biennial Meeting, Leipzig, Germany, R. Seppelt, A.A. Voinov, S. Lange, D. Bankamp (Eds.) PDF
  13. ↑ Manici L. M. , Bregaglio S., Fumagalli D., Donatelli M. 2014. Modelling soil borne fungal pathogens of arable crops under climate change, International Journal of Biometereology
  14. ↑ Maiorano A, Cerrani I, Fumagalli D, Donatelli M, 2013. New biological model to manage the impact of climate warming on maize corn borers. Agronomy for Sustainable Development,
  15. ↑ Confalonieri R., Francone C., Cappelli G., Stella T., Frasso N., Carpani M., Bregaglio S., Acutis M., Tubiello, F.N., Fernandes E., 2012. A multi-approach software library for estimating crop suitability to environment.Computers and Electronics in Agriculture 90: 170-175.
  16. ↑ Donatelli M., Bregaglio S., Confalonieri R., De Mascellis R., Acutis M., 2014. A generic framework for evaluating hybrid models by reuse and composition – A case study on soil temperature simulation, ISSN 1364-8152, Environmental Modelling & Software
  17. ↑ Stella T., Frasso N., Negrini G., Bregaglio S., Cappelli G., Acutis M., Confalonieri R., 2014. Model simplification and development via reuse, sensitivity analysis and composition: A case study in crop modelling. Environmental Modelling & Software, 59:44–58
  18. ↑ Confalonieri R., Donatelli M., Bregaglio S., Tubiello F.N., Fernandes E. 2012. Agroecological Zones Simulator (AZS): A component based, open-access, transparent platform for climate change Crop productivity impact assessment in Latin America. In: International Environmental Modelling and Software Society (iEMSs), 2012 International Congress on Environmental Modelling and Software, Managing Resources of a Limited Planet, Sixth Biennial Meeting, Leipzig, Germany, R. Seppelt, A.A. Voinov, S. Lange, D. Bankamp (Eds.) PDF
  19. ↑ Bregaglio, S.; Donatelli, M.; Confalonieri, R. 2013. Fungal infections of rice, wheat, and grape in Europe in 2030-2050.Agronomy for Sustainable Development 33: 4,767-776
  20. ↑ Bregaglio, 2012. Definition and implementation of plant disease simulation models in interaction with crop models, Ph.D. Thesis, University of Milan PDF
  21. ↑ Bregaglio, S., Cappelli, G., Donatelli, M., 2012. Evaluating the suitability of a generic fungal infection model for pest risk assessment studies. Ecological Modelling 247, 58-63
  22. ↑ Bregaglio S., Donatelli M., Confalonieri R., Acutis M., Orlandini S., 2011. Multi metric evaluation of leaf wetness models for large-area application of plant disease models. Agricultural and Forest Meteorology, 151: 1163-1172.
  23. ↑ Bregaglio S., Donatelli M., Confalonieri R., Acutis M., Orlandini S., 2010. An integrated evaluation of thirteen modelling solutions for the generation of hourly values of air relative humidity. Theoretical and Applied Climatology 102:429-438
  24. ↑ Donatelli M., Bellocchi G., Habyarimana E., Bregaglio S., Baruth B., 2010. AirTemperature: Extensible Software Library to Generate Air Temperature Data, SRX Computer Science, vol. 2010
  25. ↑ Confalonieri R., Bellocchi G., Donatelli M., 2010. A software component to compute agro-meteorological indicators. Environmental Modelling & Software, 25:1485-1486
  26. ↑ Donatelli M., Bellocchi G., Habyarimana E., Confalonieri R., Micale F., 2009. An extensible model library for generating wind speed data. Computers and Electronics in Agriculture, 69:165-170
  27. ↑ Carlini L., Bellocchi G., Donatelli M., 2006. Rain, a software component to generate synthetic precipitation data. Agronomy Journal, 98: 1312-1317
  28. ↑ Donatelli M., Carlini L., Bellocchi G., 2006. A software component for estimating solar radiation. Environmental Modelling and Software 21, 3:411-416
  29. ↑ Donatelli M., Bellocchi G., Carlini L., 2006. Sharing knowledge via software components: models on reference evapotranspiration. European Journal of Agronomy 24, 2:186-192
  30. ↑ Acutis M., Donatelli M., Lanza Filippi G. 2008. PTF: an Extensible Component for Sharing and Using Knowledge on Pedo-Transfer Functions, International Congress on Environmental Modelling and Software. Proceedings of the iEMSs Fourth Biennial Meeting, Barcelona, Catalonia 7–10 July 2008: 759-765 PDF
  31. ↑ Cappelli, G., Bregaglio, S., Romani, M., Feccia, S., Confalonieri, R., 2014. A software component implementing a library of models for the simulation of pre-harvest rice grain quality. Computers and Electronics in Agriculture, 104, 18-24
  32. ↑ Donatelli M., Rizzoli A., 2008. A design for framework-independent model components of biophysical systems. International Congress on Environmental Modelling and Software, Proceedings of the iEMSs Fourth Biennial Meeting, Barcelona, Catalonia 7–10 July 2008: 727-734 PDF
  33. ↑ GNU Lesser General Public License
  34. ↑ Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
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