Scenarios can be defined in an XML format file which defines the alphabet, configuration
and membrane structure. XML format is an ideal for representing nested entities such as
membranes and compartments. However, XML format can be really hard to read so it is
not recommended its manipulation as the system requires the file to be perfectly formatted.
The optimal strategy for editing an XML file would be defining a scenario step-by- step guided by the system of interfaces. This procedure will automatically create your scenario.
If desired, you can download and edit it in an text editor with XML validation capabilities. Once edited, we can upload resulting file with other name. Be really careful as manipulating rules in an XML file can produce a very unpredictable behaviour if your are not used with the simulator's workflow.
In order to run your scenario, please, download zipped-ARES simulator here and follow the instructions placed on it
Please, note that XML scenarios has 2 XML, both required in order to work and compressed in a zip. If you want to check an example of this kind of files you can download it here.
Citing ARES (actual version):
Marcelino Campos, Rafael Capilla, Carlos Llorens, Rafael Canton, Andres Moya, Jose-Maria Sempere, Teresa Coque, Val Fernandez-Lanza, Fernando Naya, Ricardo Futami, Fernando Baquero
Multi-Hierarchical Dynamics of Antimicrobial Resistance Simulated in a Nested Membrane Computing Model
bioRxiv 306100; doi: https://doi.org/10.1101/306100
Citing ARES (former version):
Marcelino Campos, Carlos Llorens, José M. Sempere, Ricardo Futami, Irene Rodriguez, Purificación Carrasco, Rafael Capilla, Amparo Latorre, Teresa M. Coque, Andres Moya and Fernando Baquero.
2015. A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES).
Biology Direct 2015, 10:41.