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 perfecty formatted.
The optimal strategy for editing an XML file would be defing a scenario step-by-step guided by the system and, when finished, 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.
You can download any previously defined scenario in an XML format file in "Run" section by clicking on the "Download" button next to each scenario.
This XML file can be uploaded to the system for running and generating outputs as any regular scenario created in the system. Just upload file, select scenario, set number of iterations and click on "Run".
Optionally, you can provide an auxiliar file defining the magnitudes for each bacterial lineage following this format for recalculating its actual size in all output generated files. Available magnitudes are:
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.