XML Generator


When ARES executes a simulation, the following set of files is generated:

  • SCENARIO.xml file which contains the SIMULATION in XML format. This file contains the SIMULATION structure, configuration, specification and rules built from the user's SIMULATION definition. Although this XML can be edited, it is not recommended as XML is a hard to manipulate format.

  • magnitudes.csv is a comma-separated values file that consists in a table that reflects the magnitude of each bacterial lineage type defined in current SCENARIO.

  • SCENARIO.csv file is a comma-separated values file that represents the count of each element(membranes and objects) in each iteration. Thus, it contains as many rows as the number or iterations set on running the SIMULATION's SCENARIO.
    The first row defines the element that is being tracked with the following notation ELEMENT(HIERARCHY). An example would be a column labeled as "A1(B1-H1-P1-ECO)" where we track the count of A1 substance located inside B1 bacterial lineage cells of H1 host that inhabits P1 environment of SIMULATION named ECO.
    The second row defines the initial configuration of the SIMULATION previous to its execution.
    Following rows represent the SIMULATION configuration in each iteration steps.

  • A set of csv files derived from SCENARIO.csv which groups element counts by membrane levels.
    While SCENARIO.csv tracks the counts of the whole SIMULATION, which can be hard to manipulate specially in complex SIMULATIONs, we can also find subsets representing environment level (P-like.csv), reservoir level (RS-like.csv), host level (H-like.csv) and bacterial lineage level (B-like.csv) files.

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:

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.

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