ARES
XML Generator

Environments

Specifications:
Rules:
  • ... rate of individuals of type ... present in this region will emigrate to region ... each ... hours
  • Each iteration, ... rate of host ... transfers ... percent of its bacterial organism to host ...
  • In this population there are always ... treatments of ... at the same time. Each treatment has a duration of 7 days with doses every 6 hours where each dose kills ... % of microbiomes the first hour and ... % the second hour.
  • The maximum capacity of this region is for ... individuals

Hosts

Rules:
  • During a treatment of antibiotic ..., ... % of intestinal bacteriums are lost
  • The maximum population size of a microbiome within this region is ... computational units of cells

Bacterial lineages

Specifications:
Rules:
  • Bacterial cell transfers plasmid ... with its resistance genes to other bacterial cell ... with frequency ....
  • Bacterial cells grow at a rate of ... (from 1.0 to 2.0)
  • Resistance gene ... inhibits antibiotic ...
  • The bacteria lose Plasmid/Resistance Gene ... at a rate of ...
  • The bacteria suffer a compensatory mutation at a rate of ... and compensate ...% of the cost of gen/plasmid ...
  • The bacteria suffer a compensatory mutation at a rate of ... and compensate ...% of the cost of plasmid (alone or carrying any gene) ...
  • The gaining of the Plasmid (alone or carrying any gene) ... reduces the ability of replication in this bacteria in a rate of ...
  • The gaining of the Plasmid/Resistance Gene ... reduces the ability of replication in this bacteria in a rate of ...
  • The gen/plasmid ... provides a ... % of resistance against the antibiotic ...
  • The maximum number of plasmid … per bacterial cell is …
  • The rate of mutation to obtain the gene ... in this bacterial type is ...

Request new rules/specifications

Fill this form if you want us to add a new rule or specification to the system. Administrators will study its validity and applicability and will notify when rule is implemented.

Before submitting, take a look at the rules and specifications at the left for getting familiar with its definitions and syntax. Please, be as specific and concrete as possible.

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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.



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