ARES
Antibiotic Resistance Evolution Simulator

P-membranes

Specifications:
  • The activity of antibiotic/biocide ... lasts ... days|weeks|months|years
  • The maximum capacity of this region is for ... individuals
  • The maximum population size of a microbiome within this region is ... computational units of cells.
Rules:
  • Counter clock ... cleans this region every day and the material cleaned is removed
  • Counter clock ... introduces ... milligrams|micrograms of antibiotic ... per day in hosts type ... per day.
  • Counter clock ... releases ... milliliters/milligrams of biocide ... per day in this region
  • Individuals of type ... present in this region emigrate to region ... at a rate of ...
  • Individuals of type ... transmit his microbiome to other individuals of type ... at a rate ...
  • This region transfers its content in B-like membranes and objects to region ... (it can either be RS or H) at a rate ...
  • When this region reaches its maximum capacity for individuals/objects ... it dows not allow new individuals/objects to stay in and/or expulses the excess

Reservoir-rules

Specifications:
  • The activity of antibiotic/biocide ... lasts ... days|weeks|months|years
  • The maximum bacterial cells capacity of this region is ... per milligram of food|milliliter of water
  • The maximum population size of a microbiome within this region is ... computational units of cells.
Rules:
  • ... micrograms of substance ... kills bacterium gram negative/positive
  • Counter clock ... adds ... micrograms/milligrams of substance ... per day in this water/food supplier
  • Counter clock ... cleans this RS region every day and the material cleaned is removed
  • Counter clock ... creates ... milligrams/kilograms of food per day in this RS region
  • Counter clock ... creates ... milliliters/liters of water per day in this RS region
  • This region contaminates region ... (it can be either P or RS) with ...% of its content in B-like membranes and objects every ... days/weeks/months/years
  • When an individual of type ... eats/drinks in this region the later transfers to him its content in B-like membranes and objects according to the concentration of items in region and the food/water he eats/drinks
  • Within this RS region, substance ... enters bacterial cells at a rate of ... micrograms/milligrams

H-rules

Specifications:
  • In the starting configuration indiviuals of this type are aged ... days|weeks|months|years old
  • The activity of antibiotic/biocide ... lasts ... days|weeks|months|years
  • The life expectancy of individuals of this type is ... days|weeks|months|years
  • The maximum population size of a microbiome within this region is ... computational units of cells
  • The rate of birth among the population of this individual type is ...
  • When individuals of this type become food they correspond to ... milligrams|kilograms of food
Rules:
  • ... milliliters/milligrams of biocide ... kills individual
  • Each individual drinks ... milliliters/liters of water per day
  • Each individual eats ... grams/kilograms of food per day
  • Faecal droppings of these individuals become food (that already includes its microbial content) for individuals of type ... (and then go to RS region ...)
  • If individual dies it becomes food (that already contain the whole microbiome) for other ... individuals (and then go to RS region ...)
  • If Individual does not drink the amount of water established per day, the individual dies because of dehydratation after ... days/weeks/months
  • If individual does not eat the amount of food established per day, he dies by starvation after ... days/weeks/months
  • If the number of bacterial cells of lineage ... is greater/lower than ... cells then the host dies
  • Individual releases its microbiome to the environment with rate ...
  • Individual transmits its microbiome to other individual of type ... at a rate ...
  • Individuals predate/collect individuals/objects ... with a probability of ...
  • Substance ... enters/leaves individual at a rate of ... milligrams/day
  • The rate of birth among the population of individuals is ...
  • When individual eats regularly he releases ... milligrams/grams/kilograms of faecal droppings that go to the environment together with ...% of its microflora, selected randomly
  • Within individuals, substance ... enters in a bacterial cell at a rate of ...

B-rules

Specifications:
  • ... micrograms of substance ... kills gram negative/positive bacterial cell
  • Bacterial cell members of the same/different genetic exchange community conjugate with a frequency of ...
  • Bacterial cell transfers plasmid ... with its resistance genes to other bacterial cell ... with frequency ....
  • Bacterial cells express substance ... at a rate ...
  • Bacterial cells grow at a rate (from 1.0 to 2.0)
  • Bacterial genomes lose resistance gene ... at a rate ...
  • Plasmids ... are naturally degraded at a rate ...
  • Plasmids ... lose resistance gene ... at a rate ...
  • Plasmids ... transfer resistance gene ... to other plasmids ... at a rate ...
  • Plasmids ... transfer resistance gene ... to the bacterial genome at a rate ... and vice versa
  • Resistance gene ... inhibits antibiotic ...
Rules:
  • ... micrograms of substance ... kills gram negative/positive bacterial cell
  • Bacterial cell members of the same/different genetic exchange community conjugate with a frequency of ...
  • Bacterial cell transfers plasmid ... with its resistance genes to other bacterial cell ... with frequency ....
  • Bacterial cells express substance ... at a rate ...
  • Bacterial cells grow at a rate (from 1.0 to 2.0)
  • Bacterial genomes lose resistance gene ... at a rate ...
  • Plasmids ... are naturally degraded at a rate ...
  • Plasmids ... lose resistance gene ... at a rate ...
  • Plasmids ... transfer resistance gene ... to other plasmids ... at a rate ...
  • Plasmids ... transfer resistance gene ... to the bacterial genome at a rate ... and vice versa
  • Resistance gene ... inhibits antibiotic ...

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:
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.