Learn the basics!

Understand Alchemist

A description of the entities that the simulator supports.

The world of Alchemist

The first step to take in order to use the simulator, is to answer the question

what does Alchemist simulate?

The model

The world of Alchemist is composed of the following entities:

  • Molecule
    • Name of a data item
    • If Alchemist were an imperative programming language, a molecule would have been the abstraction of variable name
  • Concentration
    • Value associated to a particular molecule
    • If Alchemist were an imperative programming language, a concentration would have been the abstraction of value associated to a variable
  • Node
    • Container of molecules
    • Container of reactions
    • Lives inside an environment
  • Environment
    • The environment is the Alchemist abstration for the space. It is a container for nodes, and it is able to tell:
      1. Where the nodes are in the space - i.e. their position
      2. How distant are two nodes
      3. Optionally, it may provide support for moving nodes
  • Linking rule
    • Is a function of the current status of the environment that associates to each node a neighborhood
  • Neighborhood
    • An entity composed by a node (centre) and a set of nodes (neighbors)
  • Reaction
    • Any event that can change the status of the environment is a reaction
    • Each node has a (possibly empty) set of reactions
    • It is composed of a (possibly empty) list of conditions, one or more actions, and a time distribution
    • The frequency at which it happens depends on:
      1. A static “rate” parameter
      2. The value of each condition
      3. A “rate equation”, that combines the static rate and the value of conditions, giving back an “instantaneous rate”
      4. A time distribution
  • Condition
    • A function that takes the current environment as input, and outputs a boolean and a number
    • If the condition does not hold (i.e. its current output is false), the reaction to which it is associated cannot run
    • The number in output may or may not influence the reaction speed (i.e. the average number of times the reaction “happens” every time unit), depending on the reaction and its time distribution.
  • Action
    • Models a change in the environment.

The following image is a pictorial view of such model:

Alchemist model

The behavior of the system is described in terms of reactions. As such, here it is a pictorial representation of a reaction:

Alchemist reaction

Incarnations

As you can see, names are given after classical chemistry terms. This is mostly for historical reasons: Alchemist has been initially conceived as chemical-oriented multi-compartment stochastic simulation engine, able to support compartment (node) mobility, still retaining high performance.

However, Alchemist is not limited to that. The key of its extensibility is in the very loose interpretation of molecule and concentration. Those two terms have a very precise definition in chemistry, but in Alchemist they are respectively

  1. a generic identifier, and
  2. a piece of data of some type

An incarnation of Alchemist includes a type definition of concentration, and possibly a set of specific conditions, actions and (rarely) environments and reactions that operate on such types. In other words, an incarnation is a concrete instance of the Alchemist meta-model. In addition, a proper Alchemist incarnation must also define:

  • A mean for translating strings into named-entities (molecules)
  • A mean for obtaining a number given a node, a molecule and and a string representing a property
  • A mean for building incarnation-specific model entities given an appropriate context and a parameter String

These functionalities are required in order to support a uniform access to different incarnations.

Different Incarnations can model completely different universes. For instance, if the concentration is defined as a positive integer and proper actions and conditions are provided, Alchemist becomes a stochastic simulator for chemistry featuring interconnected and mobile compartments.

The standalone distribution comes with:

More details on how to use each of the included incarnations will be provided after this introductory chapter.

The tool

The core part of the tool is the incarnation-agnostic simulation engine. Its current implementation is based on Gibson and Bruck’s Next Reaction, extended to support addition and removal of reactions, and improved using input and output contexts for reactions, in order to prune as much as possible the dependency graph. More details on that are demanded to this scientific paper on Journal of Simulation.

The engine’s entry point is the simulation. It is equipped with support for commands like play, pause and stop, and can be equipped with an output monitor. The output monitor can be a graphical interface, a logger, or any kind of environment inspector.

The tool also includes a graphical interface developed in Java Swing and a command line interface.

We suggest starting your journey into the Alchemist world by looking at the next tutorial page: how to write simulations.