Sepro18

Sepro - Method for modeling and simulation. Inspired by biochemistry.

See Introduction slides

Requirements

• Swift 5.0

Dependencies:

• DotWriter - for generating Graphviz output.
• Swift Log - Swift logging
• Commander - Command line argument parsing

Build

swift build

Run examples

Command sepro MODEL STEPS runs the model for given number of steps and generates output into ./out/dots.

swift run sepro run Models/linker.sepro 10

Sepro Commands:

* `run` - run a simulation
* `shell` - interactive shell
* `symbols` - dump model symbols
* `version` - display version

Use --help to get more information about the commands.

Run command options:

  -o DIR            Output directory. Default: ./out
  -w WORLD          World name to initialize simlation. Default: main

Language Reference

Model is composed of model objects: actuators, structures and worlds. Each element of the model is identified by a symbol.

Symbol definition:

DEF TAG open
DEF TAG closed
DEF TAG hungry

DEF SLOT next
DEF SLOT site
DEF SLOT complement 

Actuators

There are two kinds of actuators: unary ACT and binary REACT. The unary actuator operates on a selection of objects matching the WHERE selector pattern. The symbols of type tag are tested against object's tags and symbols of type slot are tested against object's bindings. ! operator negates the presence - denotes absence of given symbol.

The selector is followed by list of transitions which have form IN subject transitions. In unary actuators the subject is THIS, in binary actuator the subject can be LEFT or RIGHT representing left side of the selector or right side of the selector respectively. The subject can be made indirect by adding indirection slot such as THIS.site or THIS.next.

Transitions can be:

• SET tag to set a tag.
• UNSET tag to unset a tag.
• BIND slot TO target to create a new binding.
• UNBIND slot to remove a binding.

In unary transition if the target for a binding is the same as the selected object then it is referred to as THIS. In binary binding we can't refer to the object of the same "hand" (by design), only to the object from the other hand which we call OTHER.

Unary actuators:

ACT move
    WHERE (crawler node.next)
    IN THIS
        BIND node TO node.next

ACT detach
    WHERE (crawler !node.next)
    IN THIS
        UNBIND node
        SET free


ACT bind_complement
    WHERE (polymerase init t_site.nucleotide c_site.nucleotide)
    IN THIS
        UNSET init
        SET shift

    IN THIS.t_site
        BIND complement TO c_site

Binary actuators:

REACT close_box
    WHERE (box open) ON (lid free)
    IN LEFT
        SET closed
        UNSET open
        BIND top TO OTHER
    IN RIGHT
        UNSET free

REACT r_origin
    WHERE (polymerase !t_site !c_site)
        ON (nucleotide origin)
    IN LEFT
        BIND t_site TO OTHER

Initial State

The initial state is described through structures and worlds. Structure is a simple graph definition with list of objects and bindings (edges). The object definition has form: OBJ name (tags). The scope object's name is only the structure the object is contained in. The binding has form BIND object.slot TO target_object. Only objects defined within the same structure can be used for the bindings.

Example structures:

STRUCT triangle
    OBJ a (node)
    OBJ b (node)
    OBJ c (node)
    BIND a.next TO b
    BIND b.next TO c
    BIND c.next TO a


STRUCT strand
    OBJ n1 (nucleotide G origin)
    OBJ n2 (nucleotide A)
    OBJ n3 (nucleotide T)
    OBJ n4 (nucleotide T)
    OBJ n5 (nucleotide A)
    OBJ n6 (nucleotide C)
    OBJ n7 (nucleotide A)
    BIND n1.next TO n2
    BIND n2.next TO n3
    BIND n3.next TO n4
    BIND n4.next TO n5
    BIND n5.next TO n6
    BIND n6.next TO n7

The initial state of a simulation is defined by world which can be though as "ingredients" of the simulated universe. The world items are specified as count (tags) for copies of free-standing objects and count structure_name for copies of a given structure.

Example world:

WORLD main
    3 (free nucleotide A)
    3 (free nucleotide C)
    3 (free nucleotide T)
    3 (free nucleotide G)
    1 strand
    1 (polymerase)

Data

Model can have (meta) data associated with it. The data is not relevant to the simulation itself, but might be used by the simulator or a visualisation component. The data has form: DATA (tags) "text". The tags are being used by the tools as a key either by chosing all items that contain particuliar tag or all items that match all the tags. One has to refer to the tool documentation to learn how the key is used.

Example data:

DATA (dot_style nucleotide) "rounded"
DATA (dot_color A) "salmon"
DATA (dot_color C) "slateblue"
DATA (dot_color T) "sandybrown"
DATA (dot_color G) "skyblue"
DATA (dot_style polymerase) "filled"
DATA (dot_fillcolor polymerase) "gold"

Author

Stefan Urbanek [email protected]

Thanks

Thanks to Ľubomir Sepro Lanátor.