A join-calculus-based programming language for exploring description, simulation, and visualization of biochemical systems modelled as concurrent, rate-limited processes.
tonyg/stoj
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
--------------------------------------------------------------------------- StoJ README --------------------------------------------------------------------------- StoJ is a polyadic, asynchronous stochastic pi calculus with input join and no summation. Rates are associated with a join, not with a channel. StoJ Copyright (c) 2004, 2005 LShift Ltd. Copyright (c) 2004, 2005, 2010 Tony Garnock-Jones Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Lexical structure: --------------------------------------------------------------------------- - comments start with // and extend to the end of the line - "new", "stop" and "rec" are keywords - float syntax is [0-9]+(\.[0-9]+)? - ints are just [0-9]+ - identifiers start with a letter and may contain letters, digits and underscores Syntax: --------------------------------------------------------------------------- process :== process_atom "|" process | process_atom process_atom :== "rec" id "." process_atom | "new" annotated_idlist "." process_atom | id (* a process variable reference *) | "stop" | id "<" idlist ">" | id "<" idlist ">" "*" int (* clone output *) | branch | "(" process ")" branch :== prefix (suffix)? prefix :== ID "(" idlist ")" "&" prefix (* join *) | ID "(" idlist ")" suffix :== "->" "[" float "]" process_atom | "->" process_atom idlist :== (* empty *) | idlist_nonempty idlist_nonempty :== id | id "," idlist_nonempty annotated_idlist :== ann_id | ann_id "," annotated_idlist ann_id :== "!" ID | ID --------------------------------------------------------------------------- "rec" binds a process variable. A naked identifier references a process variable. When using "new", prefixing a new channel name with "!" causes events on that channel to be logged to stdout as part of the program output. Use "!" to mark channels you wish to have timing and event data for. The "row limit" in the CGI interface places a limit on the number of logged data rows (time vs. per-channel counts) per run. Suffixing an output with "*" and a count, as in h<> * 50 causes a number of duplicates of the message to be placed atomically on the channel. In the example just above, 50 copies of <> would be placed on channel h, similar to: (h<> | h<> | ... ... ... | h<>) Annotating an input prefix with a rate, h() & cl() ->[0.03] (hcl<> | ...) causes that reaction to be processed via Gillespie's algorithm. Any unrated arrow proceeds at an infinite rate - as soon as the join to the left of the arrow is enabled, the comm takes place.
About
A join-calculus-based programming language for exploring description, simulation, and visualization of biochemical systems modelled as concurrent, rate-limited processes.
Resources
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published