Released version of GUI (#5)
* The most recent version of ReactICS GUI. * Small fixes + folder structure update + help file included. * Added export to XML (for data sharing with GUI) * Released GUI version. * Automatic update of the reactants set panel + help content.
This commit was merged in pull request #5.
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Marcin Piątkowski
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reactics-gui/resources/help/index.html
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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="UTF-8">
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<title>ReactICS GUI Help</title>
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</head>
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<body>
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<hr>
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<center><a name="top"><h1>ReactICS - Distributed Reaction Systems Model Checker</h1></a></center>
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<hr>
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<p align="justify">
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<b>ReactICS</b> is a toolkit that allows for verification of Reaction Systems.
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The toolkit consists of two separate modules implementing:
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<ul>
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<li>Methods using binary decision diagrams (BDD)
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for storing and manipulating the state space of the verified system.</li>
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<li>Methods translating the verification problems into satisfiability modulo theories (SMT).</li>
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</ul>
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</p>
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<p align="justify">
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<b>ReactICS GUI</b> offers a graphical user interface allowing for editing the reaction system details
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and model checking using BDD module.
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</p>
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<p align="justify">
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More on <b>ReactICS</b> can be found at <a href="https://reactics.org">The Reactics Webpage</a>.
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</p>
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<br/>
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<hr/>
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<h2>Table of contents</h2>
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<ul>
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<li><a href="#reaction-systems">Reaction systems</a><br/></li>
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<li><a href="#gui">Application functions</a><br/></li>
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<li><a href="#rs-edit">Reaction system editor</a><br/></li>
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<li><a href="#ctx-edit">Context automaton editor</a><br/></li>
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<li><a href="#trs-view">Transition system viewer</a><br/></li>
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<li><a href="#model-checking">Model checking</a><br/></li>
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</ul>
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<br/>
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<hr/>
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<a name="reaction-systems"><h2>Reaction Systems</h2></a>
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<hr/>
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<p align="justify">
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<b>Reaction Systems</b> are a formalism inspired by the functioning of living cells.
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They allow for specifying and analysing computational processes in which reactions operate on sets of molecules.
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</p>
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<p align="justify">
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The behaviour of a reaction system is determined by the interactions of its reactions, which are based on
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the mechanisms of facilitation and inhibition.
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The formal treatment of reaction systems is qualitative and there is no direct representation of the number
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of molecules involved in reactions.
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</p>
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<p align="justify">
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A <b>Distributed Reaction System</b> is a computational model in which multiple autonomous processes (aka. agents)
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interact locally through rule-based reactions.
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Each agent operates independently (without any central controller—coordination),
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processing inputs and producing outputs based on predefined reactions,
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and their collective behavior leads to complex system dynamics.
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</p>
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<p align="justify">
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More on reaction system can be found at <a href="https://www.reactionsystems.org">The Reaction System Webpage</a>
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</p>
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<center><a href="#top">Back to top</a></center>
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<br/>
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<hr/>
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<a name="gui"><h2>Application functions</h2></a>
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<hr/>
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<p align="justify">
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<b>ReactICS GUI</b> allows to:
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<ul>
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<li>Edit the reaction system structure (the number of processes/agents, reactions for each process/agent, etc.)</li>
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<li>Edit the context automaton structure (adding/removing states and transitions,
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edit context for active processes/agents, setting guards for transitions, etc.). </li>
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<li>Preview of the state space represented as a transition system.</li>
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<li>Verification of properties defined by formulas using rsCTLK semantics.</li>
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<li>Save/load the reaction system structure to/from XML file.</li>
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<li>Export/import the reaction system to/from RSSL file.</li>
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<li>Export the reaction system structure and behaviour to ISPL file.</li>
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</ul>
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</p>
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<center><a href="#top">Back to top</a></center>
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<br/>
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<hr/>
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<a name="rs-edit"><h2>Distributed reaction system editor</h2></a>
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<hr/>
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<p align="justify">
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The structure of distributed reaction system can be edited using the following buttons from the distributed reaction system control panel:
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<center><img src="img/rs-ctrl-buttons.png"/></center>
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<ul>
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<li><b>New process</b> - Creates a new empty process.</li>
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<li><b>Remove</b> - Removes selected processes.</li>
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<li><b>Copy</b> - Makes copies of selected processes (together with all reactions).</li>
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<li><b>Rename</b> - Renames a selected process. Note that process names should be unique.</li>
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<li><b>Move up</b> - Moves selected process up the list of all processes.</li>
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<li><b>Move down</b> - Moves selected process down the list of all processes.</li>
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</ul>
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</p>
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<p align="justify">
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The details of a single process can be edited using the following buttons in the process panel:
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<center><img src="img/process-edit-button.png"/></center>
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<ul>
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<li><b>Add reaction</b> - Creates a new reaction. The details of the reaction should be specified in dialog shown below.</li>
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<li><b>Edit reaction</b> - Allows to edit the details of a selected reaction using dialog shown below.</li>
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<li><b>Remove reaction</b> - Removes a selected reaction.</li>
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</ul>
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</p>
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<center><img src="img/reaction-details.png"/></center>
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<p align="justify">
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Verification of formulas against a system specification is done after selecting desired formulas
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and clicking <b>Evaluate</b> button.
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The result of the verification (<b>True</b>/<b>False</b>), as well as time and memory used are presented next to each verified formula.
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</p>
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<center><img src="img/model-checking.png"/></center>
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<p align="justify">
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Clicking the <b>Reset</b> button resets the status of the model checking.
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Note that updating the reaction system specification (the list of processes, details of the reactions or the content automaton structure)
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the results of model checking, if any, are reset automatically.
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</p>
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<center><a href="#top">Back to top</a></center>
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<br/>
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<hr/>
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<a name="ctx-edit"><h2>Context automaton editor</h2></a>
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<hr/>
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<p align="justify">
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To create or edit the context automaton structure a proper edit mode should be set using the <b>edit mode panel</b>.
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</p>
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<br/>
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<center><img src="img/ctx-automaton-panel.png"/></center>
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<p align="justify">
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The type of the newly created object (state or edge) is set by checking the proper toggle button.
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With no button checked, one can transform the net by moving states around, etc.
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(see below for more details).
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</p>
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<br/>
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<h3>States</h3>
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<p align="justify">
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A new state is created by left-clicking the edit area (the main part of the component).
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As it is customary in automata theory, states are numbered separately starting from 1.
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The types of states are distinguished by shape and colour:
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the initial state is depicted as a square, all other states are depicted as circles.
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Moreover, hovering the mouse above a state allows to see its full description containing both
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its name and its (distinct) number.
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</p>
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<br/>
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<center><img src="img/ctx-automaton-state.png"/></center>
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<p align="justify">
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The details of a state can be edited by right-clicking the existing
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state and choosing the right option from the popup menu:
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<ul>
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<li><b>Set as initial</b> - Makes the selected state the initial state of the context automaton.</li>
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<li><b>Set label</b> - Allows to set the custom label for the selected state. Note that state labels have to be unique.</li>
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</ul>
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</p>
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<br/>
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<center><img src="img/ctx-automaton-state.png"/></center>
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<h3>Edges</h3>
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<p align="justify">
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A directed edge between two states is created by left-clicking both its endpoints in correct order.
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Each edge may contain several transitions, each of them defined by a <i>context</i> (additional entities
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provided for active processes/agents) and a <i>guard</i> (a condition required by the transition to execute).
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The list of transitions may be edited by right-clicking the existing
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edge and choosing the <b>Nondeterministic transitions</b> popup menu.
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</p>
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<center><img src="img/ctx-automaton-transition-edit.png"/></center>
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<p align="justify">
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Hovering the mouse above an edge allows to see the full list of transitions
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including context and guards.
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</p>
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<center><img src="img/ctx-automaton-edge-details.png"/></center>
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<br/>
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<h3>Removing context automaton elements</h3>
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<p align="justify">
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Switching the toggle button <b>Delete</b> on allows removing context automaton elements.
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Each left-clicked element is removed from the automaton grapn.
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Moreover, the entire context automaton graph may be deleted by clicking the <b>Clear</b> button.
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</p>
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<br/>
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<h3>Transforming the context automaton graph</h3>
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<p align="justify">
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Any state of the automaton may be picked and dragged around the edit area to obtain the desired graph shape.
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It is also possible to select multiple states and move them together at the same time.
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After <b>CTRL + left-click</b> on a particular state the entire automaton graph is shifted to be centered
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on the clicked state.
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Checking the <b>Lock relative nodes positions</b> checkbox locks the relative positions of the states.
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In that case, dragging a single state moves the entire automaton graph.
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Moreover, using mouse scroll the automaton graph view can be zoomed in and out.
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</p>
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<center><a href="#top">Back to top</a></center>
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<br/>
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<hr/>
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<a name="trs-view"><h2>Transition system viewer</h2></a>
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<hr/>
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<p align="justify">
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The component offers the visualisation of the transition system representing the state space of the reaction systems.
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The initial state is depicted as a square, all other states are depicted as circles.
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There is a directed edge connecting the state S<sub>i</sub> to the state S<sub>j</sub>
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if S<sub>f</sub> is reachable from S<sub>i</sub> by a single computation step of the reaction system.
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</p>
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<p align="justify">
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The component has two separate instances represented by two separate tabs in the application window.
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The first visualises the complete state space of the reaction system,
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where each state is represented by sets of entities possessed by each agent and the current context automaton state.
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The second visualises the compressed state space, where context automaton states are ignored
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(states are represented only by the sets of entities possessed by each agent).
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</p>
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<p align="justify">
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Computation is done by pressing <b>Update transition system</b> button.
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The reaction system structure should be loaded from the file or edited manually for the computation to be possible.
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</p>
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<p align="justify">
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Note that no matter in which component the <b>Update transition system</b> button
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is pressed, the transition system structure will be updated in both.
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</p>
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<p align="justify">
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Hovering the mouse above a state allows to see its full description: entities possessed by each process/agent
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and the context automaton state (not present in the case of the compressed graph).
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</p>
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<center><img src="img/ctx-automaton-edge-details.png"/></center>
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<br/>
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<h3>Transforming the transition system graph</h3>
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<p align="justify">
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Any state of the transition system may be picked and dragged around the edit area to obtain the desired graph shape.
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It is also possible to select multiple states and move them together at the same time.
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After <b>CTRL + left-click</b> on a particular state the entire transition system graph is shifted to be centered
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on the clicked state.
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Checking the <b>Lock relative nodes positions</b> checkbox locks the relative positions of the states.
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In that case, dragging a single state moves the entire transition system graph.
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Moreover, using mouse scroll the transition system graph view can be zoomed in and out.
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</p>
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<center><a href="#top">Back to top</a></center>
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<br/>
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<hr/>
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<a name="model-checking"><h2>Model checking</h2></a>
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<hr/>
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<p align="justify">
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Model checking is handled by the component at the bottom of the application window.
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The properties of the analysed system are expressed as formulas following <b>rsCTLK</b> syntax.
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</p>
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<p align="justify">
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The list of formulas may be modified using the following buttons:
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<ul>
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<li><b>Add formula</b> - Creates an empty formula. The details of the formula should be specified in dialog shown below.</li>
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<li><b>Edit formula</b> - Allows to edit the details of a selected formula using dialog shown below.</li>
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<li><b>Remove formulas</b> - Removes selected formulas.</li>
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</ul>
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</p>
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<center><img src="img/formula-details.png"/></center>
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<p align="justify">
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Verification of formulas against a system specification is done after selecting desired formulas
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and clicking <b>Evaluate</b> button.
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The result of the verification (<b>True</b>/<b>False</b>), as well as time and memory used are presented next to each verified formula.
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</p>
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<center><img src="img/model-checking.png"/></center>
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<p align="justify">
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Clicking the <b>Reset</b> button resets the status of the model checking.
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Note that updating the reaction system specification (the list of processes, details of the reactions or the content automaton structure)
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the results of model checking, if any, are reset automatically.
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</p>
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<center><a href="#top">Back to top</a></center>
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<br/>
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<br/>
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</body>
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</html>
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