EcoMata User Manual
Contents
1.2. the state whose q value is 1 0 and modify state s name or q value Once the q value is modified all the states are resorted immediately Attention add delete state or change state q value will affect fishing pressure s schema auto adaptive constraints and customized automaton queries batch in query panel It is strongly recommended to determine these qualitative states before edit the rest ecosystem To customize icon on the working panel click on Browse button choose a picture file If the file is a valid picture file it will be resized to 48x48 and displayed on the working panel Once you save current ecosystem model all the customized icons will also be saved To restore the default icon click on Default button 5 1 2 2 Species Model Library In Add Species Mode this panel shows all the species model in local library A species model has all the basic information such as biomass P B Q B and the qualitative states Click on Add button to add a species in the top left corner of the graphic editor Click X button to remove permanently a model from the library which can not be undone Use Import Species and Export Species in File menu to import export species models into from this local library To save one species in current ecosystem as a species model into the library switch to Move Mode click on a species icon and then click on Save button on the properties panel Attention all the species model must have different names An
3. EcoMata User Manual EcoMata User Manual Version 1 0 June 2010 Page 1 EcoMata User Manual Table of content 1 Introduction 2 Representation of trophic network 3 Installation and Starting Program 3 1 Installation 3 2 Starting Program 4 Menu 4 1 File Menu 4 2 Tool Menu 4 3 Option Menu 5 Editor 5 1 Graphic View 5 1 1 Tool Bar 5 1 2 Property Panel 5 2 Synthetic View 5 3 Automaton Editor 5 3 1 Schematized 5 3 2 Auto Adaptative 5 3 3 Custom 6 Generate Automaton 7 Query 7 1 About verifyta 7 2 Launch Queries 7 3 Use Batch 7 4 Text Query Result Format Page 2 EcoMata User Manual 1 Introduction EcoMata is designed for generate manipulate and verify qualitative models of marine trophic networks in order to provide information for fishing administration 2 Representation of trophic network In this application we use ecopath model to represent an ecosystem Species in the system has the following attributes Biomass Initial biomass of a species which will be considered as normal level P B Production Biomass ratio Q B Consumption Biomass ratio Qualitative states Represented by q B B Fishing pressures in the system has the following attributes F Basic capture rate Percentage of biomass captured Type Fishing schedule type Schematized Auto Adaptative or Customized Qualitative states Fishing force represented by q F F Disturbance in the system has the following attribut
4. Option Menu A pop up window appears when you click on Parameters menu Language Language setting Selecting Auto option leaves the program to detect the best language to use Three languages are actuelly supported English French and Simplified Chinese UPPAAL path This path indicates uppaal s launcher script file but not uppaal jar itself For Microsoft Windows users it is highly recommended to write a batch file You do not have to set this path if you do not wish to view automaton file in UPPAAL Verifyta path This path is very important for query since the model checking procedure depends entirely on it Attention UPPAAL provides executable files both for Windows and Linux Make sure that you have picked the right one Display Names Check this option to have species and external forces names displayed in graphic editor Display DC Check this option to have dc value on dc arrow displayed in graphic editor EcoSystem Background Species Background Pressure Background Disturbance Background Change background color of these elements Note 1 These settings are saved once you close the application 2 Color settings are local You will see different background color if you open your saved file on others computer 5 Editor We have two principal parts on the Network Editor tab one floatable tool bar on top of the panel and an editor area The editor area has three view tabs in which we can edit the ecosystem in di
5. anges of state according to time point To change state at a specified time point click on the corresponding black point Attention This is a linked action which means if you change state at one time point all the states of the following time point who have the same state will be changed to new state For example in the figure below any change at the time point 3 will change the following time point until time point 7 To make a periodic chronogram draw chronogram in the first period at the start position indicate the first period s start inclusive and end inclusive positions in two spinner click Duplicate button the period will be copies on the rest of the time points For example adjust start to 4 and end to 9 means duplicate a period of 6 time units from the 10 time unit Click on Reset button to restore the chronogram in its default initial state 5 3 2 Auto Adaptative This is a constraints editor It simulate the changes of state according to changes of other automatons This kind of automaton is passive If the depending automaton stay stable it will never evaluate Since the fishing pressure automatons are normally source of evaluation it is recommended that the Startup State should be other state than Normal In the table below pick the state you want the fishing pressure toggle to when the species state changes 5 3 3 Custom This section is designed for advanced users who know well timed automatons Here you can edi
6. e this species in the model library Fishing button In this mode click on any empty space in the working area to add a fishing pressure into current ecosystem model Disturbance button In this mode click on any empty space in the working area to add a natural disturbance into current ecosystem model Arrow button In this mode drag from any species icon and drop on another species icon or fishing icon or disturbance icon to create a consumption relation If the relation is valid and has been successfully added into ecosystem it will remain on the working area Note that the arrow points to biomass transformation direction LA Q Q Zoom buttons Click on these three buttons change zoom scale of graphic view The first button restore zoom to 1 1 the button zoom in by adding 0 1x until 2 0x and the button zoom out by subtracting 0 1x until 0 5x Page 6 EcoMata User Manual 5 1 2 Right Side Panel This panel shows Properties Panel in Move Mode hand button and shows local species model library in Add Species Mode fish button 5 1 2 1 Properties Panel In Move Mode click on any icon or arrow to show this panel We can edit any string numerical and enumerative property such as biomass P B Q B directly To edit the qualitative states click on the Edit button A dialog window will appear We can add up to 5 states by clicking on a button delete a state by clicking on the button except
7. ecosystem in another file name Import Species Export Species To share same species among ecosystems and to avoid input the same data we can use these two menus to import export species models into from local library See chapter 5 for more detail Export Query XML Save current query history in a structured XML file This is useful before regenerate automaton since the regeneration clears query history Export Query Text Save current query history in plain text file The export text format will be explained in Query section Exit Exit program 4 2 Tool Menu Generate Order manually a regeneration of automaton We do not quite need this command since every time we toggle to query panel we will be asked to confirm a regeneration if there is any change made in ecosystem Report Display automaton generation report A new window will pop up Basic characteristics and detail information will be displayed separately in two area Use Detail button to show hide detail information area Open Automaton Open last generated automaton in UPPAAL if UPPAAL s path is currently set Note that the opened automaton in UPPAAL is a copy of automaton file That s to say any change made in UPPAAL will be ignored If you would like to modify or create manually a fishing automaton please go to automaton editor Page 4 EcoMata User Manual Export Image Take a graphic snap shot of current ecosystem and save it in a png picture file 4 3
8. es Mortality Similar to F of fishing pressure Percentage of biomass s reduction Type How the disturbance happens Event to simulate a random event like volcanic eruption and programmed to simulate a periodic influence like global warming 3 Installation and Starting Program 3 1 Installation The software installer is usually a zip package No special install procedure is needed You can unzip the package and store anywhere you want Since the program is purely in Java the only difference between install packages is the JREs included in the package Make sure that you have downloaded the right version according to your system type Attention 32bits version does not work on 64bits system If you have already JDK or JRE installed on your system you can download the stand alone version But make sure that environment variable is correctly set JAVA HOME for Microsoft Windows and JAVAHOME for Linux based system 3 2 Starting Program Once you unzip the package find run_xx script in program folder Double click it and click launch on the pop up window for Linux If the system type is right an application window will appear 4 Menu Page 3 EcoMata User Manual 4 1 File Menu New Create an empty ecosystem model Load Load an existing ecosystem from disk Save Save current ecosystem customized icons if any automaton if generated query batch if any query history if any to disk Save As Save current
9. fferent way 5 1 Graphic View Here we edit the trophic network in graphic mode And only in this mode the buttons on the tool bar are activated Page 5 EcoMata User Manual 5 1 1 Tool Bar The selected button indicates current mouse action Hand button Click this button switches to move mode We can select drag delete element in the working area and edit elements properties on the right side panel Click on any icon or arrow to select it Drag a rectangular area to select multiple elements Drag the selected icons to move them to a new place and all arrows leaving from or pointing to these icons will be automatically adjusted To delete one or more element click to select them and press Delete key on keyboard When you select one and only one element in the system its properties are displayed at the right side panel When you click in the empty area in the working area ecosystem s properties will be displayed These properties are mainly relative to automaton generation Please refer to chapter 6 for more explanation ath Fish button In this mode click on any empty space in the working area to add a species into current ecosystem model The right side panel shows archived species models Drag one of them in the graphic panel to create an instance Click on cross button to remove it from the library In Move Mode click a species icon in graphic panel and click Save button in the property panel to add one sav
10. fied situation like always never reachable and Page 9 EcoMata User Manual which date query the situation composer is enabled Check the boxes to select states Select no state for one species means this species is not concerned in this query Select more than one state for one species means an OR relation between the selected states 7 2 2 Queries Always Vileness To test a situation is always verified during simulation time Never Security To test a situation will never happen during simulation time Reachable To test if a situation will happen at a specified time point WhichDate To test if a situation will happen If yes the first occurrence time point WhichStates Enumerate all possible situations at a specified time point Synthesis Carry out a synthesis analysis within simulation time The interval of time point is specified in ecosystem s properties 7 2 3 Use batch If you wish to launch several time consuming queries like which date query batch is a better choice To add a query to batch list select query type compose query states and select time point if necessary instead of click on Launch button click Add Batch button in the middle panel of the query window You will find a brief description of the query in the left bath list panel To change the queries order click the query which you would like move in the list window click Move Up or Move Down button to adjust its position in the l
11. is in Low state or in Danger state and species sp1 is in Normal state can happen as early as possible at time point 12 WhichStates Data type Integer Result type List lt Map lt String String gt gt Example Which State Query Time 10 Result lt sp0 Normal gt lt sp1 Normal gt lt sp2 Low gt lt sp0 Normal gt lt sp1 Low gt lt sp2 Low gt Meaning 2 situations can happen at time point 10 1 Species sp0 is in Normal state and species sp1 is in Normal state and species sp2 is in Low state 2 Species sp0 is in Normal state and species sp1 is in Low state and species sp2 is in Low state Synthesis Datal type Integer Data2 type Integer Result type Map lt String Map lt String List lt Integer gt gt gt Example Synthesis Time Limit 60 Time Unit 12 Result lt sp0 lt Danger 0 0 0 0 0 0 gt lt Low 0 1 2 2 2 2 gt lt Normal 1 1 2 2 2 2 gt lt High 0 0 1 1 1 0 gt gt lt spl lt Danger 0 0 1 1 1 0 gt lt Low 0 1 2 2 2 2 gt lt Normal 0 1 1 0 0 0 gt lt High 0 0 0 0 0 0 gt J gt Meaning Time Point 0 12 24 36 48 60 sp0 Page 12 EcoMata User Manual Danger 0 0 0 0 0 0 Low 0 1 2 2 2 2 Normal 1 1 2 2 2 2 High 0 0 1 1 1 0 sp1 Danger 0 0 1 1 1 0 Low 0 1 2 2 2 2 Normal 0 1 1 0 0 0 High 0 0 0 0 0 0 These numbers represent the occurrence number of each state at the specified time point Page 13
12. ist To remove a query from the list select it in the list window click on Remove button To clear the query list click Clear button That will remove every query from the list after your confirmation Finally click Launch button on the batch editor panel to launch the batch During the batch the pop up progress indicator is different from the one when you launch one query at a time Firstly a batch progress will indicate which query is in progress Secondly an extra Pass button is added Click on Pass button will abandon the current query and start the next one while click on Cancel button will stop entirely the batch process In batch mode neither pop up result dialog nor pop up error message dialog will be shown during the whole query processing All output will be appended in the result text panel The text output format will be explained in the next chapter Attention Page 10 EcoMata User Manual 1 No semantic verification is performed when you insert a query in batch list It will be done when the query is effectively launched 2 Every time you delete a species or edit any state information including add a state delete a state or modify state order of any species in the ecosystem it is strongly recommended to verify the query composition when you return to query panel because the information recorded in the query batch list can not be updated 7 2 4 Text Query Result Format Here we explain the text form query info
13. rmation format The primitive types like Integer Boolean and String are directly displayed The structured types like Map List and Set are displayed in the following format Map lt Key Value gt lt Key Value gt List Item Item Set Same as List Always Data type Map lt String Set lt String gt gt Result type Boolean Example Always Query States lt sp0 Normal High gt lt sp1 Normal gt Result true Meaning Species sp0 is always in either Normal state or High state and species sp1 is always in Normal state Never Data type Map lt String Set lt String gt gt Result type Boolean Example Never Query States lt sp0 Danger Low gt lt sp1 Danger gt Result true Meaning Species sp0 is never neither in Danger state nor in Low state and species sp1 is never in Danger state Reachable Datal type Map lt String Set lt String gt gt Data2 type Integer Result type Boolean Example Reachable Query States lt sp0 Normal Low gt lt sp1 Normal gt Time 10 Result true Meaning At time point 10 it is possible that species sp0 in Normal state or Low state and sp1 is in Normal state Page 11 EcoMata User Manual WhichDate Data type Map lt String Set lt String gt gt Result type Integer Example Which Date Query States lt sp0 Low Danger gt lt sp1 Normal gt Result 12 Meaning The situation that species sp0
14. s according to their similarity on invariant and guard value This value is limited between 6 and 24 Normally 12 is a good choice A larger value makes more precise query result but a slower query speed because of a larger amount of states A smaller value leads to loss of precise and either a faster speed or a slower speed due to the amount of regrouped transitions on one state After each generation the program evaluates the generated automaton According to its complexity a message will displayed to inform that the query process may be slow 7 Query On the query panel we can launch queries on current ecosystem 7 1 About verifyta Before launch any query make sure that you have downloaded UPPAAL and have verifyta program in its package This file is essential for query processing 7 2 Launch queries To launch a query select query type in the combo box compose one situation and or select the time point and click the Launch button next to the combo box A pop up progress indicator dialog will appear to show current progress of the query If you would like to abandon a query click Cancel button on the dialog When the query is correctly finished another pop up window will appear to display the query result And the query s information including selected states time point and the result will be appended in the result text panel on the bottom of the application window 7 2 1 Compose a situation To launch the queries which need a speci
15. t the automaton just almost like in UPPAAL Except that right click on the edge to add a nail and right click on a nail to remove it Attention 1 We memories always the last automaton generated for the fishing pressures That s means if you edit the automaton then change the automaton type to others than custom once you regenerate the hole ecosystem model all the changes you have made to Page 8 EcoMata User Manual automaton will be lost 2 Every time you delete a species or edit any state information including add a state delete a state or modify state order of any species or fishing pressure in the ecosystem it is strongly recommended to verify all the strings such as invariant on the states select guard sync and update on the transitions 6 Generate Automaton We have some more explanation for the properties of ecosystem which will make different effect to automaton generation Time limit This option means that the simulation is limited in how may time units Note that longer time limit will bring more states in automaton since some slow evaluation are ignored when the time limit is shorter than evaluation time In the time relative queries such as Reachable and Which State time point can be chosen only between 0 and time limit Synt Step This option will not change automaton generation but synthesis query Regroup Since there are too many transit state between main state in automaton we regroup these state
16. y import action import menu or save button will fail if any existing model in the library has the same name as the model to be added 5 2 Synthetic View Here we have a global synthetic view of every element in the ecosystem The entire panel is vertically divided into 5 zone Ecosystem s properties species fishing pressures disturbances and DC value table We can add delete species fishing pressure or disturbance in this panel except that everything added will be found at top left corner of the graphic view panel We can modify directly the properties even modify states In the DC table change one value from zero to non zero adds a relation between two element with specified DC value while change one value from non zero to zero deletes this relation The disabled box means a opposite relation exists already and it is impossible to add this relation Page 7 EcoMata User Manual 5 3 Automaton Editor In this panel we can edit fishing pressure s automaton type and also disturbance whose type is programmed Choose firstly the fishing pressure in the left combo box and then choose automaton type in the right combo box Different editor will appear according to the automaton type that you have chosen Attention when you change fishing pressure s state q value or carry out any change on fished species state it is strongly recommended to verify these automatons 5 3 1 Schematized This is a chronogram editor It simulate the ch
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