User Manual
Contents
1. a shows patch X A yellow B blue C red and b shows patch Y A grey B red C green 122. BlenX is a very powerful and general software tool its input language is necessarily quite complicated and not easy to learn LIME is tailored toward ecosystem modeling and users with no background in programming can use it almost immediately Figure 1 illustrates the flow of data in this process The user is directly concerned only with the LIME source code the BlenX output files are processed by other programs in the BetaWB suite BlenX Output Files Figure 1 LIME and BlenX Data Flow The Appendix shows an example of the use of LIME and BlenX on a simple metacommunity model 2 Getting Started Before using LIME the user must install the BetaWB suite This package is available for free from the CoSBi website http www cosbi eu index php research prototypes beta wb LIME is also available from CoSBi http www cosbi eu index php prototypes lime The first step is to create the LIME source file which should be a plain text file Any basic text editor such as Notepad or Wordpad will suffice The next steps require the use of a command line interface This is a window that is available in all versions of the Windows operating system The user interacts with it by entering lines of text through the keyboard and reading output from programs on the monitor To open a command line interface the user clicks Start Run enters cmd in the text box that opens and clicks OK The command line interface opens and awaits a command from th
3. duration steps 1000 interactions BumbleBee pollinates DayLily with rates 1 and 2 BlueJay eats BumbleBee with rates 0 2 and 0 1 birth and death dynamics DayLily is born with rate 1 DayLily dies with rate 1 BumbleBee is born with rate 0 5 BumbleBee dies with rate 0 6 BlueBird is born with rate 0 1 BlueJay dies with rate 0 11 initial population 10 DayLily 100 BumbleBee 5 BlueJay When it is input to LIME an error message is produced BlueBird undeclared species in birth and death dynamics These species are not declared in the interactions part After BlueBird is changed to BlueJay in line 12 LIME can rerun the source file and this time it will successfully generate the prog and types files Next the model is augmented by specifying three patches duration steps 1000 interactions BumbleBee pollinates DayLily with rates 1 and 2 in CenterPatch BumbleBee pollinates DayLily with rates 1 and 2 in LeftPatch BumbleBee pollinates DayLily with rates 1 and 2 in RightPatch BlueJay s feeding rate is distributed over all patches BlueJay eats BumbleBee with rates 0 2 and 0 1 birth and death dynamics DayLily is born with rate 1 in CenterPatch DayLily dies with rate 1 in CenterPatch BumbleBee is born with rate 0 5 in CenterPatch BumbleBee dies with rate 0 6 in CenterPatch DayLily is born with rate 1 2 in LeftPatch DayLily dies with rate 1 in LeftPatch BumbleBee is born with rate 0 5 in RightPatch Bum
4. The Microsoft Research University of Trento Centre for Computational and Systems Biology Q oF N D1C 3001 311110 11010040 Language Interface 0110100107 for Modelling Ecol 01101101010 or Modelling Ecology CoSBiLab LIME User Manual Ozan Kahramano ullar Ferenc Jord n and James Lynch The Microsoft Research University of Trento Centre for Computational and Systems Biology Version 1 0 lime cosbi eu Date 24 06 2010 You may use copy reproduce and distribute this software for any non commercial purpose subject to the restrictions in CoSBi SSLA This software comes as is with no warranties This means no express implied or statutory warranty includ ing without limitation warranties of merchantability or fitness for a particular purpose any warranty against interference with your enjoyment of the software or any warranty of title or noninfringement There is no warranty that this soft ware will fulfilll any of your particular purposes or needs Also you must pass this disclaimer on whenever you distribute the software or derivative works LIME User s Guide 1 Introduction LIME is a software aid for individual based modeling of ecosystems It enables ecologists to describe ecosystem dynamics in a simple intuitive language which is then translated into a format readable by the BlenX simulator BlenX outputs some data files that can be used to analyze and visualize the results of the simulation Because
5. bleBee dies with rate 0 6 in RightPatch BlueJay s birth and death rates are distributed over all patches BlueJay is born with rate 0 1 BlueJay dies with rate 0 11 patch dynamics DayLily moves from CenterPatch to LeftPatch with rate 2 DayLily moves from LeftPatch to CenterPatch with rate 2 BumbleBee moves from CenterPatch to LeftPatch with rate BumbleBee moves from LeftPatch to CenterPatch with rate BlueJay moves from CenterPatch to LeftPatch with rate 0 BlueJay moves from LeftPatch to CenterPatch with rate 0 woorooO u initial population Only CenterPatch is initially occupied 10 DayLily in CenterPatch 100 BumbleBee in CenterPatch 5 BlueJay in CenterPatch When it is input to LIME the prog and types files are generated but because the patch named Rightpatch is isolated from the other patches warnings are generated Warning patch CenterPatch is isolated from the patches RightPatch Warning patch LeftPatch is isolated from the patches RightPatch Warning patch RightPatch is isolated from the patches CenterPatch LeftPatch Warnings are not necessarily errors but they inform the user of possibly unintended conse quences The patches can be connected by adding some commands to the patch dynamics section DayLily moves from CenterPatch to RightPatch with rate 2 0 DayLily moves from RightPatch to CenterPatch with rate 2 0 BumbleBee moves from CenterPatch to RightPatch with rate 1 0 BumbleBee moves from RightPatch t
6. e user The user may want to navigate to the folder containing the LIME source file by using the cd command It is also convenient to have a copy of the LIME program lime exe in the same folder To compile a LIME source file and produce the two BlenX files the user types lime followed by the name of the source file The convention is that whatever the name of the source file is the two BlenX files begin with the same name with the suffixes prog and types appended This is illustrated by the following example The first command cd lime files changes the active directory to lime files which is a folder containing a LIME source file named lotkavolterra The second command lime lotkavolterra produces the two files lotkavolterra prog and lotkavolterra types as indicated by the message output by the LIME program cx C WINDOWS system32 cmd exe Jo x C Documents and Settings gt cd lime files C Documents and Settings lime files gt lime lotkavolterra The files lt lotkavolterra prog gt and lt lotkavolterra types gt are generated C Documents and Settings lime files gt Figure 2 Invoking LIME Still using a command line interface the BlenX simulator sim exe is then invoked ev C WINDOWS system32 cmd exe 5 x C Documents and Settings gt cd lime files C Documents and Settings lime files gt lime lotkavolterra The files lt lotkavolterra prog gt and lt lotkavolterra types gt are generated C Documents and Settings
7. eclared in the interactions and the initial populations parts These two sets of species should be the same 2 Empty Patch undeclared patches in initial population These patches are not declared in the interactions part 3 There are two sentences for the plant pollinator interaction for the species A and B in patch P There are two sentences for the birth of the species A in patch P There are two sentences for the initial quantity of the species A in patch P There are two sentences for the movement of the species A from patch P to Q gt a he No interaction is specified Interactions cannot be empty 8 Species A are in the initial population but they are not declared in the interaction dynamics There is a mismatch between the species declared in the interactions and the initial populations parts These two sets of species should be the same 9 The identifier A is used to denote both a patch and a species The identifiers that describe patches and species should be different 5 Examples The following examples are not intended to be biologically significant rather they illustrate the process of developing a model by starting with a simple system and repeatedly correcting errors and adding more details The model has three species a plant daylily a pollinator of the plant bumblebee and a predator bluejay The first version has only one patch and an error
8. ed over all patches for that species 3 4 Patch Dynamics Section This section begins with a line that reads patch dynamics followed by commands that specify the migration rates These rates do not need to be the same in each direction A moves from P to Q with rate xx xx A moves from Q to P with rate yy yy 3 5 Initial Population Section Following a line that reads initial population are lines that specify the starting populations for each species nn A in P where nn is the initial population size of species in patch P 3 6 Comments Any line beginning with a double slash is a comment and has no effect on the specification of the model Comments have at least two uses First even though LIME code is not difficult to read there could be sections of code whose purpose is not obvious and comments could clarify them Second comments provide an easy way to temporarily delete commands without erasing them simply by inserting double backslashes at their beginning 4 Errors If there are syntactic errors in the source file then LIME cannot generate the BlenX input files Instead error messages are displayed on the monitor to help the user find and correct the errors Typical errors involve incomplete redundant or contradictory specifications as these examples show 1 Species A are in the initial population but they are not declared in the interaction dynamics There is a mismatch between the species d
9. egative real value In fact BlenX allows the rate to be 00 which means the change will occur instantaneously Instantaneous waiting times are not used in LIME More technically the waiting time until the change occurs is an exponential random variable whose parameter is the rate and consequently the reciprocal of the rate is the average waiting time until the change occurs If the rate of a particular change depends on the patch in which it occurs then there must be a LIME command specifying the rate for each patch But if the rate is the same for all patches one command which does not mention any patch suffices This feature is called distributivity and can be applied to any command in section two or three In addition if all the birth and death rates are 0 then section three can be omitted Similarly if there are no migrations between patches then section four can be omitted If no command in any section mentions a patch then the system has one unnamed patch 3 1 Duration Section This section consists of one line which describes the length of time that the simulation will run It has two forms duration time tt tt or duration steps nn In the first instance tt tt is a real number denoting the total running time of the simulated process In the second nn is the number of changes that the process undergoes before terminat ing 3 2 Interactions Section Following the keyword interactions are lines of text that specify the d
10. ep start B_Prog B Prog 1 let B Rep X bproc r BrRep_X ex Bex_X ey Bey_X rep start B Prog let BY bproc r Br_Y ex Bex_Y ey Bey_Y rep start B_Prog B_Prog let B_Rep_Y bproc r BrRep_Y ex Bex_Y ey Bey_Y rep start B Prog let C_X bproc r Cr_X ex Cex_X ey Cey_X rep start C_Prog C Prog 1 let C Rep X bproc r CrRep_X ex Cex_X ey Cey_X rep start C_Prog let C_Y bproc r Cr_Y ex Cex_Y ey Cey_Y rep start C_Prog C_Prog let C_Rep_Y bproc r CrRep_Y ex Cex_Y ey Cey_Y 10 rep start C_Prog when A_Rep_X inf split A_X A_X when A_Rep_Y inf split A_Y A_Y when B_Rep_X inf split B_X B_X when B_Rep_Y inf split B_Y B_Y when C_Rep_X inf split C_X C_X when C_Rep_Y inf split C_Y C_Y run 5 AX 5 B_X 15 CX SAY 5 BY 15 C_Y The translated TYPE file of the BlenX programme Ar X ArRep_X Aex_X Aey_X Ar_Y ArRep_Y Aex Y Aey_Y Br X BrRep X Bex X Bey X Br Y BrRep Y Bex_Y Bey Y Cr X CrRep X Cex X Cey X Cr Y CrRep Y Cex Y Cey Y hh Aex_X Cex_X 0 40 Aex_Y Cex_Y 0 40 Aey_X Cey_X 0 40 Aey_Y Cey_Y 0 40 Bex_X Cex_X 0 80 Bex_Y Cex_Y 0 80 Bey_X Cey_X 0 80 Bey Y Cey Y 0 80 11 b Figure 5 The population size of three species in two habitat patches during the simulation
11. g pproc if ex Aex_X then if ey Aey_X then if ex Aex_Y then if ey Aey_Y then if ex Aex_X then pproc if ex Bex_X then if ey Bey_X then if ex Bex_Y then if ey Bey_Y then if ex Bex_X then if ex Bex_Y then pproc if ex Cex_X then if ey Cey_X then if ex Cex_Y then if ey Cey_Y then if ex Cex_X then ex ey ex ey start endif ch r ArRep_X endif start endif ch r ArRep_Y endif delay 1 0 ch r Ar_Y ch ex Aex_Y ch ey Aey_Y start endif if ex Aex_Y then delay 1 0 ch r Ar_X ch ex Aex_X ch ey Aey_X start endif if ex Aex_X then die 0 00010 endif if ex Aex_Y then die 0 00010 endif ex ey O ex ey die 0 die 0 ex ey ex ey ch 10 die inf die inf die inf die inf start endif ch r BrRep_X endif start endif ch r BrRep_Y endif 00010 endif 00010 endif endif endif endif endif 0 r CrRep_X endif if ex Cex_Y then ch 10 0 r CrRep_Y endif let A_X bproc r Ar_X ex Aex_X ey Aey_X rep start A_Prog A_Prog let A_Rep_X bproc r ArRep_X ex Aex_X ey Aey_X rep start A Prog let A Y bproc r Ar_Y ex Aex_Y ey Aey_Y rep start A_Prog A Prog 1 let A Rep Y bproc r ArRep_Y ex Aex_Y ey Aey_Y rep start A Prog let B X bproc r Br_X ex Bex_X ey Bey_X r
12. lime files gt sim lotkavolterra prog lotkavolterra types BetaWB Simulator version 2 2BETA lt Win32 gt Simulation lotkavolterra prog spec lotkavolterra prog E out lotkavolterra prog C out lotkavolterra prog V out C Documents and Settings lime files gt Figure 3 Invoking the BlenX Simulator There are two versions of the simulator one for a 32 bit PC and one for a 64 bit PC The results of the simulator are saved in several output files which can then be analyzed with other programs in the BetaWB package For details see http www cosbi eu index php research prototypes beta wb 3 LIME Commands Command names and names of species cannot contain blank spaces and they are case sensitive This is also true of LIME source file names The LIME source file consists of five sections that specify the dynamics and spatial structure of the ecosystem Each section begins with a keyword that identifies the section The space of the system is organized into discrete regions called patches The second and third sections specify the dynamics within each patch and the fourth section describes migrations between patches The system is stochastic i e these changes are discrete events that occur unpredictably but with certain probabilities The rate of a change is a measure of how soon it is likely to occur The larger the rate is the sooner the change is likely to occur It is not a probability because it can be any nonn
13. o CenterPatch with rate 0 5 BlueJay moves from CenterPatch to RightPatch with rate 0 8 BlueJay moves from RightPatch to CenterPatch with rate 0 3 Appendix Example of LIME and BlenX Applied to a Model Ecosystem Figure 4 The simplistic metacommunity model with three species A B and C in two identical habitat patches X and Y A and B prey on C with rates 0 4 and 0 8 respectively Only species A migrates with rate m 1 Death rate for both A and B in both patches equals d 0 0001 while birth rate for C in both patches equals b 10 Initial population sizes are given by to equalling 5 for A and B whiletg equals 15 for C The user friendly LIME model specification to be translated into BlenX duration steps 2000 interactions A eats C with rates 0 4 and 0 4 in X B eats C with rates 0 8 and 0 8 in X A eats C with rates 0 4 and 0 4 in Y B eats C with rates 0 8 and 0 8 in Y birth and death dynamics A dies with rate 0 0001 in X B dies with rate 0 0001 in X C is born with rate 10 in X A dies with rate B dies with rate 0 0001 in Y 0 0001 in Y C is born with rate 10 in Y patch dynamics A moves from X to Y with rate 1 0 A moves from Y to X with rate 1 0 initial population 5 A in X 5 B in X 15 C in X 5 Ain Y 5 B in Y 15 C in Y The translated PROG file of the BlenX programme steps 2000 lt lt BASERATE inf gt gt let A_Prog let B_Prog let C_Pro
14. ynamics of the food web and other interactions between pairs of individuals There are four types of interactions illustrated by these examples A eats B with rates xx xx and yy yy in P Here A and B are predator and prey respectively and P is the name of a patch There are two possible outcomes of a predation event either A simply kills B with rate xx xx or A kills B and reproduces with rate yy yy A facilitates B with rate xx xx in P Within patch P A has a beneficial effect on B causing B to reproduce with rate xx xx Omitting in P distributes the rate over all patches A and B compete with rate xx xx in P Within patch P A and B are mutually antagonistic and both individuals will die as the result of an interaction Omitting in P distributes the rate over all patches A pollinates B with rates xx xx and yy yy in P Within patch P pollination of B by A causes A to reproduce with rate xx xx and B to reproduce with rate yy yy Omitting in P distributes the rate over all patches In any of these commands the phrase in P can be omitted meaning that the rate is distributed throughout all patches 3 3 Birth and Death Dynamics Section The first line reads birth and death dynamics The succeeding lines of text specify the birth and death rates of the various species in each patch A is born with rate xx xx in P A dies with rate xx xx in P Again if the patch is not specified then the birth and or death rates are distribut
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