Avida-ED User Manual
Contents
1. gt Save Images Export data to comma delimited file MENU File gt Export Analysis Drag full dish 7 Average Fitness vs Time updates anywhere into Analyze window 025 Graph of selected properties of population s Set color for each population gt l in a T 1 Set properties to Time updates e Population s Populations Variables graph and line name and x Update200 red i Average Fitness thick FA style None remove button 2 g 10 Avida ED Manual v 1 4 9 27 06 Robert T Pennock Glossary Avida Pronounced Aveeda From A life artificial life in Spanish vida life Avida is the evolutionary computation engine at the heart of Avida ED Avidian Pronounced Ah vid ian An organism in the Avida environment Death In Avida ED an Avidian will die of old age if it does not self replicate within a given number of instructions set here as 20 times its genome length It may die earlier if another Avidian divides and one of the daughter cells 1s placed by chance onto its spot on the grid overwriting it Fitness Metabolic rate divided by gestation time Holding the environment constant if organism X has twice the fitness of organism Y it means that it on average X will reproduce twice as fast as Y This fitness measure is objective in that it measures non relative things metabolic rate and gestation time It is important to realize that in terms of natural select2. 7 06 Robert T Pennock complex sequence of instructions to perform The simplest of these functions not takes a minimum of 6 instructions we think The most complex tasks exclusive_or equals take a minimum of 19 instructions we think The ability to perform a task multiplies the org s basic metabolic rate by the task s energetic value Metabolic Rate Each organism has a value called metabolic rate associated with it which indicates how fast the organism is able to execute instructions Metabolic rate is a unitless quantity merit and is only meaningful when compared to the merits of other organisms Thus if organism X has twice the merit of organism Y than X should execute twice as many instructions in any given time frame Therefore if the gestation times of X and Y are the same and X has twice the merit of Y then on average X will reproduce twice as fast as Y see also fitness SIP Single Instruction Processing unit A unit of energy in Avida Not yet explicit in Avida ED Time Avida time is internally constant and 1s measured in updates Avida standard time is not constant relative to real time a single update for a large population takes longer in real time than an update for a small population Update An update is the unit of time in Avida ED Avida time is internally constant but is not constant relative to real time a single update for a large population takes longer in r
3. Avida ED Manual v 1 4 9 27 06 Robert T Pennock Avida ED User Manual General Avida ED Workspace Viewer chooser Freezer A Viewer chooser buttons Switch between lab bench views Viewers BEE sian 7 Organism ae AE Analysis B Lab bench Three lab bench options 1 Population View Lab Bench Petri dish amp stats viewpanes iis example empty Ti Org Clicked on Report Population Statistics j Name Population Size Fitness Avg Fitness Metabolic Rate 7 Avg Metabolic Rate Gestation Avg Gestation Age updates Avg Age updates Ancestor Functions Times Performed Functions Orgs Performing Not Not Nan Nan And And Orn Orn Oro 0 Ant iji Ant Xor Nor Equ Xor Equ Average Fitness 0 6 f f 0 4 0 2 0 0 2 0 4 0 6 H TTT TT TTT TT Loe Ws rir TT 0 6 0 4 0 2 0 0 2 0 4 0 6 Time updates Average Fitness x Avida ED Manual v 1 4 9 27 06 Robert T Pennock 2 Organism View Lab Bench Genetiscope sis no instruction 3 Analysis View Lab Bench Data graphing amp analysis amp Drag A Full Petri Dish Into This Window To Analyze It 1000 5 800 T T T 7 T 400 600 Time updates Populations Variables Average Fitness None C The Freezer e Storage shelves for Empty Petri dishes environmental settings but no orgs Ful
4. S a E x f 7 z E m Metabolic Rate vI Mmtabolic Rate E m Gestati Evg CBstation B Age updates gvo Age updates l m ncesto B a z E f a LW 5 Functions Times Performe d unctigns Orgs Performing E E E Not Net L m L m a NM m m And E agf E Orn z LI m m Om Oro a m a M m m Ant E t E m Nor m i E Xor a Na E a E Equ xy a L ba L m a EW C C a C C a a n E munun eee Nass E meN E E E i F ipp EE 4 example empty eee ec ee eee ee E E 0 00 E E E 7 E E P Zoom 11 m m TT T TT ry Era ER rT alt 0 4 0 2 0 0 2 0 4 0 6 L m Time updates E a Average Fitness C BEB BBB BPR RP RRP Ree eee eee eee Environmental Settings Per Site Mutation Rate 2 0 World Size 30 x 30 cells Ancestral Organism s What resources are available in the environment strength of reward shown in parentheses E Moder Hard Very Hard Brutal x 2 x 4 x 8 x 16 x 32 v se v andose v orose v norose v equose v nanose v or v antose v xorose dish front Organism clicked on stats report Population statistics Population data graph m Flip to Petri Avida ED Manual v 1 4 9 27 06 Robert T Pennock Dish viewpane front Population 52 default empty eae Switch over to icon amp environmental name controls Petri dish grid Pull down menu to change what information 1s Colo
5. eal time than an update for a small population Update 1s defined as the passage of enough SIPS executions of single instructions such that each organism on average has executed 30 instructions however more fit organisms will most likely have executed more and les fit organisms will have executed less 175
6. ent chance that an instruction is incorrectly copied So if the per site mutation rate is 1 there 1s a 1 chance that when an instruction is copied it will end up as any one of the 26 possible instructions one of which is itself so it could mutate back to itself With a 1 per site mutation rate if 100 instructions are copied one of them will be mutated on average although this number could be higher or lower in any instance World size Sets the maximum number of Avidians that can exist in the population The two numbers specify the number of Avidians per row and per column So 10 x 10 a population of 100 organisms Ancestral seed organism s The organism s the population begins from Drag in or out additional organisms at the beginning of a run Environmental Resource Settings Avidians can receive extra energy if they evolve the ability to metabolize nutrients Here you can set what nutrients are available in the environment Exact Repeatability Many steps in an Avida evolutionary run happen randomly e g what mutations will occur in the genome into what cell a new organism will be placed Avida ED Manual v 1 4 9 27 06 Robert T Pennock at division so each run will be slightly different even with the same general environmental values as in nature This 1s the default setting However if you need to repeat a run e g for a demonstration you can switch this to exactly replicate the sequence with t
7. he same mutations and values Offspring placement When an offspring is born it can either be placed at random in any of the eight cells adjacent to its parent or anywhere at random in the population If the cell 1s already occupied the org there 1s overwritten Pause Run Manually Automatically If you set a specific number ahead of time the run will pause when this many updates have passed If you set the run to stop manually it will continue indefinitely until it is paused using the button under the Petri dish Freeze Petri Dish Button Push snowflake button to save either just the environmental configuration by saving an empty Petri dish or else the environment plus the organisms by saving a full Petri dish Avida ED Manual v 1 4 9 27 06 Robert T Pennock 2 Genetiscope Organism genome viewer Functionality Observe the genome of an individual organism Play a movie of the genome instructions operation Choose how much of the genetic machinery is visible Save viewer images Basic Controls Drag an organism from the freezer A progress bar will indicate that the organism 1s being readied for viewing Press play pause to start stop the movie of the genome s execution Use the scrub bar to move back and forth in the movie Press flip arrow button for the checkbox controls These toggle on off which components of the genetic machinery are shown Note Currently only the instr
8. ion the fitness of an organism must be compared to the organisms it competes with An organism with a fitness of 3 will have a selective advantage in a population where every other organism has a fitness of 1 whereas this same organism with a fitness of 3 will be at a selective disadvantage in a population where every other organism has a fitness of 10 Genome This is the genetic code of an Avidian It consists of a string list of instructions comprised of the instruction set Its biological analogy is an organism s DNA In Avida ED the size of the genome is fixed at a length of 50 instructions Gestation The number of instructions it takes for an organism to reproduce Instruction Set The genome of an Avidian is comprised of a series of simple computer instructions There are 26 instructions in the basic set Different instructions are symbolized by the lower case letters a through z and by different colored dots in the organism viewer Metabolic Functions Organisms may gain additional energy by evolving abilities to perform special metabolic functions or tasks These tasks are logic functions performed on either one or two 32 bit numbers The organism must manipulate these numbers with the instructions in its genome In Avida ED there are 9 functions that that may be evolved not nand and or not or and not neither or exclusive or equals All functions require some ee Avida ED Manual v 1 4 9 2
9. l Petri dishes fixed environment settings and frozen orgs Individual organisms removed from a Petri dish Freezer F Empty Petri Dishes default example no_mutations T PRF Full Petri Dishes example Update200 w amp Organisms ancestor Drag and drop freezer items to or from an open lab bench e Right click Ctrl click item in freezer to rename delete export or open it Avida ED Manual v 1 4 Robert T Pennock ll Lab Benches 1 Petri Dish Bench View Population amp environment settings Functionality Evolve a population in a Petri dish Click on an individual organism and observe its stats Observe whole population stats in real time Graph population stats in real time Basic Controls 9 27 06 Drag a Petri dish empty or full or one or more organisms into the Petri dish bench from the freezer to begin a new run Flip arrow button Switch between Petri dish front view and its environment settings Save images of populations in viewer MENU File gt Save Images Export data to comma delimited file MENU File gt Export Analysis See Pee eee 2 Be ip to m example empty Dish viewpane front Dish viewpane rear Environment settings POU PePeePePeeeeeeeeeeeeeee e 3 ime Updates 1 Fitness E BHHRHHEHEEG wOrg Clicked on Report BopulMion Statistics E E Settings m a z Name Populagion Size L a L E Fitness m S
10. n menu for property to Time updates graph Pull down property menu Pick the property of the population to graph in real time Options include Average Metabolic Rate Average Fitness Average Gestation Time and Number of Organisms in the population Vertical axis Units change depending upon property being graphed The scale dynamically changes during a run to accommodate the evolving population Time axis Time in updates since beginning of run of this population Avida ED Manual v 1 4 9 27 06 Robert T Pennock Environmental settings amp controls Flip to E F example Petri Dish Environmental Settings Per Site T ES Oriq S1Ze Mutation Rate Per Site Mutation Rate World Size control slider amp control e y 30 x 30 cells Ancestral Organism s a Ancestral seed ancestor organism s Offspring placement Place offspring O Near their parent gt Anywhere randomly setting Environmental What resources are available in the environment s strength of reward shown in parentheses resources settings Easy Moderate Hard Very Hard Brutal x 2 x 4 x 8 x 16 x 32 F notose F andose v orose v norose wv equose F nanose F ornose v antose F xorose Exact repeatability s Experimental D Repeatablity Mode O iraan a mani SSS control Pause Run i P Run Manually A setting didin Gs Freeze Petri dish button Freeze Petri Dish Per site mutation rate This rate reflects the perc
11. r scale being displayed legend Zoom level amp Update control Penah 199 _ Fitness gt Zoom 11 g Play Pause Freeze dish button D Population icon amp name Drag icon to freezer to save Flip arrow switch Go to environmental settings for this Petri dish Petri dish grid More or less is visible depending upon the size of the grid Use scroll bars and or zoom control if grid extends beyond window Color Scale Legend During a run the color scale will automatically adjust as numbers increase or decrease Scaling will appear in parentheses The spectrum will thus always show relative values but particular colors will represent different absolute values as a population evolves Special colors Black indicates an empty cell and white indicates a cell whose value is above the maximum portrayed on the scale as the scale readjusts to accommodate this new value it will be colored appropriately Update Avida internal time in number of updates since the beginning of a run Pull down menu Select a feature of the population to indicate by color Options Ancestor Metabolic Rate Fitness Gestation Time Genome Size Zoom Set the zoom level for the Petri dish Play pause button Starts and temporarily stops a run Freeze button Save the population and or environmental settings to the freezer Avida ED Manual v 1 4 Robert T Pennock Stats viewpanes Organism Clicked on Sta
12. tistics Report Org Clicked on Report Name aaalk E Fitness 0 50810 Metabolic Rate 94 0 Gestation 185 Age updates l Ancestor ancestor Functions Times Performed Not 0 Nan And Orn Oro Ant Nor Xor oO oo 020 202 OC KF Equ 9 27 06 Name Avida ED automatically assigns names to new varieties of Avidians as they evolve in a population The square s color matches the color of the selected Avidian in the current Petri dish grid Basic Statistics The following stats related to the selected organism are listed in real time Fitness Metabolic Rate Gestation instructions Age updates Functions list Metabolic functions listed in ascending order of complexity that the organism may have evolved the ability to perform If Times Performed is 0 the organism has not performed that function yet in this lifetime or never does Organisms get more energy SIPs if they perform more complex functions Population statistics Click buttons to highlight orgs in dish that have these phenotypes Same properties as above but data is for the population as a whole Population Statistics Population Size 366 Avg Fitness 0 35294 Avg Metabolic Rate 67 Avg Gestation 192 Avg Age updates 4 Functions Orgs Performing Not 151 ee 5 d Z gt O O 3 Sei 2iieiis coo oO ONO Avida ED Manual v 1 4 9 27 06 Robert T Pennock Population data graph Pull dow
13. uction head options are available 1 default workspace freezer ancestor organism mpe A Switch Over to O Q Settings e Prat can animation icon amp Mna 0 controls name S Ant 0 7 Xor 0 cc C c 0 cE Cy Shows movie of an org s genome A y oa lt Shows what the genome s instructions n E en u Wabaul ta Execule c c r h alloc y This instruction 0 Q E as it runs are doing E asaan woven co of no instruction SCceqpad Time line amp Play Pause ca FA Beginning Scrub bar Pa a Organism icon amp name Name of the organism whose genome is being viewed Flip arrow switch Go to animation settings for the genetic machinery Scrub bar Move forward or backward in the movie after it has rendered Play pause button Starts and temporarily stops movie Save images of orgs in viewer MENU File gt Save Images Avida ED Manual v 1 4 9 27 06 Robert T Pennock 3 Analyzer Lab Bench Data graphing amp analysis Functionality Graph one or two data sets from a population Analyze graphed data as a whole or close up in selected sections Basic Controls Drag full Petri dish s from the freezer onto the analyzer lab bench Use pull down menus to choose what information you wish to graph you can graph two things at once and the corresponding color for that information Click drag within the graph to show just that segment Save images of graphs MENU File
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