OntoAvida: ontology for Avida digital evolution platform.

A CPU cycle is the amount of time it takes the virtual CPU of a digital organism in Avida to execute a single instruction code in its memory.

The instruction code 'Divide-Erase' is an instruction code of the transsmt instruction set that attempts to divide off a finished offspring copy. It uses whatever memory space the write-head is currently pointing to as the offspring's genome. If this instruction code fails, the memory space is cleared and the organism's heads are reset. Note that this instruction code is equivalent to the instruction code 'h-divide' of the heads_default instruction set.

The instruction code 'Head-Move' is an instruction code of the transsmt instruction set that will cause the instruction pointer ?IP? to jump to the position in memory of the flow-head. This instruction code can be modified by one 'Nop' instruction code, which specify which head to move to the position pointed to by the flow-head. Note that this instruction code is equivalent to the 'mov-head' instruction code of the heads_default instruction set.

The instruction code 'Head-Pop' is an instruction code of the transsmt instruction set that pops a position of the ?B? stack and moves the instruction pointer ?IP? to that position. This instruction code can be modified by one or two 'Nop' instruction codes, which specify which stacks are compared. The first 'Nop' instruction code specifies which head (read-head, write-head, flow-head, or instruction pointer) is used, and the second 'Nop' instruction code specifies from which stack the position is popped.

The instruction code 'Head-Push' is an instruction code of the transsmt instruction set that pushes the position of the instruction pointer ?IP? onto the ?B? stack. Note that this instruction code differs from the instruction code 'Inst-Read' in that it pushes the location of the specified head rather than the value at that position. This instruction code can be modified by one or two 'Nop' instruction codes, which specify which stacks are compared. The first 'Nop' instruction code specifies which head (read-head, write-head, flow-head, or instruction pointer) is used, and the second 'Nop' instruction code specifies on which stack the position is pushed.

The instruction code 'IO' is an instruction code of the transsmt instruction set that outputs the 32-bit binary number stored at the top of the ?B? stack, checking it for any logic operation that may have been performed on the two 32-bit binary numbers stored in its input buffers. It also places a randomly generated 32-bit binary number from the environment onto the ?B? stack. Input-output instruction codes can be executed either only once or many times during the time it takes to generate an offspring. This means that a digital organism can take input numbers from the environment more than once before replicating and can compute the result of more than one logic operation. This instruction code can be modified by one or two 'Nop' instruction codes. The first 'Nop' instruction code specifies the input stack, and the second 'Nop' instruction code specifies the output stack. If only one 'Nop' instruction code is used, the same stack is used for both the input and output values. Note that the 'input-output' instruction code of the heads_default instruction set can only be modified by one 'nop' instruction code (i.e., the same register is used for both the input and output values).

The instruction code 'If-Equal' is an instruction code of the transsmt instruction set that compares the value on the top of the ?A? stack to the value on the top of the ?B? stack. If they are equal, the next instruction code (after a modifying 'Nop' instruction code, if one is present) is executed. If they are not equal, that next instruction code is skipped. This instruction code can be modified by one or two 'Nop' instruction codes, which specify which stacks are compared.

The instruction code 'If-Greater' is an instruction code of the transsmt instruction set that compares the value on the top of the ?A? stack to the value on the top of the ?B? stack. If the value of the ?A? stack is greater that the value of the ?B? stack, the next instruction code (after a modifying Nop' instruction code, if one is present) is executed, otherwise it will be skipped. This instruction code can be modified by one or two 'Nop' instruction codes, which specify which stacks are compared.

The instruction code 'If-Less' is an instruction code of the transsmt instruction set that compares the value on the top of the ?A? stack to the value on the top of the ?B? stack. If the value of the ?A? stack is less that the value of the ?B? stack, the next instruction code (after a modifying 'Nop' instruction code, if one is present) is executed, otherwise it will be skipped. This instruction code can be modified by one or two 'Nop' instruction codes, which specify which stacks are compared.

The instruction code 'If-Not-Equal' is an instruction code of the transsmt instruction set that compares the value on the top of the ?A? stack to the value on the top of the ?B? stack. If they are not equal, the next instruction (after a modifying 'Nop' instruction code, if one is present) is executed. If they are equal, that next instruction code is skipped. This instruction code can be modified by one or two 'Nop' instruction codes, which specify which stacks are compared.

The instruction code 'Inject' is an instruction code of the transsmt instruction set that acts similarly to the instruction code 'Divide-Erase', but instead of dividing off a "free-living" organism, it attempts to "infect" a host digital organism with its parasite genome contained in the memory space pointed to by the write-head. This instruction code allows a digital organism to become a parasite digital organism.

The instruction code 'Inst-Read' is an instruction code of the transsmt instruction set that pushes the instruction code pointed ?IP? to by the read-head onto the ?A? stack and advances the read-head by one position. This instruction code can be modified by one or two 'Nop' instruction codes. The first 'Nop' instruction code specifies which head (read-head, write-head, flow-head, or instruction pointer) is used, and the second 'Nop' instruction code specifies on which stack the instruction pointer is pushed.

The instruction code 'Inst-Write' is an instruction code of the transsmt instruction set that pops the instruction code on the ?A? stack and writes it into the memory location pointed to by the write-head ?WH?, and and advances the write-head ?WH? by one position. This instruction code can be modified by one or two 'Nop' instruction codes. The first 'Nop' instruction code specifies which head (read-head, write-head, flow-head, or instruction pointer) is used, and the second 'Nop' instruction code specifies from which stack the instruction is read.

The instruction code 'Nop' is an instruction code of the transsmt instruction set that does nothing or modifies the behavior of the instruction code preceeding it by changing the virtual CPU component that it affects (stack or head), or acts as part of a template to denote positions in a digital organism's genome. Note that most operations that use 2 'Nop' instruction codes to specify which stacks to use can also be parameterized by a single 'Nop' instruction code, in which case the second modifier is assigned the next stack in sequence (e.g., C->D, D->A, etc.).

The instruction code 'Nop-A' is an instruction code of the transsmt instruction set that does nothing or modifies the stack being used by default to the stack A or the head being used by default to the instruction pointer.

The instruction code 'Nop-B' is aninstruction code of the transsmt instruction set that does nothing or modifies the stack being used by default to the stack B or the head being used by default to the read-head.

The instruction code 'Nop-C' is an instruction code of the transsmt instruction set that does nothing or modifies the stack being used by default to the stack C or the head being used by default to the write-head.

The instruction code 'Nop-D' is an instruction code of the transsmt instruction set that does nothing or modifies the stack being used by default to the stack D or the head being used by default to the flow-head.

The instruction code 'Push-Comp' is an instruction code of the transsmt instruction set that pops a value off of the ?B? stack and pushes it onto the complement stack (i.e., the stack two over in sequence), in this case, the ?D? stack. This instruction code can be modified by one or two 'Nop' instruction codes, which specify the source and the destination stacks, respectively.

The instruction code 'Push-Next' is an instruction code of the transsmt instruction set that pops a value off of the ?A? stack and pushes it onto the next stack in sequence (the ?B? stack). This instruction code can be modified by one or two 'Nop' instruction codes, which specify the source and the destination stacks, respectively.

The instruction code 'Push-Prev' is an instruction code of the transsmt instruction set that pops a value off of the ?B? stack and pushes it onto the previous stack in sequence (the ?A? stack). This instruction code can be modified by one or two 'Nop' instruction codes, which specify the source and the destination stacks, respectively.

The instruction code 'Search' is an instruction code of the transsmt instruction set that reads in the sequence of 'Nop' instruction codes that follows it, and searches for the location of a complement template (e.g., B:C:D -> D:A:B) in a digital organism's genome. If the complement is not found, a value of 0 will be pushed to the top of the B stack. If a complement is found, the distance between the current instruction code being executed and the beginning of the complement will be pushed onto the B stack, the size of the template will be pushed on the A stack, and the flow-head will be moved to the end of the complement template.

The instruction code 'SetMemory' is an instruction code of the transsmt instruction set that selects which memory space is active (I.e., which memory space the flow-head is pointing to). The memory spaces can be labeled with up to 4 'Nop' instruction codes. If no 'Nop' instruction codes are given, the memory space containing the currently executing digital organism is selected. If a 'Nop' instruction code is provided that does not yet exist, a new memory space is created.

The TransSMT hardware is the hardware type that allows host-parasite interactions to take place in Avida.

The instruction code 'Val-Add' is an instruction code of the transsmt instruction set that pushes the sum of values from the top of the ?B? and ?C? stacks onto the B stack. This instruction code can be modified by one or two 'Nop' instruction codes, which specify which stacks are added.

The instruction code 'Val-Copy' is an instruction code of the transsmt instruction set that pushes a copy of the value at the top of the ?B? stack onto the ?B? stack. This instruction code can be modified by one or two 'Nop' instruction codes, which specify the source and the destination stacks, respectively. In this case, if only one 'Nop' instruction code is used, the value is copied and pushed onto the same stack as the source.

The instruction code 'Val-Dec' is an instruction code of the transsmt instruction set that decrements the value at the top of ?B? stack by one. This instruction code is destructive (I.e., it pops the old value off the stack).

The instruction code 'Val-Delete' is an instruction code of the transsmt instruction set that pops off a value from the ?B? stack. This instruction code may be modified by one 'Nop' instruction code, which determines from which stack to remove a value.

The instruction code 'Val-Div' is an instruction code of the transsmt instruction set that pushes the result of the integer division of the value from the top of the ?B? stack by the value at the top of the ?C? stak onto the B stack. This instruction code can be modified by one or two 'Nop' instruction codes, which specify which stacks are divided. If there is an arithmetic error caused by the division, the instruction code fails and does not return a value.

The instruction code 'Val-Inc' is an instruction code of the transsmt instruction set that increments the value at the top of ?B? stack by one. This instruction code is destructive (i.e., it pops the old value off the stack).

The instruction code 'Val-Mod' is an instruction code of the transsmt instruction set that pushes the remainder from integer division between the value from the top of the ?B? stack by the value at the top of the ?C? stak onto the B stack. This instruction code can be modified by one or two 'Nop' instruction codes, which specify which stacks are divided. If there is an arithmetic error caused by the division, the instructioncode fails and does not return a value.

The instruction code 'Val-Mult' is an instruction code of the transsmt instruction set that pushes the result of multiplying the values from the top of the ?B? and ?C? staks onto the B stack. This instruction code can be modified by one or two 'Nop' instructions, which specify which stacks are multiplied.

The instruction code 'Val-Nand' is an instruction code of the transsmt instruction set that computes the bitwise NAND logic operation on the values at the top of the ?B? and ?C? stacks. The result of this operation is pushed onto the top of the B stack. This instruction code can be modified by one or two 'Nop' instruction codes, which specify which stacks are used for computing the logic operation. Note that this is the only logic operation provided by the instruction set.

The instruction code 'Val-Shift-L' is an instruction code of the transsmt instruction set that shifts the value at the top of the ?B? stack over one bit to the left, effectively multiplying the value by two and ignoring any potential overflow. This instruction code can be modified by one 'Nop' instruction code, which specifies which stack is used.

The instruction code 'Val-Shift-R' is an instruction code of the transsmt instruction set that shifts the value at the top of the ?B? stack over one bit to the right, effectively dividing the value by two and rounding down. This instruction code can be modified by one 'Nop' instruction code, which specifies which stack is used.

The instruction code 'Val-Sub' is an instruction code of the transsmt instruction set that pushes the result of substracting the values from the top of the ?B? and ?C? stacks onto the B stack. This instruction code can be modified by one or two 'Nop' instruction codes, which specify which stacks are substracted.

The instruction code 'add' is an instruction code of the heads_default and heads_sex instruction sets that reads in the contents of the BX and CX registers and sums them together. The result of this operation is then placed in the ?BX? register. This instruction code can be modified by one 'nop' instruction code, which specify which register is used to place the result of this operation.

The default analyze configuration file.

The analyze configuration DETAIL command is an analyze configuration command that, after the execution of an analyze configuration RECALC or RECALCULATE command, writes statistics of the genomes of the digital organisms (one per line) loaded in a batch and executed in analyze mode to an output file.

The analyze configuration LOAD_ORGANISM command is an analyze configuration command that loads a single genome in a batch from a digital organism file.

The analyze configuration LOAD_SEQUENCE command is an analyze configuration command that loads a single genome in a batch from a genome instruction sequence.

The analyze configuration PURGE_BATCH command is an analyze configuration command that remove the genomes of all digital organisms loaded in a batch.

The analyze configuration RECALCULATE command is an analyze configuration command that runs all of the genomes loaded in the current batch through a test virtual CPU and records the measurements taken (fitness, gestation time, etc.). This command overrides any values that may have been loaded in with the genomes. The "use_resources" flags means whether or not the test virtual CPU will use resources when it runs. If the "use_random_inputs" flag is set, then digital organisms will be provided with new, random input 32-bit binary numbers for each trace as they would experience during an experiment performed using the standard mode of Avida. By default, the same inputs are provided every time to digital organisms in analyze mode. Phenotypic plasticity information is not available from the analyze configuration RECALCULATE command (you should use the analyze configuration RECALC command with "num_trials X", where X is greater than 1, for phenotypic plasticity statistics).

The analyze configuration RECALC command is an analyze configuration command that performs the same operations as the analyze configuration RECALCULATE command but has a few additional features (e.g., computes phenotypic plasticity). If "num_trials" is set to greater than one, random inputs will be used to gather phenotypic plasticity information. Please note that phenotypic plasticity analysis performed by using the analyze configuration RECALC command will reset genome statistics to the values for the most likely phenotype. Implicit phenotypic plasticity analysis (e.g. by not calling RECALC or calling RECALC with "num_trials 1") will not re-evaluate the genome statistics in this manner and instead rely on the initial values or those values from a single recalculation.

The analyze configuration TRACE command is an analyze configuration command that shows step-by-step the status of all of the virtual CPU components and the genome of a digital organism during the course of its execution in analyze mode. The filename used for each trace will be the genotype's name with a ".trace" appended. Four parameters need to be specified: the name of the folder that will contain the trace files, whether the digital organism uses resources (1) or not (0) when running in analyze mode, the update at which resources will be available (-1 if resources are not used), and whether the environment configuration file provides new random input numbers to the digital organisms (1) or not (0) everytime the analyze mode is called.

The analyze configuration command is a directive included in the analyze configuration file that is used for loading, manipulating, and saving data from an experiment performed in the analyze mode of Avida.

An analyze configuration file is a configuration file that involves loading the genomes of digital organisms in one or more batches to perform additional tests after an evolutionary experiment in Avida has been completed.

The analyze mode is an execution mode of Avida consisting of performing an experiment where the genome of a single digital organism is executed in a test virtual CPU to compute its properties.

The 'and' logic operation is a logic operation on two bitstrings that returns 1 if and only if both inputs are 1 (otherwise it returns 0).

The 'and-not' logic operation is a logic operation on two bitstrings that only returns 1 if for each bit pair one input is 1 and the other input is 0 (otherwise it returns 0).

The digital file that executes Avida.

The default avida configuration file. This file is actually an excellent guide to itself; every option has a description of what it does and what its options are.

An avida configuration command is a directive included in the avida configuration file that is used for setting up all the basic conditions for performing an experiment in the standard mode of Avida.

An avida configuration file is a configuracion file that set up all the basic conditions for performing an experiment in Avida.

An avida experiment is an experiment carried out in Avida using digital organisms.

A batch is a digital storage space where the genomes of the digital organisms are loaded before being executed in analyze mode.

A buffer is a digital storage space that a digital organism uses to receive information or return the processed results.

A complementary template is a sequence of 'nop' instructions that are found, in the heads_default and heads_sex instruction sets, by taking each 'nop' instruction that makes up that template, and shifting it to the next in alphabetical order, looping around at the end. Thus, 'nop-A' -> 'nop-B' -> 'nop-C' -> 'nop-A'. In the transsmt instruction set, the complement is the template where each 'Nop' is shifted over in sequence by 2, such that the complement of the complement recovers the original template: 'Nop-A' -> 'Nop-C' -> 'Nop-A' and 'Nop-B' -> 'Nop-D' -> 'Nop-B'.

A configuration command is a directive included in a configuration file that make up a configuration file in Avida.

A configuration file is a digital file that stores settings that are specific to a particular software.

The instruction code 'dec' is an instruction code of the heads_default and heads_sex instruction sets that reads in the contents of the ?BX? register and decrements it by one. This instruction code is destructive (I.e., it pops the old value off the register), and can be modified by one 'nop' instruction code, which specifies which register is used.

The default file containing a digital organism that is defined by the default instruction set and the default hardware type.

The default file containing a parasite digital organism that is defined by the transsmt instruction set and the transSMT hardware type.

The default hardware is the default hardware type used in Avida.

A digital file is an information content entity which conforms to a specificacion or format and which is meant to hold data and information in digital form, accessible to software agents.

A digital genome is a circular list of instruction codes that can be executed sequentially by the virtual CPU of a digital organism.

A digital organism is a self-replicating computer program that mutates and evolve within a user-defined computational environment.

A digital organism file is a digital file containing the list of instruction codes that constitutes the genome of a digital organism in Avida.

A digital organism memory is a digital storage space that a digital organism uses to hold a sequence of instruction codes to be executed. The memory space is initialize to the genome of the digital organism, but it will be modified over the lifetime of the digital organism, typically as an offspring is produced. As section of the memory is then divided off to initialize the offspring. Memory is treated as circular, such that execution will loop back to the first instruction code after the last instruction code has been executed.

The digital phenotype of the logic9 environment that a digital organism that is not capable of computing any logic operation has.

The digital phenotype of the logic9 environment that a digital organism computing the logic operation 'not' has.

The digital phenotype of the logic9 environment that a digital organism computing the logic operations 'not', 'not-and', 'and', 'orn-not', 'or', 'and-not', 'not-or', 'exclusive or' and 'equals' has.

A digital phenotype is a unique combination of logic operations that the digital organism performs on 32-bit one- and two-binary input numbers. Any two digital organisms that compute the same logic operations are considered to have the same phenotype.

A digital storage space is a memory or disk space of a computer that is used to retain digital data.

A digital tandem repeat is a string of two or more instruction codes within a digital transcriptome that are executed sequentially more than once by a digital organism.

A digital transcriptome is a list of the instruction codes that have been executed by the virtual CPU of a digital organism during its replication.

The instruction code 'divide-sex' is an instruction code of the head_sex instruction set that attempts to divide off a finished offspring copy. But, instead of placing it in the population immediately, its offspring is stored until the offspring of another digital organism is produced, at which time they recombine their genomes and the two recombinant products are placed into the population.

The default environment configuration file. The default environment provides a digital organism with new, random input strings every time an 'input-output' instruction code ('IO' for the transsmt instruction set) is executed. The genome of a digital organism can harbor one or several input-output instructions that can be executed either only once or many times during the time it takes to generate an offspring. This means that the organism can take input numbers from the environment more than once before replicating and can compute the result of more than one logic operation.

An environment configuration REACTION command is an environment configuration command that allows us to set up a computational function that can be used by a digital organism to consume or produce resources when it performs certain logic operations. By defining reactions, a digital organism can be rewarded or punished for performing the logic operations that triggers them.

An environment configuration RESOURCE command is an environment configuration command that allow us to set up a computational quantity (i.e., resource) that can be used to modify the fitness of a digital organism. The resource can be a global quantity or a quantity that vary from cell to cell within the world grid.

An environment configuration command is a directive included in the environment configuration file that is used for xxx from an experiment performed in the standard mode of Avida.

An environment configuration file is a configuration file that set up the way a digital organism interacts with its computational environment in Avida.

The 'equals' logic operation is a logic operation on two bitstrings that returns 1 if both bits are identical, and 0 if they are different.

The default events configuration file.

An event configuration Exit command is an event configuration command that allows us to specify the end of an experiment performed in the standard mode of Avida.

An event configuration InjectRange command is an event configuration command that allows us to add digital organisms to the world grid at any time during the course of an experiment performed in the standard mode of Avida.

An event configuration SavePopulation command is an event configuration command that allows us to save the state of the entire population of digital organisms to a file at any time during the course of an experiment performed in the standard mode of Avida.

An events configuration command is a directive included in the events configuration file that is used for controlling the events that need to occur throughout the course of an experiment performed in the standard mode of Avida. An event configuration command will be triggered either a single time or periodically. The format for each command is: 'type' 'timing' 'event' 'arguments'. The type determines what kind of timings the event will be based off of (i.e., immediate 'i', based on update 'u', or based on generation 'g'). The timing should only be included for non-immediate events. If a single number is given for timing, the event occurs at that update/generation. A second number can be included (separated by a colon ':') to indicate how often the event should be repeated. And if a third number is listed (again, colon seperated) this will be the last time the event can occur on. The event is simply the name of the action that should be performed, and the arguments detail exactly how it should work when it is triggered.

An events configuration file is a configuration file that controls the events that need to occur throughout the course of an experiment in Avida.

This file consists of a list of events that will be triggered either singly or periodically. The format for each line is: 'type' 'timing' 'event' 'arguments'. The type determines what kind of timings the event will be based off of (i.e., immediate [i], based on update [u], or based on generation [g]). The timing should only be included for non-immediate events. If a single number is given for timing, the event occurs at that update/generation. A second number can be included (separated by a colon ':') to indicate how often the event should be repeated. And if a third number is listed (again, colon seperated) this will be the last time the event can occur on. The event is simply the name of the action that should be performed, and the arguments detail exactly how it should work when it is triggered.

The 'exclusive-or' logic opertation is a logic operation on two bitstrings that returns 1 if one but not both of the inputs are 1 (otherwise it returns 0).

An executable file is a digital file that executes a process.

A thread of execution is the smallest sequence of programmed instructions that can be managed independently by a scheduler, which is typically a part of the operating system.

An experiment is a scientific procedure undertaken to make a discovery, test a hypothesis, or demonstrate a known fact.

A flow-head is the head that marks the beginning of a loop in a digital organism's memory space to jump the instruction pointer back to from the loop's end.

The instruction code 'get-head' is an instruction code of the heads_default and heads_sex instruction sets that copy the position of the instruction pointer ?IP? into the CX register. This instruction code can be modified by one 'nop' instruction, which specifies which head its position will be copied.

The instruction code 'h-allow' is an instruction code of the heads_default and heads_sex instruction sets that allocates additional memory for the digital organism up to the maximum it is allowed to use for its offspring.

The instruction code 'h-copy' is an instruction code of the heads_default and heads_sex instruction sets that reads the contents of the digital organism's memory at the position of the read-head and copy that to the position of the write-head. If a non-zero copy mutation rate is set, a test will be made based on this probability to determine if a mutation occurs. If so, a random instruction code (chosen from the full instruction set with equal probability) will be placed at the write-head instead.

The instruction code 'h-divide' is an instruction code of the heads_default instruction set that attempts to divide off a finished offspring copy. The original digital organism keeps the state of its memory up until the read-head. The offspring's memory is initialized to everything between the read-head and the write-head. All digital organism's memory past the write-head is removed entirely.

The instruction code 'h-search' is an instruction code of the heads_default and heads_sex instruction sets that will read in the template that follows it, and find the location of a complement template in the code. The BX register will be set to the distance to the complement from the current position of the instruction pointer, and the CX register will be set to the size of the template. The flow-head will also be placed at the beginning of the complement template. If no template follows, both BX and CX will be set to zero, and the flow-head will be placed on the instruction immediatly following the 'h-search' instruction code.

A hardware type is the way the memory of a digital organism and the execution threads are managed by Avida.

A head is a mechanism that reads data from or writes data to the digital organism's memory space.

The heads_default instruction set is the default instruction set in Avida.

The heads_sex instruction set is the instruction set that allows digital organisms reproduce sexually in Avida.

A host digital organism is a digital organism whose CPU-cycles can be stolen by another digital organism.

The instruction code 'if-label' is an instruction code of the heads_default and heads_sex instruction sets that reads in the template that follows it, and tests if its complement template was the most recent series of instruction codes copied. If so, it executes the next instruction code, otherwise it skips it. This instruction code is commonly used for a digital organism to determine when it has finished producing its offspring.

The instruction code 'if-less' is an instruction code of the heads_default and heads_sex instruction sets that compares the ?BX? register to its complement. If ?BX? is the lesser of the pair, the next instruction code (after a modifying 'nop' instruction code, if one is present) is executed. If it is greater or equal, then that next instruction code is skipped. This instruction code can be modified by one 'nop' instruction code, which specifies which register is compared.

The instruction code 'if-n-equ' is an instruction code of the heads_default and heads_sex instruction sets that compares the ?BX? register to its complement. If they are not equal, the next instruction code (after a modifying 'nop' instruction code, if one is present) is executed. If they are equal, that next instruction code is skipped.

The instruction code 'inc' is an instruction code of the heads_default and heads_sex instruction sets that reads in the contents of the ?BX? register and increments it by one. This instruction code is destructive (i.e., it pops the old value off the register). This instruction code can be modified by one 'nop' instruction code, which specifies which register is used.

The instruction code 'input-output' is an instruction code of the heads_default and heads_sex instruction sets that takes the contents of the ?BX? register (i.e., a 32-bit binary number) and outputs it, checking it for any logic operation that may have been performed on the two 32-bit binary numbers stored in its input buffers. It also places a randomly generated 32-bit binary number from the environment into the ?BX? register. This instruction code can be modified by one 'nop' instruction code, which specifies which register is used. Input-output instruction codes can be executed either only once or many times during the time it takes to produce an offspring. This means that a digital organism can take input numbers from the environment more than once before replicating and can compute the result of more than one logic operation.

An input buffer is the buffer that a digital organism uses to receive information.

An instruction code is a group of bits that instruct the computer to perform a specific operation. Each intruction code may be followed by a series of options that define how that instruction code should be used. In Avida, each position of a digital organism genome consists of an instruction code.

An instruction-pointer is the head that determines the next instruction code to be executed by the virtual CPU of a digital organism. After each execution, the instruction pointer is automaticall advanced (unless the instruction code executed dictates otherwise).

An instruction set is a list of instruction codes that a digital organism can hold in its genome (i.e., its genetic language).

An instruction set file is a digital file containing the instruction set that defines the genetic language of a digital organism in Avida (i.e., the instruction codes that a digital organism can hold in its genome). The name of the instruction set may not be the same as the name of the file containing the instruction set (i.e., one file may contain multiple instruction sets).

An instruction set file containing the instruction set that allows digital organisms reproduce sexually in Avida.

An instruction set file containing the default instruction set in Avida.

An instruction set file containing the instruction set that allows host-parasite interactions to take place in Avida.

The instruction code 'jump-head' is an instruction code of the heads_default and heads_sex instruction sets that reads in the value of the CX register, and the move the instruction pointer ?IP? by that fixed amount through the organism's memory. This instruction code can be modified by one 'nop' instruction code, which specifies which head to move.

A logic environment where 77 logic operations are listed in the environment configuration file.

A logic environment where 9 logic operations are listed in the environment configuration file.

A computational environment that defines the logic operations that are listed in the environment configuration file.

A logic operation is a mathematical function in which each bit is treated independently of all the other bits in a binary number. Thus if a logic operation 'and' was performed between two bitstrings, the first bit of the first string would be added to the first bit in the second string, the second bit to the second bit and so on.

A merely-viable digital organism is a digital organism that does not compute any logic operation (i.e., it can only produce an offpring).

The instruction code 'move-head' is an instruction code of the heads_default and heads_sex instruction sets that will cause the instruction pointer ?IP? to jump to the position in memory of the flow-head. This instruction code can be modified by one 'nop' instruction code, which specifies which head to move to the position pointed to by the flow-head.

A multiple-trait digital organism is a digital organism that computes more than one logic operation.

The instruction code 'nand' is an instruction code of the heads_default and heads_sex instruction sets that reads in the contents of the BX and CX registers (each of which are 32-bit binary numbers) and performs a bitwise NAND operation on them. The result of this operation is placed in the ?BX? register. This instruction code can be modified by one 'nop' instruction code, which specifies which register is used to place the result of this operation. Note that this is the only logic operation provided by the instruction set.

A non-plastic digital organism is a digital organism whose genome encodes the same phenotype in all environments (i.e., a digital organism that computes the same set of logic operations in all environments).

The instruction code 'nop' is an instruction code of the heads_default and heads_sex instruction sets that does nothing or modifies the behavior of the instruction code preceeding it by changing the virtual CPU component that it affects (register or head), or acts as part of a template to denote positions in a digital organism's genome. A register name (AX, BX, or CX) surrounded by question marks refers to that register being used by default when the instruction code in question is being executed, but if the instruction code is followed by a 'nop' instruction code, the 'nop' instruction code will alter the register used. A head abbreviation (IP, RH, WH, or FH) surrounded by question marks refers to that head being used as a default, when the instruction code in question is being executed, but if the instruction code is followed by a 'nop' instruction code, the 'nop' instruction code will alter the head used.

The instruction code 'nop-A' is an instruction code of the heads_default and heads_sex instruction sets that does nothing or modifies the register being used by default to the register AX or the head being used by default to the instruction pointer.

The instruction code 'nop-B' is an instruction code of the heads_default and heads_sex instruction sets that does nothing or modifies the register being used by default to the register BX or the head being used by default to the read-head.

The instruction code 'nop-C' is an instruction code of the heads_default and heads_sex instruction sets that does nothing or modifies the register being used by default to the register CX or the head being used by default to the write-head.

A nop-head notation is a two-letter notation (IP, RH, WH, or FH) surrounded by question marks that refers to that head being used as a default, when the instruction code in question is being executed. But if the instruction code is followed by a no-operation ('nop' or 'Nop') instruction code, the 'nop' or 'Nop' instruction code will alter the register used. A 'nop-A' or 'Nop-A' instruction code indicates the instruction pointer (IP); a 'nop-B' or 'Nop-B' instruction code indicates the read-head (RH); a 'nop-C' or 'Nop-C' instruction code indicates the write-head (WH); and a 'Nop-D' instruction code indicates the flow-head (FH).

A nop-register notation is a two-letter notation (AX, BX, or CX) surrounded by question marks that refers to that register being used by default when the instruction in question is being executed. But if the instruction code is followed by a no-operation ('nop') instruction code, the 'nop' instruction code will alter the register used. A 'nop-A' instruction indicates the AX register; a 'nop-B' instruction code indicates the BX register; and a 'nop-C' instruction code indicates the CX register. It does not apply to the transsmt virtual CPU because the Transsmt hardware does not use registers.

A nop-stack notation is a single-letter noation (A, B, C, or D) surrounded by question marks that refers to that stack being used by default when the instruction code in question is being executed. But if the instruction code is followed by a no-operation ('Nop') instruction code, the 'Nop' instruction code will alter the register used. A 'Nop-A' instruction code indicates the stack A; a 'Nop-B' instruction code indicates the stack B; a 'Nop-C' instruction code indicates the stack C; and a 'Nop-D' instruction code indicates the stack D. It only applies to the transsmt virtual CPU, because the TransSMT hardware does not use registers.

A nop notation is a single or two capital letters (IP, RH, WH, or FH for heads; AX, BX, and CX for registers; and A, B, C, D for stacks) surrounded by question marks that refer to the head, register, or stack being used as a default.

The 'not' logic operation is a logic operation on a single bitstring that returns 1 at a bit position if the input is 0 at that bit position, and 0 if the input is 1.

The 'not-and' logic operation is a logic operation on two bitstrings that returns 0 if and only if both inputs at the corresponding bit positions are 1 (otherwise it returns 1).

The 'not-or' logic operation is a logic operation on two bitstrings that returns 1 only if both inputs are 0 (otherwise it returns 0).

The 'or' logic operation is a logic operation on two bitstrings that returns 1 if either the first input, the second input, or both are 1 (otherwise it returns 0).

The 'orn-not' logic operation is a logic operation on two bitstrings that returns 1 if for each input bit pair one input bit is 1 or the other is 0 (otherwise it returns 0).

An output buffer is the buffer that a digital organism uses to return the processed results.

Note that this is a much more specific class than that referred to by MeSH Journal article (D016428).

A parasite digital organism is a digital organism capable of stealing CPU-cycles from another digital organism.

A plastic digital organism is a digital organism whose genome encodes distinct phenotypes in different environments (i.e., a digital organism that computes different logic operations in different environments).

The instruction set 'pop' is an instruction code of the heads_default and heads_sex instruction sets that removes the top element from the active stack, and places it into the ?BX? register. This instruction code can be modified by one 'nop' instruction code, which specifies which register is used.

The instruction code 'push' is an instruction code of the heads_default and heads_sex instruction sets that reads in the contents of the ?BX? register, and places it as a new entry at the top of the active stack.This instruction code can be modified by one 'nop' instruction code, which specifies which register is used.

A read-head is the head that determines what instruction code is copied by the virtual CPU of a digital organism when a 'h-copy' instruction code is executed ('Val-Copy' instruction code if the transsmt instruction set is used).

A register is a digital storage space that a digital organism uses for storing a single number. The default virtual CPU contains three registers (XA, XB, and XC), each of which is made up of 32 bits. All math-based instruction codes operate on the registers, and various instruction codes will move the values in the registers around.

The instruction code 'set-flow' is an instruction code of the heads_default and heads_sex instruction sets that moves the flow-head to the memory position specify by the ?CX? register. This instruction code can be modified by one 'nop' instruction code, which specifies which register is used to move the flow-head.

The instruction code 'shift-l' is an instruction code of the heads_default and heads_sex instruction sets that reads in the contents of the ?BX? register, and shifts all of the bits in that register to the left by one, placing a zero as the new rightmost bit, and truncating any bits beyond the 32 maximum. For values that require fewer than 32 bits, it effectively multiplies that value by two. This instruction code can be modified by one 'nop' instruction code, which specifies which register is used.

The instruction code 'shift-r' is an instruction code of the heads_default and heads_sex instruction sets that reads in the contents of the ?BX? register and shifts all of the bits in that register to the right by one. In effect, it divides the value stored in the register by two, rounding down. This instruction code can be modified by one 'nop' instruction code, which specifies which register is used.

A single-trait digital organism is a digital organism that computes a single logic operation.

A stack is a digital storage space that a digital organism uses for storing numbers. The default virtual CPU and the transsmt virtual CPU have two and four stacks, respectively, used for storing numbers. In the default virtual CPU, the 'push' and 'pop' instruction codes are used to move numbers between the registers and the stack, and the 'swap-stk' instruction toggles the active stack in use. A digital organism can theoretically store an arbitrary amount of data in the stacks, but for practical purposes the maximum stack depth is limited to ten.

The standard mode is an execution mode of Avida consisting of performing an experiment where populations of digital organisms evolve in a open ended computational environment (i.e., standard or transsmt virtual CPU).

The instruction code 'sub' is an instruction code of the heads_default and heads_sex instruction sets that reads in the contents of the BX and CX registers and subtracts CX from BX. The result of this operation is then placed in the ?BX? register. This instruction code can be modified by one 'nop' instruction code, which specifies which register is used to place the result of this operation.

The instruction code 'swap' is an instruction code of the heads_default and heads_sex instruction sets that swaps the contents of the ?BX? register with its complement. This instruction code can be modified by one 'nop' instruction code, which specifies which register is used.

The instruction code 'swap-stk' is an instruction code of the heads_default and heads_sex instruction sets that toggles the active stack in the virtual CPU. All other instruction codes that use a stack will always use the active one.

A template is a sequence of no-operation instruction codes ('nop' or 'Nop', for the heads_default and transsmt instruction sets, respectively) used to mark regions of code within a digital organism's genome.

A transcriptome-robust digital organism is a digital organism that executes the same transcriptome in all environments (i.e., a digital organism that executes the same instruction codes in all environments).

A transcriptome-sensitive digital organism is a digital organism that executes distinct transcriptomes in different environments (i.e., a digital organism that executes different instruction codes in different environments).

The transsmt instruction set is the instruction set that allows host-parasite interactions to take place in Avida.

An update is the amount of time during which a digital organism executes on average 30 instruction codes from its genome.

A world grid is the topology of the world where digital organisms live.

A world grid cell is a unit that make up the world grid.

A writ- head is the head that determines the position of a digital organism's memory space where the instruction code is going to be copied to by the virtual CPU of a digital organism.