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**************************************** BSIM v1.00 A Biological Simulater (C) Copr. 1988 Paul H. Deal All Rights Reserved This is a shareware program. To register see REGISTRATION INFORMATION on page 9 **************************************** INSTRUCTIONS CONTENTS page line INTRODUCTION ----------------------------------- 1 29 Physical characteristics ----------------------- 1 49 Biological characteristics --------------------- 2 73 Chemistry -------------------------------------- 2 85 RUNNING THE SIMULATION ------------------------- 2 103 Master menu ------------------------------------ 2 105 First input screen ----------------------------- 3 154 Second input screen ---------------------------- 4 220 Entering genomes ------------------------------- 6 330 SAMPLING --------------------------------------- 7 364 EXPERIMENT POSSIBILITIES ----------------------- 8 438 REGISTRATION INFORMATION ----------------------- 9 466 INTRODUCTION BSIM is a computer simulation program which generates a 'pseudo- ecology' that can serve as an analog for actual biological systems. The program generates 'organisms' as a function of a simulated genome which specifies the rules whereby the organisms will interact with a simulated physical environment. The model for the program is a microbial aquatic ecosystem, but many of the features of the system are more general and it can be used to conceptualize a broader range of natural ecosystems. While the system does have an underlying simulated chemistry the reactions are highly simplified and it is not intended to reproduce the biochemistry or physiology of actual systems. Such simulation is well beyond the scope of this program. It is intended, rather, to be a model for the study of the concepts of population dynamics, mass flow in ecosystems, and evolution. BSIM operates in two basic modes: 1: Stagnant - simulates a 'pond' or unstirred 'flask' environment. 2: Circulated - simulates a stirred laboratory 'flask' environment. Physical characteristics Both modes: * isolated from outside biology. * choice of open or closed to atmospheric gases; if open there is the option of adjusting the equilibrium solution values for CO2 and O2, if closed the initial concentrations of CO2 and O2 are selected. * choice of running in the light or dark; light intensity is selectable when running in the light. * aqueous. * temperature and pH are assumed constant and optimum. Stagnant: * substances move by diffusion only - concentration gradients are homogeneous in the horizontal dimension, variable in the vertical dimension. Circulated: * stirred - this is the 'flask' mode in which it is assumed that mixing tends to produce a homogeneous distribution of substances in both horizontal and vertical dimensions. Biological characteristics Both modes: * simulated organisms are abstractions of real organisms with their morphology and physiology determined by a pseudo-genome consisting of 13 elements. * genome elements are mutable. * organisms carry out metabolism through a simplified carbon chemistry. * organisms are capable of reproduction. Chemistry Both modes: * chemistry is based on a generalized carbon flow model. * only oxygen and carbon are considered in the model; other elements are assumed, but not computed. * calculations are based on model reactions which must be considered as summaries of complex biochemical pathways consisting of numerous individual reactions and not as complete reactions in and of themselves. * mass flow of carbon and oxygen is balanced, but tracking of energy or other elements is not undertaken; the direction of energy flow is, however, taken into account and where a reaction requires energy a source for that energy must be available before the reaction can take place. * detailed simulation of biochemistry is beyond the scope of this model. RUNNING THE SIMULATION Master Menu The command 'GO' loads and executes a program called 'VPEB'. 'VPEB' produces a master menu for operating the simulator and its associated utilities. It also permits browsing and printing the program documentation. The master menu appears as follows: ------------------------------------ | VIEW INSTRUCTIONS | ------------------------------------ | VIEW EXPT. MANUAL | ------------------------------------ | PRINT INSTRUCTIONS | ------------------------------------ | PRINT EXPT. MANUAL | ------------------------------------ | RUN BSIM | ------------------------------------ | RUN CTGEN | ------------------------------------ | RUN MIXGEN | ------------------------------------ | RUN LOOKGEN | ------------------------------------ | RUN GRAPHB | ------------------------------------ | RUN PLOTB | ------------------------------------ up down enter escape Cursor up/down arrow keys can be used to move a highlight bar to the desired function. Pressing enter will then execute that function. If this is the evaluation version of 'BSIM', the lower five functions and the experimenter's manual will not be available. Attempting to run these will result in a 'file not found' error. However, BSIM itself is complete and all its features are fully implemented in the evaluation as well as the registered versions. If preferred, each of these functions can be run directly, without invoking the menu. At the DOS prompt, type the appropriate commands. To view documentation, type 'VIEWDOC', to print documentation, type 'PRNDOC', and in all other cases type the command name as seen in the menu (without typing 'RUN'). VIEWDOC and PRNDOC can be used to view or print other documentation as well; in fact, they will handle any ASCII type files that can be loaded in available memory. The command 'BSIM' loads and initiates execution of the main program. First Input Screen Press any key to remove the logo and present the first input screen as follows: Max population size = 4321 ------------------------------------ | Reseed/New | N | ------------------------------------ | Stagnant/Circulating | S | ------------------------------------ | Open/Closed | O | ------------------------------------ | Random/Defined | R | ------------------------------------ up down rewrite(BKSP) enter(F10) abort(ESC) help(F5) Max population, given in the upper left hand corner, indicates the number of organisms supportable by the available memory in your computer. Dynamic memory is used to generate the organisms and this process can, in some cases, exhaust memory. If that happens the simulation will continue with the letters ML posted on the display screen in the lower right hand corner indicating that operation is currently memory limited. During memory limited operation an arbitrary limit will be imposed on the number of offspring which can be produced. This limit will not reflect the constraints of the simulation program so care in interpreting results is in order. A max population of less than a thousand will generally not be adequate for useful experiments. The cursor may be moved from line to line by using the up and down arrows. Each of the four options has two choices which may be selected by entering the appropriate letter in the space provided. The default choices are displayed. Backspace erases the current choice. The F5 function key brings up a help screen appropriate to the topic indicated by the current cursor postion. Escape aborts the entire program and the F10 function key enters all the choices currently on the screen and moves to the next screen. Below is listed the information that appears on the appropriate help screens. Reseed/New: Type 'N' or 'R' to begin a new simulation or continue a previous run. If you choose the reseed option you must have a file available containing the saved data from a previous run and you will be prompted for the path and name of that file. When you continue a previous run you will have only limited options for changing the original settings established when that run was inititated. Stagnant/Circulating: Type 'S' or 'C' to choose between a non-circulating, 'pond' type simulation and a circulating mode comparable to a stirred flask. In the stagnant mode, conditions may differ from top to bottom of the simulation. In the circulating mode, conditions will be homogenous except for light intensity (light is absorbed by the 'medium', hence is at its highest intensity at the top of the simulation). Open/Closed: Type 'O' or 'C' to choose between having the head space gases in equilibrium with a selected atmospheric value or having the simulation 'sealed' from the outside world. Random/Defined: Type 'R' or 'D'. The Random choice will cause the simulation to be initiated with organisms of random genetic composition. The Defined option allows you to enter up to 3 genomes of your choice or will allow seeding with a collection of known genomes. Second Input Screen After entering the choices on the first input screen a second input screen will appear as follows: ----------------------------------------- | Inhibitors(A to L) | NONE | ----------------------------------------- | Mutagen conc(0 to 10000) | 100 | ----------------------------------------- | Light intensity(0 to 3000) | 1200 | ----------------------------------------- | Depth(2 to 100) | 16 | ----------------------------------------- | Oxygen(0 to 4000) | 2000 | ----------------------------------------- | Carbon dioxide(0 to 2000) | 100 | ----------------------------------------- | Reservoir size(1 to 12) | 3 | ----------------------------------------- | Starting population(1 to 2000)| 500 | ----------------------------------------- | Sol substrate conc(0 to 3000) | 1000 | ----------------------------------------- | Amount sediment(0 to 30000) | 0 | ----------------------------------------- | Num genomes(1 to 3) or (S)eed | | ----------------------------------------- up down rewrite(BKSP) enter(F10) abort(ESC) help(F5) There are eleven options possible on this screen but they will not all be available in every instance. If the reseed option was chosen many of the options on this screen will not be relevant and you will not be able to enter values for those. The last option listed is available only if you chose the defined option on the previous screen. The up and down arrow keys control cursor movement, backspace erases the current entry, and escape aborts the program. The F10 function key enters the current screen and, if the defined option is in effect, moves to the third input screen. Otherwise a seedfile is prompted for and execution of the program begins. Function key F5 brings up help screens with the following messages: Inhibitors: Twelve 'substances', letter names A to L, are available which act as 'biochemical inhibitors'. These can be added in combinations of up to six at one time to investigate the various simulated chemical pathways that may be available to any given collection of organisms. To enter an inhibitor type the appropriate letter. Mutagen: Analagous to a mutagenic factor, such as UV radiation, in natural environments. Mutagen controls the rate at which 'mutations' occur in the simulated genome. A value of 0 results in no mutations and is useful for studying the characteristics of defined populations. Light intensity: Luminance at the surface of the simulation. The value assumes that portion of the spectrum which is photosynthetically active. A value of 0 represents darkness. Depth: Effective only in the stagnant model, this variable determines the rate at which solutes diffuse vertically in the simulation. Horizontal distribution is considered to be homogeneous. Higher values are equivalent to a deeper pond. Oxygen: Sets the concentration of oxygen in the aqueous phase in equilibrium with the gas phase in open systems. Also provides the initial concentration of oxygen at the start of a new simulation whether open or closed. Carbon dioxide: Sets the concentration of carbon dioxide in the aqueous phase in equilibrium with the gas phase in open systems. Also provides the initial concentration of carbon dioxide at the start of a new simulation whether open or closed. Reservoir size: A technical factor that determines the relative effect of metabolism of each organism on the substrate pool. It is analagous to buffering capacity in a natural medium and is loosely analagous to the volume of a natural system. A low value produces a simulation in which substrate becomes limiting at low population densities. Starting population: The number of 'organisms' with which the simulation is initially seeded. Not meaningful in reseed and seeding options. Soluble substrate concentration: The concentration of soluble organic matter in the simulation at startup. Amount sediment: The total mass of sediment at the start of the simulation. Some sediment may be suspended in the aqueous phase and some may be trapped at the bottom of the simulation. The sediment serves as substrate for some biochemical pathways. Number of genomes: Allows selecting up to 3 predefined genomes when the defined option was previously chosen. The configuration for each genome will be entered on a following input screen. This option also permits entering the letter 'S' to indicate seeding from a previous run. The seed option differs significantly from reseeding in that all the input variables can be reselected. It is analagous to adding a drop of old culture to a new batch as compared to simply continuing the incubation of the old batch. Each of the first ten of the above eleven options has a default value which is listed when the screen is presented. In the first option the default is for no inhibitors; in all others it is the number indicated. The defaults were chosen to produce useful and interesting simulations, but they are by no means to be considered the best possible choices. Indeed, experimentation with these values is the heart of the simulation! Entering Genomes After pressing F10 to enter the current choices, if the defined option was chosen you will now be presented with an input screen for entering your selected genomes or prompted for the file from which a seed culture is to be taken. Below, the screen for two genomes is shown. Up to three genome entries may be selected. ----------------------------- | EEEEEEEEEEEEE | 0 | ----------------------------- | EEEEEEEEEEEEE | 0 | ----------------------------- chng window(ARROWS) (SPACEBAR) (BKSP) enter(F10) abort(ESC) help(F5) The cursor is moved by the arrow keys, spacebar, and backspace. Escape aborts the program and selections are entered using F10. Function F5, pressed at any time, calls up the following help message: This screen appears only when the defined option was previously selected and 1, 2, or 3 genomes was entered. To enter a known genome, type over the default or old genome using the letters 'E', 'F', 'G', or 'H' (upper or lower case is acceptable). The boxes on the right hand side contain the percentage of each genome which will be represented in the final population. When only one genome is entered this box is always set at 100. In all other cases the total of all boxes (2 or 3) must add to 100. An attempt to enter a value of more or less than 100 will not be accepted. When all entries have been made and, if appropriate, the path and name of the seed file has been entered, the program will begin execution. SAMPLING While the simulation runs, the keyboard is ACTIVE, so beware! Either of two interrupts can be activated (quit or sample). The interrupts will not be processed until the end of a cycle. As a consequence there may be a delay after pressing an interrupt key and the initiation of the corresponding action. If quit(q) is entered you will have the opportunity to abort the entry in case of error. If sample(s) is entered (after the above mentioned delay) a menu bar will appear at the bottom of the screen as follows: auto(a) screen(s) disk(d) printer(p) Pressing the designated keys will permit choosing where the sample is to be sent; screen, disk or printer: or, in the case of auto, allows sending a sample automatically to disk at designated intervals. The auto option permits sampling physical quantities only or may include both physical and biological components. In the latter case the samples will include all genomic types in the population, with a count of the number of organisms having each specific genome. The user must assure adequate disk space to handle the number of samples expected during the time this option is in effect. The total number of samples to be taken can be specified at the time auto sampling is initiated. If the non-automatic options are selected a question, 'Count only(y/n)?', will appear next. The yes option permits taking a sample in which the organisms will be counted but will not be listed individually. The no option causes all organisms to be listed by genome. After answering this question another menu bar will appear as follows: select(s) grid(g) rand(r) tot(t) option(s): Select produces a small box on the screen which can be moved to any desired location using the cursor keys. Pressing 's' will then sample the organisms inside the box. option(g): Grid allows the user to select a grid interval for drawing a sampling grid on the screen. By selecting row and column numbers the population within any square of the grid will be sampled. option(r): Rand permits taking a random sample of the entire population at a sampling frequency selected by the user. option(t): Tot samples the entire population. This option must be used to save the current run for future reseeding. After a sample has been taken another menu bar appears: again(a); new(n); quit sam(q); halt(h) option(a): Again permits taking a second sample with the same options as already selected. option(n): New permits taking a second sample with new options. option(q): Exits the sampling procedures and resumes running the simulation. option(h): Halts the entire program and returns to DOS. All sampling modes include a detailed physical profile of the simulation. Included are the current values of user controlled variables and a top to bottom reading of oxygen, carbon dioxide, soluble substrate, sediment, toxin, and cell mass concentrations. Light intensity is displayed as a function of depth in the culture regardless of whether mixed or stagnant. Light is absorbed by the medium and also by the included biomass. EXPERIMENT POSSIBILITIES Using the sampling options, ability to reseed, seed, and define cultures, and the control over physical and chemical parameters provided by the program model, it is possible to simulate a wide variety of biological experiments and techniques in an environment where results can be obtained in minutes or hours as compared to days or weeks in the laboratory or field. Among the possiblities are: Selection by enrichment for organisms of a given capability. Evolution of new capabilities under a variety of conditions. Dynamics of competitive exclusion in a controlled environment. Observation of growth dynamics of a population including: exponential growth senescence decline substrate exhaustion waste buildup. Stress effects on populations. Genetic drift. Isolation and characterization of pure cultures. Sampling techniques and concepts. The above list is not exhaustive and many other experimental areas may suggest themselves as experience with the simulation is gained. It is hoped that this simulation will serve as a useful tool in helping students to develop concepts in specific areas of biology. REGISTRATION A registration number is provided with each copy of BSIM. The number may be seen by typing 'B' at the main program menu. The number will appear in the box containing 'RUN BSIM' immediately following 'BSIM'. Unregistered copies display the number: 000000-100-0000000. This is a shareware program and, as such, is not free software. If you find the program useful, please register by sending your name and address along with the registration fee of $29.95, to: Paul H. Deal P.0.B. 1398 Moriarty, N.M. 87035 Registered owners will receive the following items: 1: A technical description of the program. 2: Five supplementary utilities to assist in program analysis. 3: An experimenter's manual with experiments illustrating the following concepts: 1: Statistical sampling error. 2: Systematic sampling error. 3: Growth curve. 4: Competitive exclusion. 5: Enrichment isolation. 6: Evolution. 7: Mutualism. 8: Commensalism. 9: Parasitism. 10: Mutation rate. Thank you for trying the program. Any suggestions or comments you might have can be sent to the above address and will be greatly appreciated. END OF BSIM INSTRUCTION DOCUMENT