Teaching Software

Details of two teaching programs, developed by Professor Bill Foley, Dr Neil Jessop & Dr Andrew Illius, Edinburgh) are given below.


Digestion in Mammals (computer simulation)

Introduction and rationale behind the model

This computer programme aims to simulate the digestive processes occurring in herbivorous mammals. A range of options is available to specify body size, characteristics of the digestive tract and characteristics of food eaten. Thus you can run any number of virtual experiments to examine the effects of body size, digestive anatomy and food characteristics on the ability of mammals to meet their energy requirements. The model has been derived from programmes described by Illius and Gordon (1991, 1992).

Previously, digestive physiology experimentation in undergraduate classes has been limited to enzyme assays but this programme gives you the opportunity to conduct sophisticated simulations.

Mechanics of the programme

The programme is written in Delphi and runs in a  Windows environment. It will not run on a Mac. There are four windows, a welcome screen, an input screen and two screens for output. The two output screens are combined for printing. Ensure that you enter your name or some other identifying character on each screen that you print in case it gets mixed with the work of others. To print a page click on the printer icon on the top of the screen. You move between the screens either by clicking on the icons on the top left of the screen you are working on or by choosing the window from the main menu bar. Note that you can only exit the programme by clicking on the exit icon the exit command under “File” on the main menu bar is not working for some reason. There are certainly some other bugs in that not every possible combination that you wish to test is feasible. It is hard to predict this in advance but you will certainly encounter the situation.

Getting started

The best way to get started is to spend a short time familiarizing yourself with the programme and its options so that you can move between the screens confidently. The notes below provide details of what some of the options and terms mean since we have not completed a context-sensitive “Help” file yet. Keep referring to these notes during this familiarization process. Remember that the point of simulations like these is the freedom to ask “what if?”questions and not try to “study” some faithful representation of a real animal.

Second, look at the list of questions that are provided below and then step back from the programme and decide what “experiments” you need to carry out to answer these questions. Some reading either from the list supplied or other sources may assist at this stage. If you can solve these questions and write the work up adequately, you can achieve a grade of Credit for the exercise. If you wish to achieve a Distinction/High Distinction grade, you will need to show evidence that you have gone beyond the set questions and conducted some of your own investigations spurred by your reading.

Screens and switches

Input Screen
Animal Note that you can pull down data on a range of different animals. Good ones to start with are “Generic Marsupial” and “Generic Eutherian”. These “animals” vary only in their maintenance requirements for energy. The maintenance requirements for the marsupials are 70% of those for eutherians as a result of their generally lower metabolic rate. The characteristics of other animals (e.g. cow, koala, greater glider, sheep etc) have been entered from data in the literature. You should not hesitate to vary these data if you wish and do not regard these “animals” as perfect representations of the real world!

Body mass can be between the range of 0.2 and 950 kg. This should cover most of the animals of interest excepting perhaps the megaherbivores such as elephant and hippo. This will be something that you change regularly because one of the questions of interest is the relationship between body size and digestive performance.

% of large particles - this is not something that you should alter until you have some feeling for the programme or have read further on the kinetics of digestion. One use might be to change this as a test of differences in the masticatory ability of animals. For example, it has been argued that many koalas die because they simply can’t chew up their food finely enough as their teeth wear.

Fermentation rate of particles. - Again leave this until you have run some simpler simulations and then you can alter this in conjunction with the % large particles switch to see the effect.

Animal Characteristics

Note that these are divided up into two categories and a number of subcategories within the groups. Basically you are now specifying the type of digestive system that you want to examine. You should decide first of all whether the animal that you want to examine is a foregut fermenter or a hindgut fermenter. Note that the hindgut switch only has an effect when you specify simple stomach.

Foregut - there are three options. Ruminant will give you a digestive system like that of the vast majority of the Order Ruminantia (sheep, cattle, giraffe, antelope); kangaroo will give you a digestive system like the members of the subfamily Macropodidae. Note that the digestive system of the rat kangaroos (Potoroidae) are not catered for by this switch.

If you choose either of these options, the hindgut options become irrelevant even though most foregut fermenters have a secondary area of fermentation in the hindgut as well. Fermentative digestion is calculated in the hindgut however, and added to the energy that the animal obtains. You will see this on the Output screens.

The final option is simple stomach to represent the stomachs found in animals that have the major region of fermentative digestion in the hindgut. This option must be paired with one of the hindgut options.

Hindgut - gives two options - sacculation is the normal condition found in most hindgut fermenters where the hindgut (caecum and/or colon) accommodates and passes digesta effectively as a single bolus. Separation of small particles occurs in small herbivores such as rabbits, koalas and greater gliders. We believe that it is an important physiological feature that allows these small animals to feed on fibrous diets.

Passage rates and % of gut DM load: These options will not concern the vast majority of you unless you get further in to the detail of the digestive process. The model can work by optimizing either the amount of digesta in the gut (Digesta load dominance) or the rate that digesta is flowing out of the gut (Passage rate dominance). Use digesta load dominance as a default.

Dominance - This relates to the method used to optimize the model. Use Digesta load dominance in all your simulations. Come and see me if you get so deeply into the model that you want to understand the effects of changing this.


This is the second major area where you can pull down preset details or alternatively, enter your own data. Food types that you can pull down are expressed as a % of the dry matter of the food that is cell contents. Ensure that you have chosen an appropriate food type See below for more details

Plant Characteristics

The major factor controlling the food is the proportion of cell wall to cell contents in the plant. Cell walls comprise things like cellulose, hemicellulose and lignin which have to be digested symbiotically. Cell contents comprise, simple sugars and starch, proteins, fats and lipids and the cell contents are presumed to be largely available to the animal. Thus the ratio of cell walls to cell contents is some indication of the quality of the diet.

The button Auto will adjust the proportion of cell walls on the basis of the cell content value that you have chosen/entered. You can alter the proportion of cell walls to cell contents beyond the preset values that appear under “Food”

The typical crude protein content of the food changes in accordance with changes in the cell content percentage but is not affected by the different food types, grass, browse and forbs (see below).

Allelochemicals are plant constituents such as tannins and phenolics which provide little usable energy to the animal and which may reduce the digestion of other plant constituents such as protein. In the model, all allelochemicals are regarded as part of the cell contents and so if you enter a value for allelochemicals it will act to reduce the valuable portion of the cell contents.

Feed type
Note that at the very bottom of the food columns there is a list of three potential dietary items, grass, browse (leaves of shrubs and trees) and forbs. ("Forbs" is the general name given to small annual and perennial dicotyledonous plants that typically occur in rangelands.). Each of these groups of plants have a different chemical composition and as a consequence a different rate of digestion. This is reflected in the box directly above called fermentability.

To begin, you should just accept the values that appear in this box for each of the combinations of food type and cell content concentration. Once you have mastered the basics you may wish to alter some of the parameters in the Fermentability box to see for example whether increasing the intrinsic rate of cell wall digestion has a major impact on animal’s meeting their maintenance requirements.

Output screens

Animal and Food Types
The first box on the output screen summarizes the information that you have entered. (Note that the term “monogastric” is incorrect and will be changed to ”simple stomach” later).

Intake and digestibility
This box is probably the most important of the five output boxes.
DMI = dry matter intake (the amount of food eaten by the animal after correction for water) and we predict that this amount of food should be divided amongst a set number of Meals/d

The data below shows where the animal obtained its energy

  • MJ/kg DM = Megajoules per kilo of dry food eaten
  • MJ/d = Megajoules per day (takes into account the total amount of food eaten (see above)
  • MM = multiples of maintenance. This is a very important result for most of the simulations that you can run. Animals have certain requirements for energy which they need to maintain themselves. MM describes how well the combination of diet and digesta anatomy that you have chosen achieve this. Sometimes the answer will be 3-4 other times, <1. In the real world an animal may not actually eat 3-4 times more food than it needs but clearly this is not something that we can model. You might regard high numbers as suggesting that on the particular diet, there is no digestive constraint. However when the MM = <1, then the animal is unable to eat enough of the food to meet its basic maintenance requirements and will start to lose body mass - again this is not something that we can model.
  • Digestibility = The overall digestibility of the diet is calculated for each different part of the gut and summed to provide a total digestibility. The fibre content and type of food is a very strong influence on this value.

Pool sizes and fractional rates of passage and fermentation
This figure shows the different pools of digesta in the gut. The model assumes that the foregut contains a pool of large particles and a pool of small particles and allows for the possibility that these leave at different rates. The same applies to the hindgut. Large particles are broken down into small particles in the foregut but not in the hindgut. In foregut fermenters, particles from the foregut are fermented and particles from the hindgut are also fermented. In hindgut fermenters, only particles from the hindgut are fermented.

The rate of fermentation is given by the numbers on the lines leading to the fermentation label (position the mouse on these for confirmation), the fraction (i.e. proportion of the total particle flow) rate of flow of particles into the different pools are given as numbers on the lines connecting the pools together as well as the faeces which are excreted.

Patterns of intake and absorption
These graphs show patterns of nutrient supply which differ between digestive strategies. You might also observe some asynchrony in nutrient supply which some would suggest might be important in metabolic control of intake. In particular watch how the pattern of absorption of short-chain fatty acids and amino acids changes depending on diet quality and gut type.

Energy supply
These stacked bar graphs show how the animal obtained its energy requirement. Herbivores can obtain energy from three sources. (i) Direct from the plant (as cell contents = cell solubles) or

(ii) indirectly as short chain or volatile fatty acids resulting from the fermentative digestion of plant cells walls by gut bacteria, protozoa and fungi. There are three major fatty acids acetic acid (CH3COOH); propionic acid (CH3CH2COOH) and butyric acid (CH3CH2CH2COOH). On the legend, these are denoted as C2, C3 and C4 respectively.

(iii) the final source of energy is microbes that have been washed out of the stomach of foregut fermenters which are digested in the midgut or small intestine.

The graph shows where the absorbed energy has come from in terms of multiples of maintenance (MM - see above).

Some Questions

  1. Conduct experiments to show the critical size that herbivorous marsupials and eutherians must be to maintain themselves on (i) different diet types (grass, forbs and browse). Is their any interaction with digestive physiology?
  2. Do foregut fermenters or hindgut fermenters rely more on fermentation as a source of energy?
  3. At what body size do hindgut-fermenting herbivores gain appreciable energy from fermentation?
  4. As pasture quality declines throughout the dry season of the northern Australian Savannah’s, both kangaroos and sheep find it increasingly difficult to maintain themselves. Collect data to answer whether sheep or kangaroos (of a similar size) are better suited to these conditions when eating a diet of grass. Collect data to show whether any difference is a consequence of digestive anatomy or different maintenance requirements.
  5. Evaluate the suggestion that small marsupial browsers gain appreciable advantage from selective retention of fine digesta particles in the hindgut.
  6. What is the pattern of short chain fatty acid absorption and amino acid absorption in both hindgut and foregut fermenters eating different qualities of diet? Explain the basis for any variation.


  • Illius, A.W. and Gordon, I.J. (1992) Modelling the nutritional ecology of ungulate herbivores - evolution of body size and competitive interactions. Oecologia 89:428-434

Thermal Balance in reptiles


This practical is a computer simulation of the thermo-physiology of reptiles. It replaces an experiment using live lizards (blue tongue skinks) that we ran previously.

Computer simulation exercises are being introduced as an important part of teaching large practical classes in Second Year level. We have done this for several reasons - primarily in relation to the ethical issues arising from the use of live animals in teaching. These include (i) large class sizes requiring large numbers of animals, (ii) long experiment times which compromise an animal's behavioural responses (iii) use of live animals minimizes student input to experimental design because procedures have had to be approved by an Ethics Committee in advance and (iv) the unwillingness of some students to do live animal experiments.

This is the second version of this programme but incorporates some new features including a scren where you can move the animal into several different microclimates.Most of the bugs should have been eliminated but we are particularly interested in your opinions and responses. If you discover bugs or conflicts please notify us by email or a note giving as much detail as possible. We can’t fix bugs during the semester without a major effort but you should be able to work around any minor problems. The model is not a perfect representation of the physiological processes but it is more than adequate for our purposes.

The programme can be run in two modes

  1. Static Mode – alows you to change aspects of the environment and animals and run the simulation over several hours.
  2. Mobile Mode – allows you to move the reptile that you have specified between three different micro-environments – the top of a rock, the shade of a rock and underneath the rock over a 24 h period. The environnmental conditions prevailing during that 24 h period can be specified.

Getting started - What some of the switches mean

i) Animal variables

Weight (kg)
The programme will accept body weights between 10g and 1000kg. You must enter the values in kilograms. Therefore the limits are 0.01 and 1000. I suggest that you focus your investigations on say three body masses. I suggest a typical value for common blue tongues is about 1kg; a small blue tongue is about 150g. You may also wish to see what happens to animals of 0.02 kg and a very large animal (obviously not a blue-tongue!) of 20kg. While you will not be able to play Jurassic Park, you will certainly gain an idea of the thermal inertia of large reptiles which may give you some insights into the debate about "hot-blooded dinosaurs".

Body temperature
The body temperature range is 2° C to 50° C. The programme will accept higher temperatures but performance maybe erotic outside this range. The typical range that a lizard might experience is between about 10° C and 40oc. I know of one species in the Middle-East that has a preferred maximum of 42° C.

Eccritic temperature
Selection of the correct eccritic temperature is very important. The major weakness of the model is that it relies too much on the selected eccritic temperature. The eccritic temperature is the preferred or selected body temperature of an animal and will generally be between 32 and 40° C. You should use a lower eccritic temperature for smaller animals - for example a 20g animal may have an eccritic temperature of say 30° C whereas large animals will have eccritic temperatures of 38° C to 40° C. The programme will accept a greater range but again the further you go from the ranges seen in the real world, the less reliable will be the simulations.

(ii) Environmental variables

Julian day
The Julian Day is simply the number of the particular day of the year. For example, January 1 is "1"; July 1 is "181" and December 31 is "365". Variations in this setting serve to vary the angle of the sun above the horizon and so vary the intensity and duration of solar radiation. It should have no effect if you move the animal into the shade.

Air temperature
The range of air (or ambient) temperatures accepted by the programme is between 0 and 100° C but 50° C is about the upper ambient temperature measured on earth I suggest that you go no higher than this. Most previous experiments have been performed at air temperatures between 20° C and 40° C.

This programme was developed with colleagues in Scotland and used Northern Hemisphere equations for the angle of the sun. For the Southern Hemisphere you need to enter the value as a negative.

  • Hobart 49oS Brisbane 27oS
  • Melbourne 37oS Townsville 19oS
  • Sydney 33oS Cape York 12oS

Time past Midnight
This should be self-explanatory and serves to allow variations in solar load.

(iii) Options

The behaviour switch allows the animal to defend or reach an eccritic temperature by behavioural means (as well as any physiological means). For example if radiant heat load is too high, typical behaviours might be to move to a shaded area. Alternatively, an animal might bask in sunlight to allow its body temperature to increase more rapidly.

Skin colour
The skin colour of many lizards changes as their body temperatures change. Although this is not very noticeable in blue-tongues, other species such as the Spiny tailed Lizard of the Middle-East goes from dark brown to almost pure white as body temperature approaches 42oC.

The Shade/Exposed switch allows you to remove the input of solar radiation. In effect at the same air temperature you should see a much more rapid rate of heat transfer and hence body temperature change when solar radiation is allowed. In the absence of solar radiation heat transfer will mainly be effected by convection. An interesting "experiment" might be to allow behaviour and move the animal into shade and then into exposed conditions.

Mobile Mode
There are some additional switches when running the animal in “Mobile”mode Note in particular that you can change the speed of the simulation with the sliding switch. You should use slow settings to give you time to observe what is happening to the body temperature and make a decision as to where to move the icon “animal”.

Note that the graph now covers a 24 h period.

(iv) Mechanics and printing

The screen will hold a several graphs at any one time. This will enable you to plot say and animal heating from 20° C to 40° C and then cooling from 40° C to 20° C. You will then need to either print the two graphs (Print Graphs) or the screen (Print Form) or else clear the screen (Clear Graph) before starting another "experiment". "Print data" will print a list of all the data from which the graphs were plotted. At present there is no facility to export the data to a spreadsheet.

The programme also produces a plot of Heart rate vs Body temperature. However, at this stage the Heart rate graph cannot be printed - even if it is on the screen when you click on "Print Form". You should make notes of the heart rate data and output the data if you want to use those results. You can move the Heart rate graph around the screen by clicking and dragging or double clicking will erase it completely.

The Animal and Environment variables can be changed by typing a new value in the box.

Some advice
To answer questions about the degree of physiological control that lizards have over their body temperature, you will need to do some controlled experiments. I suggest that initially you do this in “Static Mode”. This means (i) turning behaviour "off" (ii) removing the effect of solar radiation by putting the animal in shade. This will then be equivalent to many of the experiments reported in the literature. I suggest the following approach

  1. read these notes again!
  2. spend a short session playing with the programme to see what it can do.
  3. read some of the references so that you know what experiments will be worthwhile doing. There are far more possible combinations than are either necessary or sensible. Try not to vary too many factors.
  4. design some useful experiments to answer the questions you have identified from your reading.
  5. Perhaps then ask how modifying one further factor might change your conclusion.

Build up your investigations in this way rather than simply changing a number of factors randomly or simultaneously.


  • Bartholomew, G.J. and Tucker, V.A. (1963) Control of changes in body temperature, metabolism and circulation by the agamid lizard Amphibolurus barbatus. Physiological Zoology 36: 199-218.
  • Bartholomew, G.J. (1982) Physiological control of body temperature. Pages 167-211 in C. Gans (ed) Biology of the Reptilia. Volume 12 (Physiology C). Academic Press: New York.
  • Fraser, S. and Grigg, G.C. (1984) Control of thermal conductance is insignificant to thermoregulation in small reptiles. Physiological Zoology 57:392-400