From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!mojo.eng.umd.edu!cs.umd.edu!news.umbc.edu!haven.umd.edu!purdue!lerc.nasa.gov!magnus.acs.ohio-state.edu!mail-news-gateway From: rumpf.1@osu.edu (Robert Rumpf) Newsgroups: bionet.general,bionet.molbio.evolution,bionet.software Subject: DNA ML Questions Date: 1 May 1995 17:18:00 -0400 Organization: The Ohio State University Lines: 17 Sender: root@magnus.acs.ohio-state.edu Message-ID: NNTP-Posting-Host: charm.magnus.acs.ohio-state.edu Xref: biosci bionet.general:14957 bionet.molbio.evolution:2766 bionet.software:11948 We've been using Fast DNAml to do some phylogenetic trees and have some general questions about ML algorithms in general: Is it necessary to bootstrap ML trees, since the ML algorithm is in itself a statistical procedure? Also, should we expect bootstrap values to be inherently lower with the ML algorithm (as opposed to parsimony or distance methods)? We've run trees on a various data sets of 37 taxa with over 2000 characters and found that the ML algorithm consistently gives us MUCH lower bootstrap values...thanks for any and all help! _____________________________________________________________________ Bob Rumpf (rumpf.1@osu.edu) OSU Molecular Genetics: "We MAKE Friends" _____________________________________________________________________ *** Magic: The Gathering: It's not just a hobby anymore... *** http://calvin.biosci.ohio-state.edu/~rrumpf/rrumpf.html _____________________________________________________________________ From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!biosci!not-for-mail From: ismb95@biu.icnet.uk Newsgroups: bionet.biology.computational,bionet.software Subject: ISMB-95 REGISTRATION DETAILS Date: 1 May 1995 20:36:47 -0700 Organization: Imperial Cancer Research Fund Lines: 257 Sender: biohelp@net.bio.net Approved: comp-bio-moderator@net.bio.net Distribution: world Message-ID: <3o2v1aINN860@beadle.lif.icnet.uk> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.biology.computational:631 bionet.software:11955 REGISTRATION INFORMATION ISMB-95 ======= The Third International Conference on Intelligent Systems for Molecular Biology July 16 - 19, 1995 Robinson College, Cambridge, England * FULL REGISTRATION MATERIAL AND LIST OF ACCEPTED PAPERS NOW ON WWW * ftp://ftp.icnet.uk/icrf-public/ismb/ismb95.html * Date for early registration discount 4th June * -------- This file contains: Description of ISMB-95 Tutorials ASCII Text form of Registration Form (See WWW for full registration pack) -------------------------------------------------------------------------- TUTORIALS All tutorials will be offered on Sunday, July 16. There will be parallel sessions geared for introductory issues and advanced issues. Tutorial costs are 50 UKpounds for a single tutorial (65 UKpounds including lunch) and 95 UKpounds for two tutorials (including lunch). INTRODUCTORY AM TUTORIALS (July 16, 1995, 10.00am - 1.00 pm): T1 Molecular Biology for the Computer Scientist (Shankar Subramaniam) A description of the fundamentals of Molecular Biology, specifically aimed at the computer scientist. Topics to be covered include: the macromolecules of living systems,nucleic acid structure and function,protein structure and function, metabolism, energy flows, evolution and experimental methods in molecular biology. T2 Intelligent Systems for the Molecular Biologist (Doug Brutlag) An overview of the intelligent system technologies that have been applied to molecular biology. Includes knowledge representation, machine learning, advanced database methods, knowledge-based simulation, and other techniques. All topics will be taught using examples from everyday molecular biology research,and this tutorial is intended to be accessible to biologists without computational training. ADVANCED AM TUTORIALS (July 16, 1995, 10.00am - 1.00 pm): T3 Protein Structure Prediction (Sean O'Donoghue and Burkhard Rost) A review of the state of the art of computational techniques used in experimental determination of structure, and in the theoretical prediction of protein function and 1D, 2D, and 3D structure. Issues covered include: similarities and differences between the calculation methods used in deriving structures from X-ray crystallography and NMR spectroscopy; principles and methods relevant to closing the gap between known protein sequences and known structures; methods for testing and validating predicted structures. T4 Machine Learning Approaches to Molecular Biology (Pierre Baldi) A broad overview of the applications of machine learning to problems in molecular biology. Discussion of statistical induction and modelling, and its relevance to these methods. Discussion of the Bayesian framework, Cox-Jaynes axioms, hierarchical modelling, and model fitting and optimization. The latter portion of the tutorial will be dedicated to a detailed treatment of Hidden Markov Models and Stochastic Grammars. INTRODUCTORY PM TUTORIALS (July 16, 1995, 2.15 pm - 5.45 pm): T5 Linguistics of Biosequences (David Searls) Biological sequences viewed as strings in a language. Formal language theoretic aspects of DNA and protein sequences. Review of proofs of the positions of biologically relevant languages in the Chomsky hierarchy, closure properties under biological operations, and the important role of syntactic ambiguity in genetic material. Applications of grammar-based approaches to biological sequences, including syntactic pattern recognition and representation of inter-and intra-molecular interactions in three-dimensional structure. T6 Protein Evolution (Bill Pearson) This tutorial will present a review of our ability to look back through evolutionary time using protein sequences and protein structures. Doolittle's classification of ancient, middle-aged and modern proteins will be used to examine different modes of protein evolution, looking both at sequences and structures. The evidence for and against an informative role for exon structure will be discussed. Strengths and weaknesses of using similarity to infer homology, and exploration of the confidence limits that can be placed on inferences of homology and structural similarity will be a focus of the tutorial. The statistics of sequence similarity scores, information content and scoring matrices, and the strengths and weaknesses in current comparison methods will be summarized. ADVANCED PM TUTORIALS (July 16, 1995, 2.15 pm - 5.45 pm): T7 Computational Methods for Molecular Docking (Gerhard Klebe,Thomas Lengauer) Chemical and computational issues in the inference of molecular docking. Types of chemical interactions, phases of the docking process, and enthalpic and entropic methods for evaluating docking potential. Approaches to computing receptor-ligand interactions, including algorithms, data structures, computationally efficient models, and validation methods, presented from an application-oriented viewpoint. T8 Statistical Foundations of Multiple Sequence Alignment and Structure Prediction (Chip Lawrence) The significance of statistical methods for multiple sequence alignment, and their conceptual foundations. Boltzman-like models of residue frequencies, permuted data likelihood, expectation maximization and Gibs sampling. Refinements in the method to include multiple elements (gaps) and manage the flexibility vs. sensitivity tradeoff. Incorporating structure into the calculation, including protein threading and stochastic context free grammars for RNA alignment. -------------------------------------------------------------------------- ISMB-95 REGISTRATION FORM NAME: .............................................................. AFFILIATION: .............................................................. ............................................................. ADDRESS: ............................................................. ............................................................. ............................................................ PHONE: ............................. FAX: ............................... E-MAIL: ..................................................................... Are you:- Full-time Student* ...... Other ...... Male ...... Female ...... * Please include proof of full-time student status ...... Tick here if you would like information about travel support TUTORIALS (select at most one tutorial from each column) AM ...... PM ...... AM 16/7: PM 16/7: T1: Molecular Biology for the T5: Linguistics of Biosequences Computer Scientist T6: Protein Evolution T2: Intelligent Systems for the T7: Computational Methods for Molecular Biologist Molecular Docking T3: Protein Structure Prediction T8: Statistical Foundations of T4: Machine Learning Approaches Multiple Sequence Alignment to Molecular Biology and Structure Prediction ONE TWO 50 UKpounds/$85/65ecu 95 UKpounds/$155/125ecu (or 65 UKpounds/$110/85ecu (including lunch) including lunch) UKpounds/$/ecu ...... CONFERENCE REGISTRATION Early* Late Full-time student* 125 UKpounds/$200/160ecu 150 UKpounds/$240/195ecu Other 150 UKpounds/$240/195ecu 175 UKpounds/$280/225ecu UKpounds/$/ecu ...... * Early registration = before 4 June 1995 ACCOMMODATION/MEALS Accommodation Package @ 260UKpounds/$420/330ecu UKpounds/$/ecu ...... Extra Night's Accommodation (B&B) @ 50 UKpounds/$85/65ecu per night (Pre-Tutorial: 15 July Post-Conference: 19 July) Please specify date(s) .............. UKpounds/$/ecu ...... Non-Residential Lunch only @ 15 UKpounds/$25/20ecu per day (17, 18 and 19 July) Please specify date(s ) ............. UKpounds/$/ecu ...... Conference Dinner tickets @ 35 UKpounds/$60/50ecu UKpounds/$/ecu ...... TOTAL UKpounds/$/ecu ...... I enclose my cheque/money order (UKpounds, $US, ecus - please specify) made payable to Imperial Cancer Research Fund (ISMB-95) or debit my card: Access/Visa/Amex/Diners Club (please specify) Card No: Expiry Date: Signed: Date: Please list:- Any special dietary requirements .............................................................. Any special accommodation requirements (eg twin room) .............................................................. Whether wheelchair access is required .............................................................. Please state if you would like to present a poster at the Open Poster Evening - to be held on Tuesday July 18, 6.00pm - 7.30pm Yes/No Return Registration Form with payment to:- ISMB-95 Registration c/o Dr C J Rawlings Biomedical Informatics Unit 61 Lincoln's Inn Fields LONDON WC2A 3PX Fax: + 44 (0)171 269 3067 From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!cs.utexas.edu!news.sprintlink.net!noc.netcom.net!ix.netcom.com!netnews From: Latnimag@ix.netcom.com (Leighton) Newsgroups: bionet.software Subject: Population, Resources, and Ecology Software sources Date: 2 May 1995 01:40:16 GMT Organization: Netcom Lines: 10 Distribution: world Message-ID: <3o42i0$pk3@ixnews2.ix.netcom.com> References: NNTP-Posting-Host: ix-pas11-17.ix.netcom.com In bo931@FreeNet.Carleton.CA (Colbert Philippe) writes: I am looking for software (primarily CD-ROM, Laser Disc, or video) dealing with the biological, ethical, economic, and political issues involving population control, resource managment, and ecological preservation. I am particularly looking for software that would be used by the teach in class at a college level. Please let me know if there is anything out there - how good is it - does it work...thank you for your help. From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!rutgers!gatech!newsfeed.pitt.edu!hudson.lm.com!news.pop.psu.edu!ra.nrl.navy.mil!usenet From: rwadkins@cbmse.nrl.navy.mil (rmw) Newsgroups: bionet.software Subject: Skatchard analysis Date: 2 May 1995 22:26:50 GMT Organization: Naval Research Laboratory Lines: 18 Sender: -Not-Authenticated-[6745] Distribution: world Message-ID: <3o6bja$385@ra.nrl.navy.mil> References: <3o3dje$mmo@dartvax.dartmouth.edu> NNTP-Posting-Host: rmw-6900.nrl.navy.mil X-Posted-From: InterNews 1.0.1@rmw-6900.nrl.navy.mil Xdisclaimer: No attempt was made to authenticate the sender's name. In article <3o3dje$mmo@dartvax.dartmouth.edu> Timothy.J.Moser@Dartmouth.EDU (Timothy J. Moser) writes: > Is there a program available for the Mac which allows for easier > calculation of Skatchard analysis? A shareware or free program would be > best. > > Thanks in advance - Tim > I think you have to be a bit more explicit. I mean, a Scatchard analysis, while being highly error-prone (Klotz, Science 217:1247 (1982)), is really just a straight line that one could do with a hand calculator. Most curve fitting software (e.g. Kaleidagraph) would do this too. If you want something more extravagant, like von Hippel's equations, then that's a different matter. Randy From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news.starnet.net!wupost!uwm.edu!reuter.cse.ogi.edu!netnews.nwnet.net!news.u.washington.edu!root From: meir@zoology.washington.edu (Eli Meir) Newsgroups: bionet.software Subject: Bio Education Software FAQ (2 of 2) Date: 2 May 1995 03:18:54 GMT Organization: Dept. of Zoology, Univ. of Washington Lines: 716 Sender: -Not-Authenticated-[3641] Message-ID: <3o48au$t6b@nntp3.u.washington.edu> NNTP-Posting-Host: nntp5.u.washington.edu X-Posted-From: InterNews 1.0.5@quaternary.zoology.washington.edu Xdisclaimer: No attempt was made to authenticate the sender's name. (3j) Blind Watchmaker This is an implementation of the program Richard DawkinÕs used in writing his book of the same name. The screen displays a population of tree-like stick figures, each figure drawn according to a Ôgenetic codeÕ of parameters. Parameters are such things as the number of branch points, the length ratio between the larger and smaller branches, whether the figure is symetric or asymetric, the angles between branches, and so on - about 16 all together. The figures evolve through artificial selection, meaning you are presented with a series of figures on the screen which are all slightly different from each other, and you select which one you want to breed to make the next population. You can also ask the computer to ÔdriftÕ through parameter space, showing a little movie of different shapes as it goes, or you can search the space more methodically. Using this program you get a nice demonstration of how evolution can generate fairly complex shapes from pretty simple beginnings, and how selection can bring this about. The user interface is easy to figure out. The program seems to have a little trouble with newer computers. You can run it, but you canÕt multitask. However, we have an old version of the program, so perhaps this has been fixed. Computer: Macintosh Source: W. W. Norton & Company, NY Cost: Low (3k) Simlife This is a commercial game, put out by the same people that did SimCity, SimAnt, SimEarth, and more. The idea is to build an ecosystem, by designing animals and plants to put into it and then letting them run around have sex, die, etc., with evolution and mucking around from god (you). Being a commercial program, its very slick, with nice graphics and animation, sound effects, full color maps of the game world, and a well-written manual. To make a creature, you give it a number of attributes such as what types of food it eats, how it moves (swim, fly, walk), what type of movement pattern it has, how long it takes to reach maturity and start having kids, and many, many more (probably over 50 characteristics total, many of them continuously variable). You also have some control over weather, the terrain in your world, how quickly evolution happens, and other factors. SimLife is a really fun game, you could easily spend hours playing it. That said, its probably not too useful as a biology teaching tool, especially at the college level. When the game first came out, there were several discussions on the net about its utility as a teaching tool, and for the most part people gave it reserved praise at best. Still, it might be worth looking at. If nothing else, its a good way to procrastinate, and its better for your students than television. Computer: Macintosh Source: Any mail-order company Cost: Low (3l) Populus Computer: DOS Source: ecology.ecology.umn.edu (IP# 134.84.144.16) Cost: Free (3m) PopDyn This program lets you play with some basic ecology models. The included models are exponential and logistic growth, lotka-volterra competition between two species, lotka-volterra predator-prey, a four species lotka-volterra type system, and a predator / two competing prey system. The last of these is done in a separate program with a different interface. For all the others, you can change the parameters associated with each model using a novel but intuitive control on the screen. As each model runs, PopDyn shows the population sizes in one window, and a phase-portrait in a second window. The lines are color-coded for the different species, and in addition there are cute icons of each species which draw the curves. There are several options for controlling the look of the graphs, the speed and so on. You can also make parameters in the models change stochastically over time. The accompanying manual includes some exercises for students to do with the program. This is a very nice portrayal of these basic ecology models. The program is very visually appealing and easy to use, with lots of cute pictures and rudimentary but effective online help. There are a few features missing that would be nice, such as being able to scroll and change the scales on the graphs, and the ability to print. A more substantial missing feature is the ability to change the initial population sizes. But these are minor complaints, and will not bother most students. This program should be very well suited for use in an introductory ecology class where the included models are introduced to the students, especially for students without the math background to understand the equations analytically. Computer: Macintosh Source: Ron J. Etter, Biology Department, University of Massachusetts, 100 Morrissey Blvd., Boston, MA 02125. Phone: 617 -287-6613, email: etter@umbsky.cc.umb.edu Cost: Free (3n) Fish Farm This program puts you in charge of raising fish in a pond. You are the manager of the farm, and you need to figure out how best to raise the fish to maximize your profit. You can control a variety of factors including how densely you initially stock the fish, how much protein you put in the fish food, the rate at which you turn over the water, how much you aerate the water, and so on. Your job is to experiment with these different variables to find the optimal way to raise fish in your farm. The program lets you change each variable separately, make a run with that setting, and then gives you a summary of how you did in that run. As the model runs, it shows you various statistics on the screen telling you how well youÕre doing. The program will also take the data from several experiments and make graphs of profit versus different values of one of the variables. This program is quite engaging, and really makes you think about how to go about finding out an answer to a question which depends on many variables. For instance, you will have trouble finding the optimal fish growing method if you donÕt change one variable at a time. The user interface is quite clear and easy to use. Everything is done through buttons and dialog boxes where you can type in numbers, and all the information you need is on the screen. The one annoying thing about the interface is that to go from one experiment to the next you must traverse four or five dialog boxes which gets tiresome after a while. However, other than that minor complaint, this program is quite nice. Computer: Macintosh Source: Benjamin/Cummings Publishing Company, ?? Cost: Low? (4) Physiology and Neurobiology (4a) Neuro 140 This is a collection of three programs written by Larry Abbot at Brandeis University which let you play with simple models of channels, voltage or current clamped neurons, and propagating action potentials. The Channel program is a simulation of patch-clamping, where you can look at one of four channel types used in a typical axon (K and Cl leakage, fast Na and delayed rectifier K). You can stimulate or not, change the stimulus duration and intensity, ionic concentrations, and a couple other things. The output is plots of current over time. Neuron is a simulation of voltage-clamping or current-clamping a neuron. You give the neuron a voltage step or current pulse and watch what happens. You can control the pulse, change properties of the membrane, and add TTX or TEA. You can also add in a synapse though I didnÕt quite understand what this was simulating. Cable simulates an axon propogating a series of action potentials, using the cable equations. You get a view from two stationary electrodes over time, as well as a view of the potential in space (so you can watch the waves propogating - pretty nice). Again, you can change several parameters such as the stimulus, the cable dimensions, the currents involved, and more. All of these programs are quite easy to use. Each one has windows on the screen which show the graphs, and another window with with a few dialog boxes that let you change all the parameters. There is no manual, however (at least we havenÕt seen one), so you have to figure everything out on your own, and you will also need to write up your own laboratories using the programs, since there is no real on screen guidance given for what to do. The trio of programs would make a very good collection to be used in an introductory neurobiology course, as laboratory exercises to accompany the lectures and textbook. Computer: Macintosh Source: Larry Abbot, Department of Physics, Brandeis University, Waltham, MA 02254. Cost: Free (4b) Axon A fairly simple model of hogkin-huxley dynamics in a squid giant axon, where the user can set the stimulus and watch what happens to voltages, currents, and channels. Also includes voltage clamping and a few other goodies. Computer: Macintosh Source: BioQuest asdg@umdd.umd.edu or see address above under Resources. Cost: Low (single user) / High (site license) (4c) Isolated Heart Laboratories This program lets you play around with heart function. You have a choice of several different graphs that show you things like pressure in the left ventricle versus time or volume. You can change a few parameters like ÔPreloadÕ, ÔDiastolic StiffnessÕ, and ÔNumber of BeatsÕ, and see what happens on the graphs. Computer: Macintosh Source: BioQuest asdg@umdd.umd.edu or see address above under Resources. Cost: Low (single user) / High (site license) (4d) Neurosim II We have not yet seen this program. However, its advertised as being a series of modules, each of which simulates something in neurobiology and lets you play with it. ThereÕs one that simulates patch clamping a single channel, another simulating a bursting neuron, a couple modules looking at neural networks, a couple looking at cable properties and hodgkin/huxley dynamics, etc., 10 modules in all. We hope to get a demo version soon to give a better description and evaluation. Computer: DOS Source: BioSoft, PO Box 10938, Ferguson MO 63135. Tel. (314)524-8029. email: ab47@cityscape.co.uk. Cost: High (4e) Frog Dissection and other dissection tutorials This hypercard-like tutorial shows a series of pictures of what you see when dissecting a frog. You can go to a specific part of the frogs body and see a labeled version of what the inside should look like, with things identified and one-line descriptions of function. ThereÕs also a step-by-step guide to dissecting a frog, and a self-test on different parts of the frog. All pictures are in color, but they are rough sketches, not actual photos of a frog. We only have the demo version. The same company makes other tutorials for other common dissection animals, including worms, frogs, crayfish, and a few others. They also indicate that they are considering CD versions of these programs, presumably with much nicer pictures. This program is supposed to accompany an actual dissection, not replace it. I could be persuaded that this might be useful, particularly as a study guide before or after the dissection to prepare for or reinforce what has nbeen seen in an actual animal. Unless you have computers next to your dissection tables, it wouldnÕt be useful as an actual study guide for the dissection. As mentioned above in the philosophy section, we are a little sceptical that programs such as this which take a study guide and put it on the screen are all that useful, even if they are ÔinteractiveÕ. However, if you think that programs of this type will help your students, then these programs might be worth looking at. Computer: Macintosh Source: Cross Educational Software, 504 E. Kentucky Ave., Ruston, LA 71270. Tel. 1-800-768-1969. Demo version available at various anonymous ftp sites. Cost: Low (4f) NeuroLab (Note - we have only seen a demo) This is a collection of modules usable in the program Extend which let you construct and play with neural networks. Extend is a Stella-like program (see review) which lets you graphically construct and solve ODE models. Some of NeuroLabÕs introductory level modules are things like Adaptive Weighted Summation, Sigmoid, Linear, I/O Control and BP Control. These modules can be used to construct simple neural networks, such as network to do the XOR function, or much more complex networks. Using the Extend interface, you lay out the models nicely, make graphs of the results, and even animate components of the model as it runs. I am not a particular expert in this field and this is rather sophisticated, so you should check the demo yourself if youÕre interested. I think these modules would only really be useful in an upper-level modelling course where you were focusing quite a bit of time on neural networks. In that case, having these modules around might be quite nice and a big time-saver. Its also possible that an instructor could use these modules to make a neural network that students could then play with. However, due to the learning curve involved both in learning these modules and in learning how to use Extend, I am not sure this is the best way to introduce neural networks unless you are really going to spend some time on them. Computer: Macintosh Source: Mikuni Berkeley R&D Corp., 4000 Lakeside Dr., Suite 230, Richmond, CA 94806, Tel: 510-222-9880 Demo available on Info_Mac mirrors. Cost: High (4g) SymBioSys Computer: IBM (Windows) Source: Critical Concepts, 5240 S. Harper Ave., Suite #1, Chicago IL 60615, USA. (312)-324-3600. Online info at http://http.bsd.uchicago.edu/cci. Cost: High (4h) Quantitative Circulatory Physiology Computer: IBM Source: tcoleman@fiona.umsmed.edu, Biological Simulators, P.O. Box 14014, Jackson, MS 39236-4014. Cost: Low (5) Cell and Molecular Biology (5a) Genetics Construction Kit This is a problem-solving program based on fly genetics. You get a vial of flies, with certain traits, and you have to figure out the genetics of those traits by doing various crosses. The traits can range from simple dominant/recessive to multiple gene, multiple allele systems with codominance, linkage, sex-linkage, and probably more. The program has a nice intuitive interface. As a note of historical interest, I believe that this is the original BioQuest program. Computer: Macintosh Source: BioQuest asdg@umdd.umd.edu or see address above under Resources. Cost: Low (single user) / High (site license) (5b) SequenceIt! This program is a puzzle-solving program. You are presented with a completely unknown protein and asked to sequence it, using around two dozen standard (I assume) biochemical techniques, such as acid and base degradation, cleavage by various proteases, various degradation techniques, and so on. Again, this program has a very nice display and user-interface, with some cute (though probably eventually annoying) animations. I suspect students would have a lot more fun with it than with the standard cookbook chem lab exercises, since you can concentrate on the puzzle instead of the vials. Computer: Macintosh Source: BioQuest asdg@umdd.umd.edu or see address above under Resources. Cost: Low (single user) / High (site license) (5c) PurifyIt! This program is another puzzle solving program similar in design to SequenceIt! above, except here you get a flask with a number of proteins in it, and you have to purify one of them, using one of a number of standard (I assume) purification techniques such as dialysis and various gel schemes. This program seems a little unfinished, with not quite as good an interface as SequenceIt!, but basically theyÕre the same concept. Computer: Macintosh Source: BioQuest asdg@umdd.umd.edu or see address above under Resources. Cost: Low (single user) / High (site license) (5d) RateIt! In this program you are given flasks of enzymes, substrates, inhibitors, etc., and you must perform various tests to discover the kinetic properties of the enzymatic system, using standard tools and experiments of enzymoligists (is that a real term). You can change pH, temperature, etc. and do experiments to find rates of enzyme activity. You can also compare results to theoretical models such as michaelis-menton. (This program only got a short look, so there may be a lot more here). Computer: Macintosh Source: BioQuest asdg@umdd.umd.edu or see address above under Resources. Cost: Low (single user) / High (site license) (5e) Enzyme This is a combination of a hypercard stack with a simulation of enzyme kinetics. The hypercard stack provides the front-end which lets the user change parameters in the model and determine reaction rates. Has graphing capabilities for the results. Quite nicely done. This program is not, however, as comprehensive as the BioQuest version, and only includes two built-in enzymes (I donÕt see a way to add more). Computer: Macintosh, also needs Hypercard 2.2 (wonÕt work with Hypercard player). Source: David Kesler, Rhodes College. email: KESLER@ns.rhodes.edu Cost: Free (5f) MacMolecule This program allows you to build and display models of molecules. It will do any of three traditional diplay type - ball and stick, space-filling, and wire-frame. The molecules are displayed really nicely, in full-color, and you can rotate them around using the mouse (its fast! - quite impressive). They have some molecules included, and you can make your own with a word-processor. Computer: Macintosh Source: anonymous ftp sites Cost: Free (5g) Visual Genetics (Note - we have only seen a demo version) This is a series of animations designed to accompany a course in cell and molecular biology. The animations are divided into seven categories: DNA structure and replication, Protein synthesis, Cell division, Recombination and mapping, Mutation repair and regulation, Biotechnology techniques, and Cell biology. Each category has approximately 10 animations in it. The animations are more than stick-figure but less than realistic-looking, and are stopped many times to show explanatory text and labels. Along with animations, the program has multiple choice and problem-solving questions, and can also present you with a diagram which you must then label correctly. You can input your own questions if you wish. None of these were active in the demo version. In the demo version we saw, only two animations are active, a demonstration of meiosis, and an animation of several biochemical techniques for separating out proteins, dna, and rna. The meiosis animation seems useful to me as a visual aid in understanding what is happening, since meiosis is a confusing concept for many students, and the animation can show the steps fairly clearly. The biochemical techniques animation seems less useful, and I believe a good description in a textbook with nice pictures should do just as well or better at explaining the techniques. However, perhaps the television appeal of having things move on the screen will help some students to remember these techniques better than they would have through reading. In general, this package should help students who learn visually to understand and remember some introductory concepts in cell and molecular biology, as an adjunct to (but not a replacement for) a good textbook, laboratory, and video tapes of live cells. It should be especially helpful for things such as meiosis and dna replication which are somewhat complicated to visualize from a description in a textbook. Computer: Macintosh and IBM Source: BioAnimate Productions, 28 Askin St., London, Ont. N6C 1I3. Phone: 519-432-5800. Demo available from http://www.inform.umd.edu/EdRes/ Topic/AgrEnv/Biotech/Software/bio-anim Cost: Low to High (depending on number of animations purchased) (6) General purpose software useful in education (6a) Stella [EM and AS] This program lets you construct and run mathematical models using a very easy to understand graphical interface. For each element in your model, you make a box on the screen. Inside that box, you put the starting amount of that element. Then you use the mouse to draw arrows between the boxes representing flows of stuff from one box to another, or effects of one box on another. For each arrow, you type in an ordinary differential equation which specifies what that arrow does. For instance, to model growth of a tree, you might have a ÔtreeÕ box, a ÔsunlightÕ box and a ÔCO2Õ box, and arrows coming from the sunlight and the CO2 into the tree. The tree would start out with a certain mass, and the sunlight and CO2 could each be given appropriate starting values and changes over time (e.g. you could put the sun on a 24 hour cycle by modelling it with a sine wave) and you would have some equation like ÔdTree/dt = function(sunlight, CO2)Õ associated with the arrows. Then you could run this model and watch the tree grow. The growth of the tree would be represented both by the tree box filling up, and you can also make graphs of any of the variables over time. This program is really nicely designed for teaching. The learning curve is quite small, and even though the equations are not hidden from the user, the interface makes the mathematics behind the models quite transparent. Yet the mathematics is still rigorous, and once students learn to use this tool they can use it for high quality work (plenty of researches use Stella as well). Instructors could also use this program to set up models ahead of time which the students could then play with, though if one of the other programs mentioned in this FAQ does that model, its probably better to use the special program. I think Stella should be useful from advanced undergraduate level courses where modelling is discussed all the way through graduate level courses. One warning is that (as with any mathematical programs) the instructor should probably know something about numerical solution techniques if you donÕt want to get into trouble. Computer: Macintosh (and IBM ?). Source: High Performance Software Cost: Low (ask for educational pricing) (6b) Extend We have not seen this program, except as part of other teaching programs mentioned in this FAQ (NeuroLab, Environmental Decision Making). It appears to be a Stella-like modelling program, with cuter graphics and a more flexible interface. Computer: Macintosh (and IBM?) Source: Cost: High? (6c) Mathematica [EM and AS] Mathematica is a symbolic equation solver. This means that you can type in something like ÔIntegrate 2x + 5Õ and it will spit back Ôx^2 + 5x + CÕ. This is only the simplest example of what it can do. You can give much more complicated equations and ask it to integrate, differentiate, find roots, and many other mathematical operations. All functions can be plotted in many ways, and there are lots of other useful things included (fourier transforms, etc.). This program has a pretty large learning curve, but once you get over the top of the curve it is a very powerful tool for doing all kinds of modelling. As such, it should be quite useful in an advanced undergraduate course or in graduate courses with an emphasis on modelling biology. For more introductory level courses, the program could probably be used by an instructor to make a model which students could then play with. However, if one of the other programs described in this FAQ includes the desired model then you should probably use the specialized program. Computer: Macintosh, IBM, UNIX Source: Available commercially through software stores and mail-order. Cost: High (6d) Maple [EM and AS] Maple is a symbolic equation solver. See the description of Mathematica above. Maple has the advantage over Mathematica of being faster, and having better solvers. Computer: Macintosh, IBM, UNIX Source: Available commercially through software stores and mail-order. Cost: High (6e) Matlab (6f) LabView [EM and DB] LabVIEW is a very powerful data acquisition and analysis program. While the program is not made specifically for education, many people use it in physiology laboratories to make data collection easy for the students. Essentially LabVIEW is a graphical programming environment that uses the construction of 'virtual instruments' as a metaphor. The front panel (the user interface) consists of various controls and indicators (such as graphs, buttons, knobs, etc) and is built graphically by placing different components in a window, and using the mouse to move them around and resize them just the way you want them. The diagram (the 'code' that determines the instrument's behavior) is also built graphically by wiring together icons that represent various functions into a flowchart. Traditional programming structures such as loops and cases are available. A high degree of modularity is supported due to the ability of one instrument to access another as an icon within the diagram. LabVIEW ships with a large library of routines for data analysis (FFTs, statistics, etc.). As is apparent from the above description, LabVIEW does take a little skill to use. While many pre-made instruments are available which do quite a few of the things you are likely to want in a classroom, inevitably you will want to modify them. This does not take a full-blown programmer, but there is a learning curve. On the plus side, once you figure your way around LabVIEW, you will be able to make highly custom programs for each lab in your course quite easily. Such programs could include complex simulations in addition to traditional data acquisition. Also, there are many other teachers using LabVIEW for classes, so you may be able to take modules developed by others and use them as is. All in all, if you are setting up a physiology lab where you intend to use computers, then Labview is a very nice program to use for that. Computer: Macintosh, Windows, Sun Source: National Instruments, 1-800-433-3488. Cost: High (6g) SuperScope [EM and DB] Superscope is a general purpose data collection and analysis program, similar to LabView (described above). It is a very powerful research tool, but is also used in teaching. From within SuperScope, you can design 'programs' that will collect and process data in many different ways. While the design process is not as graphical as in LabVIEW, the basic idea and functionality is the same. SuperScope is more tightly focused on data acquisition and is quicker to get up and running, but less customizable. Elements of the user interface (graphs, buttons, etc.) can be positioned in a window and assigned tasks written in a macro language. However, SuperScope isn't a programming environment (for better or worse, you pick). SuperScope's macro language does include a library of data analysis routines. (We have not used Superscope extensively, and so are not providing a review). Computer: Macintosh Source: GW Instruments, 617-625-4096. Cost: High (6h) Spike Studio Spike Studio is a data acquisition and analysis program written for researchers in neurophysiology, and is also used in several neurophysiology laboratory courses. It was written by the author of this FAQ, so take this description and review with a grain of salt. The program will collect data from several brands of digitizing board (including the macintosh built-in microphone), will show the data on the screen, and includes several types of analyses including spike and burst discrimination, determining frequencies, data averaging, and some other tools commonly used by neurophysiologists. While Spike Studio is not flexible in the way that LabView and SuperScope are, it will do many of the things you would want in a teaching program. ItÕs two advantages are that it does not require any programming or much set-up on your part, and more importantly its free. Computer: Macintosh Source: anonymous ftp sites, such as info_mac or umich. Cost: Free (7) Textbooks on CD (8) Mosaic Sites and other random stuff (8a) Institute for Molecular Virology This site has lots of very pretty pictures of x-ray reconstructions of viral structures. It also has a few animations of things like a virus binding to its host, and interactive pictures where you can rotate viral structures around. In addition, this site is a good source of other information on viruses and virologists. URL: http://www.bocklabs.wisc.edu/ (8b) BioCatalog This is a collection of descriptions of software useful for biologists. They describe a few dozen packages, both commercial and public domain, with information on how to get ahold of them, but no reviews. Almost all the programs are for molecular biologists, falling into categories such as DNA, Proteins, Molecular Evolution, and so on. FTP: ftp.ebi.ac.uk Directory: /pub/databases/bio_catal URL: http://www.ebi.ac.uk/biocat/biocat.html (8c) Neurosciences on the Internet This site has a ton of cross-links to different places on the internet with interesting neuroscience content. Included are links to some programs mentioned in this FAQ. URL: http://www.lm.com/~nab/ (8d) Quantitative Training for Life Sciences This site contains a number of public domain programs for biology instruction, as well as links to other sites with more programs or demos. This site also contains a number of reviews of biology education software done by undergraduates at the University of Tennessee, in a format similar to the reviews in this FAQ. URL: http://mathsun1.math.utk.edu:8000/~gross/quant.lifesci.html (9) Acknowledments Eli Meir is a Howard Hughes Medical Institute Predoctoral Fellow (obligatory acknowledgement). Eli Meir Dept of Zoology, Univ of Washington meir@zoology.washington.edu From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nntp.uio.no!nac.no!Norway.EU.net!EU.net!howland.reston.ans.net!news.sprintlink.net!ten.net!not-for-mail From: Trent@ten.net Newsgroups: bionet.software Subject: FREE CATALOG......********* Date: 2 May 1995 12:05:03 -0700 Organization: The Total Entertainment Network Lines: 18 Sender: news@ten.net Message-ID: <595788@news.ten.net> NNTP-Posting-Host: ten.net Are you tired of paying high prices for software just to find them a week later $$'s cheaper than what you just paid. Then look no farther. Write to Escape@Shasta.com or NRVE491@Prodigy.com to recieve a free catalog on diskette. There also contests and giveaways. The catalog is very easy to go through and easy to order from, just click on what you want to purchase and the order form will print out for you. If you like what you see and also like the prices then tell your friends and give them this address. Then tell them to tell their friends. You can also write on your local BBS's or post anywhere you hang out on the Internet. I tell you this because I have been pricing around town then looking at the catalog and seeing a better price even with the added cost of the postage in this catalog. If you see me out there say HI :) and I'll tell you what I have bought. Trent Trent@TEN.net Trent@MGS.com From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!bvc.edu!yuqian From: yuqian@bvc.edu (Suicidal Freshman) Newsgroups: bionet.software,bionet.software.acedb Subject: New Dedicated Bio-tech/science/chem BBS Message-ID: <1995May2.123030.10878@bvc.edu> Date: 2 May 95 12:30:30 CDT Organization: Buena Vista College, Storm Lake, IA Lines: 27 Xref: biosci bionet.software:11961 bionet.software.acedb:580 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% A NEW BBS IS ONLINE AND NEEDS PEOPLE LIKE YOU TO HELP IT PROSPER The IDT Online Information System is now up and running and needs intelligent users such as yourselves. Anyone interested in Chemistry or Biology or any twist of the two is more than welcome. If you are a user of Oligonucleotides, there is an online order system that allows you to place your order directly into the production facility for 48 hour turnaround. THERE IS ABSOLUTELY NO CHARGE FOR USAGE. YOU DO NOT HAVE TO BE A CUSTOMER TO USE THE SYSTEM Just a sample of some of the discussion forums: Parsitology Classifieds Employment Chemical Engineering Computer Software Biochemistry Programming Molecular Medicine Genetics Organic Chemistry Oligo Design Scientific Humor BioPhysics Cell Biology Internet Topics Biomed Engineering Late Breaking News Immunology NeuroScience Suggestions The system is in place, and we are looking for good users, and a few Forum Moderators, so: Check it out: telnet 204.71.106.202 or telnet idtdna.com %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!val.AgShantz.Arizona.EDU!valeryt From: valeryt@ag.arizona.edu (Valery F. Thompson) Newsgroups: bionet.software Subject: Re: How is SigmaPlot & Stat for Windows compared to for DOS? Date: Tue, 2 May 1995 10:04:24 Organization: Muscle Biology Group, University of Arizona Lines: 34 Message-ID: References: <3nrf4t$5s0@nnrp.ucs.ubc.ca> NNTP-Posting-Host: val.agshantz.arizona.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article <3nrf4t$5s0@nnrp.ucs.ubc.ca> dcwong@unixg.ubc.ca (Donald Chun Kit Wong) writes: >From: dcwong@unixg.ubc.ca (Donald Chun Kit Wong) >Subject: How is SigmaPlot & Stat for Windows compared to for DOS? >Date: 28 Apr 1995 19:19:57 GMT >We currently have Sigmastat & Sigmaplot for DOS (latest versions). We >plan to upgrade our system to a OS/2 oe Windows environment. Does anyone >have any experience or comments on the Windows version of SigmaPlot (2.0 >plus Graph Library Bundle) and SigmaStat? Are these version sbetter than >the DOS ones? Any commetns will be apprecitaed. Thanks. > >Donald Wong >Pathology, UBC >Canada I have been using Sigmaplot for Windows version 2.00 (now 2.01 if you call and ask for it) for some time. It fixes some of the bugs in version 1.0, but still seems to have some bugs. The biggest gripe I have had with the windows version is that it cannot completely translate your Sigmaplot for DOS ver 5 files. The data and axes for the graphs come through fine, but all of the labels are gone. Basically if you need to use those files again, you should either keep the DOS version on your computer or plan to totally recreate the graphs in the windows version. Otherwise, I have been pleased with the windows version. I especially like the ability to easily place the graphs into other applications. I didn't buy the graph library. I already have templates for the graphs that I use most often so I thought it would be a waste of money for me. Sorry I have no experience with SigmaStat. Val Thompson Muscle Biology Group University of Arizona valeryt@ag.arizona.edu From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!is.bbsrc.ac.uk!pc0519.ri.bbsrc.ac.uk!user From: Andy.Law@bbsrc.ac.uk (Andy Law (Big Nose)) Newsgroups: bionet.molbio.gene-linkage,bionet.molbio.genome-program,bionet.software Subject: Bioinformatics & Genome Research Conference Date: Tue, 02 May 1995 11:45:13 +0000 Organization: Roslin Institute Lines: 15 Message-ID: NNTP-Posting-Host: pc0519.ri.bbsrc.ac.uk X-Newsreader: Value-Added NewsWatcher 2.0b24.0+ Xref: biosci bionet.molbio.gene-linkage:666 bionet.molbio.genome-program:1345 bionet.software:11959 Possibly not the correct place for this, but has anyone in the UK found a good deal on airline tickets to get to San Francisco for this conference. The prices I've been quoted via the Division's Secretary (who doesn't have time to phone every bucket shop in the country) have been horrendous. The travel operators listed by the organisers as having special deals for "those originating east of the Rockies" refuse to answer the telephone or reply to faxes. Unless I find something cheaper quick-time, I'm not going to be able to go. Thanks in advance for any help -- Andy Law ( Andy.Law @ bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!cs.tu-berlin.de!fauern!winx03!news From: weenie@wbzx07.biozentrum.uni-wuerzburg.de (Werner Wolz) Newsgroups: bionet.software Subject: Re: Email for CDC Date: 2 May 1995 22:00:56 GMT Organization: Dept. of Human Genetics Lines: 15 Message-ID: <3o6a2o$3ku@winx03.informatik.uni-wuerzburg.de> References: <3nm01f$hmn@mserv1.dl.ac.uk> NNTP-Posting-Host: wbzd11.biozentrum.uni-wuerzburg.de X-Newsreader: WinVN 0.92.6+ In article <3nm01f$hmn@mserv1.dl.ac.uk>, S.P.Cowell@exeter.ac.uk says: > >Does anyone know if there is an email address for the >Center for Disease Control >(Special Pathogens Dept) >Atlanta Georgia. > >I would be obliged for any assistance offered. > >S. Cowell >Biological & Medicinal Chemist >Exeter University > try: user@MSMAIL.EM.CDC.GOV good luck ! From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!EU.net!sun4nl!uva.nl!amc!pubmac04.amc.uva.nl!user From: not available (guest) Newsgroups: bionet.software Subject: Re: best anatomy/biology CD-ROM titles ? Followup-To: bionet.software Date: 2 May 1995 07:26:27 GMT Organization: Academic hospital of the University of Amsterdam Lines: 23 Message-ID: <3o4mr3$8f6@amcnix.amc.uva.nl> NNTP-Posting-Host: pubmac04.amc.uva.nl Message-ID: References: <3nmebv$k93@nntp.ucs.ubc.ca> Organization: acad. med. centr. Amsterdam In article <3nmebv$k93@nntp.ucs.ubc.ca>, alistair@bcu.ubc.ca (Alistair Blachford) wrote: > I've been asked for great reference software for budding biologists, something > on CD-ROM for Windows. The particular request was for things useful to > someone bound for medicine. High school level and beyond. One particular item you will want to check out: A.D.A.M. An anatomy CD-Rom with an authoring system available. Use all standard images and explanations of the CD and add your own. Cheapest version $150, complete (I seem to remember free of copyrights, ie. you are allowed to use the images for your own readers) version up to $4000. This were last year prices. runs on mac and dos The (zoology?) dept of biology of the University of Amsterdam has developed a multi-media CD which contains a complete classification system of birds. More a biology than an anatomy item. Ard From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!biosci!not-for-mail From: Timothy.J.Moser@Dartmouth.EDU (Timothy J. Moser) Newsgroups: bionet.software Subject: Skatchard analysis Date: 1 May 1995 20:36:54 -0700 Organization: Dartmouth College, Hanover, NH Lines: 6 Sender: biohelp@net.bio.net Distribution: world Message-ID: <3o3dje$mmo@dartvax.dartmouth.edu> NNTP-Posting-Host: net.bio.net Is there a program available for the Mac which allows for easier calculation of Skatchard analysis? A shareware or free program would be best. Thanks in advance - Tim From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.sprintlink.net!news.clark.net!NewsWatcher!user From: uspdi@clark.net (USPDI) Newsgroups: bionet.software Subject: Testing Computer Software Conference Date: 2 May 1995 01:58:09 GMT Organization: U.S. Professional Development Institute Lines: 82 Message-ID: NNTP-Posting-Host: uspdi.clark.net Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit S p e c i a l M e e t i n g A n n o u n c e m e n t (This announcement has been posted to several newsgroups. Please excuse any unintended duplication.) 12th International Conference and Exposition on TESTING COMPUTER SOFTWARE Defect Prevention June 12-15, 1995 Crystal Gateway Marriott * Washington, D.C. CONFERENCE FEATURES: * International speakers * Presentations of current best defect prevention practices * Presentations based on the experience of actual testing practitioners * Opportunities to share lessons and experiences with your peers * Exposition of products and services FEATURED SPEAKERS: Boris Beizer * Dorothy Graham * Tom Gilb * Robert Mays ABOUT THE CONFERENCE The Twelfth International Conference on Testing Computer Software will provide an opportunity for participants to discuss software testing issues, exchange current experiences and take a look at how others have attempted to solve common (and some not-so-common) testing problems. The conference will provide a variety of ways to participate, from the presentation of technical papers and tutorials, through informal birds-of-a-feather sessions, to tool exhibits and demonstrations. You will be able to exchange knowledge and ideas with people from a wide variety of environments and locations including those from industry, academia, and government from the United States and abroad. Conference tracks will address topics concerning the management of software testing, the application of a variety of software testing techniques, test automation and tools, and a few topics that attempt to introduce some more advanced ideas. This conference will provide essential information to all who are involved with or have an interest in software testing. This includes not only practitioners but managers and researchers as well. Featuring sessions on technology applications and management issues: Full day workshops: * Foundations of Software Testing Techniques * Software Inspection and the Defect Prevention Process * Risk Assessment in Software Projects * Hands-On Windows(TM) GUI Testing & Test Automation * Practical Test Automation Over 30 plenary and parallel sessions, organized into tracks: * Practices * Object Oriented Systems * Management * Techniques * Shrink-wrap Software * Advanced Topics In cooperation with American Society for Quality Control (ASQC) - Software Division Software Technology Support Center (STSC) Association for Computing Machinery (ACM) Conference management by: U.S. Professional Development Institute For complete program and registration information please contact: . Phone: 301/445-4400 Fax: 301/445-5722 E-mail: uspdi@clark.net (Subject: Testing Conference) Regular Mail: USPDI, 1738 Elton Road, Suite 304; Silver Spring, MD 20903-1725, USA --- From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!hubcap.clemson.edu!opusc!not-for-mail From: dean@tbone.biol.scarolina.edu (Dean Pentcheff) Newsgroups: bionet.software Subject: Re: Free graphical software for IBM-pCs? Date: 1 May 1995 21:34:57 -0400 Organization: Univ. of South Carolina, Columbia Lines: 25 Message-ID: <3o4281$agj@tbone.biol.scarolina.edu> References: <3o1tvc$39r@service1.uky.edu> NNTP-Posting-Host: tbone.biol.scarolina.edu Venkat Rajagopal writes: > O would like to know if there are any graphical software there out >on the internet. I am looking for software that would aid in drawing >figures. Somethink like Xfig would be nice. ANy info will be appreciated >Thanks You should take a look at GLE. It's a free graphing program that runs from a script of commands (rather than being a point 'n' click type of program). It produces professional-quality Postscript output, and also has drivers for a number of other devices. It runs on PCs, Unix systems (via X), and VAXen. If you're interested, check the info sheet for it at: http://tbone.biol.scarolina.edu/~dean/glelist/ And, to answer the obvious question: no, I didn't write it - I just run a mailing list to help support it. -Dean -- N. Dean Pentcheff Biological Sciences, Univ. of South Carolina, Columbia SC 29208 (803-777-3936) Internet addresses: pentcheff@acm.org or dean@tbone.biol.scarolina.edu WWW link: home page From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!news.starnet.net!wupost!uwm.edu!reuter.cse.ogi.edu!netnews.nwnet.net!news.u.washington.edu!root From: meir@zoology.washington.edu (Eli Meir) Newsgroups: bionet.software Subject: Bio Education Software FAQ (1 of 2) Date: 2 May 1995 03:12:12 GMT Organization: Dept. of Zoology, Univ. of Washington Lines: 669 Sender: -Not-Authenticated-[3641] Message-ID: <3o47uc$std@nntp3.u.washington.edu> NNTP-Posting-Host: nntp5.u.washington.edu X-Posted-From: InterNews 1.0.5@quaternary.zoology.washington.edu Xdisclaimer: No attempt was made to authenticate the sender's name. Biology Education Software FAQ Copyright 1995 by Eli Meir and the Biology Education Software Taskforce of the University of Washington All Rights Reserved This document is freely redistributable as long as absolutely no money is charged and no changes are made to the document. The latest version of this document is posted at ftp.zoology.washington.edu in /pub/doc (1) WhatÕs in this FAQ? (1a) Who is B.E.S.T. ? (1b) Where to address comments, queries, etc.. (1c) How we picked software to include here (1d) What information we include about each piece of software we review (1e) How to submit software for inclusion on this list (2) Resources for information on biology education software (2a) BioQuest (2b) CTI Centre for Biology (2c) NECUSE Biology Software Reviews (2d) Quarterly Review of Biology (3) Ecology and Evolution Software (3a) Biota (3b) Environmental Decision Making (3c) Evolve (3d) PopGen (3e) Energy Flow Stella Stack (3f) Island Biogeography StellaStack (3g) Max. Sustainable Yield Stella Stack (3h) Carbon Cycle Stella Stack (3i) Population Momentum Stella Stack (3j) Blind Watchmaker (3k) Simlife (3l) Populus (3m) PopDyn (3n) Fish Farm (4) Physiology and Neurobiology (4a) Neuro 140 (4b) Axon (4c) Isolated Heart Laboratories (4d) Neurosim II (4e) Frog Dissection and other dissection tutorials (4f) NeuroLab (4g) SymBioSys (4h) Quantitative Circulatory Physiology (5) Cell and Molecular Biology (5a) Genetics Construction Kit (5b) SequenceIt! (5c) PurifyIt! (5d) RateIt! (5e) Enzyme (5f) MacMolecule (5g) Visual Genetics (5h) Enzyme Kinetics Stella Stack (6) General purpose software useful in education (6a) Stella (6b) Extend (6c) Mathematica (6d) Maple (6e) Matlab (6f) LabView (6g) SuperScope (6h) Spike Studio (7) Textbooks on CD (8) Mosaic sites and other random stuff (8a) Institute for Molecular Virology (8b) BioCatalog (8c) Neurosciences on the Internet (8d) Quantitative Training for Life Sciences (9) Acknowledments ----------------------------------------------- (1a) Who is B.E.S.T. B.E.S.T. stands for Biology Education Software Taskforce of the University of Washington. We are not quite as official as that title makes us sound, but have done quite a bit of work looking at educational software for use in the biology classes here at UW. The group is composed of several graduate students and PhDÕs from the Department of Zoology at the UW. In addition to gathering software, we have run classes here examining biology education software, have invited notable people in the field to come and speak at our departmental seminars, and some of us are authors of educational and other software. Among the primary people involved in the group are Adrian Sun, George Gilchrist, Tarif Awad, Creagh Bruener, David Baldwin, Kevin Obrien, and Eli Meir (the author of this FAQ). We are not claiming to be especially knowledgable or gifted when it comes to educational software, nor are we claiming to be teachers who are speaking from years of experience in using computers in education. We have provided some references to articles and reviews by people who are much more knowledgable than we are. Rather, based on our experience as students, teachers, and authors of materials for undergraduate education, we aim to present what we think are the most useful pieces of software for undergraduate education in various branches of biology. We hope this will provide a starting point for instructors in other universities who are looking for good software to use in their classes. (1b) Where to address comments, queries, etc.. You can get in touch with us by emailing to best@zoology.washington.edu, or by emailing the author of this document at meir@zoology.washington.edu. You can also get us through snail mail by sending to Eli Meir B.E.S.T. Dept. of Zoology, NJ-15 University of Washington Seattle, WA 98195 (1c) How we picked software to include here In searching for educational software, we quickly realized that there is lot of stuff out there which is not very interesting. We did not want to include all of that in our list, so we have weeded out a lot of software. This weeding is obviously subjective. What one person considers junk might be exactly what another person is interested in. Originally I was going to spell out these biases in this FAQ, but due to lack of time, hereÕs a quick summary. First of all, anything that didnÕt work on a reasonably new computer and operating system was excluded. We also excluded most software which didnÕt run on a Macintosh or IBM machine, since that is what most students and teachers have access to. There is some bias towards Macintosh software, since that is the computer which most of us have sitting on our desks, but we included any good IBM software we came across as well, and have also included a small amount of UNIX software. Secondly, we have a bias against software which puts a textbook or a study guide onto the computer and claims that just the fact its on a computer screen makes it somehow superior. We also did not particularly like most software whose only innovation was a bit of hypertext capability (ie - click on a word, it gives you a definition of the word or takes you somewhere else in the document). We do like software that uses the computer to do things which would be hard or impossible to do on paper. We especially like simulations and other programs which let a student perform experiments. (1d) What information we include about each piece of software we review We have tried to write three paragraphs about each piece of software weÕve seen. The first paragraph gives our description of what the software does. The second paragraph is a short review of the software. The third paragraph gives information on how to get the software, and approximate price range if we know it. In the price range, Free means free, Low means $100 or less, and High means more than $100. These are by no means gauranteed to be accurate. We have NOT class tested most of this software, so the reviews are based on our impressions as students and teachers. In general, only one or two people have looked at each piece of software, and most titles have only been looked at by the author of this FAQ. Because of this lack of class testing and the small number of reviewers, we have limited each review to a single short paragraph which states what we see as the strengths and weaknesses of the package, and our gut feeling about how useful we think it is. We hope that this short review will help users of this document to decide what software they are interesting in looking for on their own, but do not intend it as an authoritative statement on the value of the software. Also note that we have in essence given favorable reviews to all software included here, since quite a bit of software was left off this list (well over 50% of what we looked at is not on here). If someone other than the author of this FAQ contributed to a review, their initials are given next to the software title. (1e) How to submit software for inclusion on this list We welcome new software, and will be happy to include it in the list if it meets our criteria as discussed above in (1c). However, there are a couple conditions. (I) We will only accept software for review from the authors or publishers of the software, or on an original store-bought disk with the manual. This does not mean that others cannot tell us about software theyÕve used and liked. We really want to hear about software from everyone, and if you inform us of a piece of software and tell us how to get ahold of it, we will do our best to get a copy and look at it. However, to protect us from copyright problems, virus problems, etc., we would rather only receive software from the actual authors, or from anonymous ftp sites if the software is in the public domain. When cost is a factor, we may review demo versions of software instead of the full package. (II) We prefer reviewing real copies of a piece of software, rather than a demo version, and if we have only seen a demo version then we will mention this in our review. (III) We prefer receiving software on a diskette. We also would like to see a manual, or any other documentation which exists. The documentation can be included as a file on the disk, if you prefer, in either ASCII, Microsoft Word, or Wordperfect formats (UNIX software can have documentation in standard unix formats). If you want to send software to us via the network, please inform us beforehand that you plan to send us something. For our protection, we may still request something in writing stating that you are the author (or at least a phone number). (IV) We would also welcome contributions from people outside the group here at UW. If you would like to submit a review for this FAQ, please write it in the form of the other descriptions here, and send it to us with some indication of how you have used the software and what your qualification is to review it (it doesnÕt have to be very high, but weÕd like to know). If we are satisfied that it is a fair description of the program, then weÕll include it in the next release of the FAQ. We will also try to get ahold of a copy of the program ourselves to look at. (2) Resources for information on biology education software (2a) BioQuest This is a consortium of software developers and educators which have gotten together to produce a CD full of really good biology education software. Many of their programs are described in this document, and you can get fuller descriptions of their programs by getting their Intro_to_BioQuest hypercard stack off of the internet. Before putting a piece of software on their CD, they subject it to a pretty rigorous peer review process, and make sure its been tested in many classrooms. I think that this is some of the best stuff out there, and well worth the price (which is quite cheap - under $100 last time I checked for all of their programs for a single user, more expensive for a site license). In addition to software, the BioQuest group has developed a whole philosophy of education, which they use to guide their development and selection of educational software. This philosophy revolves around the three PÕs - Problem-posing, Problem-solving, and peer-Pursuasion. They describe this philosophy better than I can here, so IÕll let you get ahold of it yourself. ItÕs well worth reading their material, even if you donÕt end up using their software. To get the Intro_to_BioQuest hypercard stack, look in: To order the BioQuest CD, send email to asdg@umdd.umd.edu, or write to Academic Software Development Group Computer Science Center University of Maryland College Park, MD 20742 For information, you can write to BioQuest@beloit.edu (2b) CTI Centre for Biology This is a gopher site which you can access with mosaic that includes reviews of some 650 pieces of software for teaching biology. The reviews are pretty short, saying the name of the software, the distrributor, what types of computer it works on, and giving a short paragraph of description. There is also a warning at the beginning that the information has not been kept up to date since 1991, although there are reviews of software that have come out since then. The big advantage to this database is that it is the most comprehensive of any weÕve seen - over 650 products are listed - so it might be a good place to start a search. Get there using Mosaic - its at Liverpool University Computer Science gopher site in the UK. (2c) NECUSE Biology Software Reviews This is a book of biology software descriptions and reviews, with more information than whatÕs included here. The 1994 version covers almost 50 titles. The reviews are organized by topic, with various indexes in the back. Along with information such as author, supplier, cost, computer system, etc., is a short description of the program, a set of poor/good/excellent grades for a number of criteria, and a synopsis of the programs strengths and weaknesses. There is also an extensive list of videodisks in the back, with just one line of description and a price and supplier. To get this book, write to Carol Ann Paul at Wellesley College, or Graham Kent at Smith College (Dept. of Biological Sciences, Smith College, Northampton, MA 01063). (2d) Quarterly Review of Biology The Quarterly Review of Biology is one of the few sources for academic reviews of software interesting to biologists. Each issue includes a few software reviews, not all of educational software, but quite a few are. The reviews are generally written by an expert in the field, and are pretty good. (3) Ecology and Evolution Software (3a) Biota This program lets you play around with differential equation models in ecology. It is very different, however, than some of the other ecology programs listed here in that it lets you mix and match classical ecological equations with each other to make systems of equations. This works as follows. You can have up to 10 different species and/or ecosystem components. Each species has an equation which governs its growth and death, for instance exponential, logistic, lotka-volterra, and so on. You may also add in interactions between the species, such as specifying one of the species as a predator on another one, again governed by classical differential or differencce equations. Each equation has a set of parameters that you can set. You then run the models and watch population sizes over time of each species. You can also sample the populations using a couple of sampling techniques, and you can specify that the sampling include error to simulate real life sampling. In addition, the program lets you add in a spatial component to the models, by having separate populations of each species in distinct spatial areas. You can have up to 200+ spatial areas, and in each one you can independently specify starting conditions. You can then specify how migration will occur between each pair of cells for each species cells. The program will give you separate population size graphs for each area when you run the model, so you can look at metapopulation dynamics, island biogeography, etc.. The user interface for Biota is particularly well-designed, given the complexity of the program, and lets you easily change equations and parameters through pop-up menus, dialogs, and maps of the different areas. Because of the ability to mix and match equations, species, and areas, you should be able to use this program to design and play with models demonstrating many concepts, from simple population growth models to moresophisticated concepts involving space and several interacting species. Nevertheless, I would be hesitant to use this in an introductory class, because despite the nice user interface the level of understanding you need to figure out whatÕs going is still fairly high. There are a lot of equations and interactions to keep track of, and you need to understand these at least superficially to be able to play with parameters, and interpret the graphs of population size in light of those parameters. Building new models that are stable is also not trivial. So I think this program would best be used in more advanced ecology courses, where either you want students to be able to play with models but donÕt want to use a full-blown modelling program such as Stella or Mathematica, or you want to be able to play with spatially-explicit models. Computer: Macintosh Source: BioQuest asdg@umdd.umd.edu or see address above under Resources. Cost: Low (single user) / High (site license) (3b) Environmental Decision Making These are a series of three modules built around a crippled version of a program called Extend. Extend seems to be a program somewhat like Stella (see review). Using the version of Extend included, you can run three different models, one of a grasslands ecosystems with fires, a second looking at logging, and a third looking at fishing. Each model has functional blocks representing things like trees, fire, logging effort, and cash. You are asked to connect the blocks together to make ecosystems, and then to connect these ecosystems to human management systems. The manual takes you through this process step-by-step. You can then play with changing selected parameters of each block, and running the model to see what happens to population sizes (or the equivelant variable) in each component of the system over time. The authors of these models want students to focus on the process of model building, and how you calibrate and use models, rather than on the models themselves, so all the parameters for each block are easily available to be played with, and the equations connecting the blocks are not shown from within the program. The models which the authors have developed are nice, and should be useful in a course looking at the interactions between people and ecosystems. The software makes it fairly easy to change parameters and add and remove links between things, though there are a lot of extraneous tools and commands that could potentially confuse non-computer literate students. However, in more than an introductory class, or if the instructor would like to modify these models instead of using them as is, then I think it would be better to go with a full-blown modelling program such as Stella, or perhaps the full version of Extend. Computer: Macintosh Source: BioQuest asdg@umdd.umd.edu or see address above under Resources. Cost: Low (single user) / High (site license) (3c) Evolve This is a population genetics simulator. It simulates evolution in a two-allele system, with natural selection, genetic drift, and gene flow. You can set separate survival and reproductive rates for each genotype per generation, number of immigrants of each genotype, percentage of each genotype which emigrates, and to simulate evolutionary bottlenecks and genetic drift you can set a maximum population size, after which the population crashes down to a lower population size (by randomly killing individuals of all genotypes). You can also use one set of parameters for a certain number of generations, then change the parameters and continue running the model, simulating environmental variability. The main interface to the program is a graph window where you can choose to plot the frequencies of each of the genotypes in the population, the allele frequencies, the population sizes of each genotype, and/or the total population size. All of these results and more are also shown in a table at the bottom of the window. To facilitate comparisons between the results from different parameters settings, you can run multiple trials and plot one trial on top of another. All the parameters are set within a single dialog box. This program is quite nicely laid out, with a lot of information and controls put into a single window and a single dialog box in a way that makes them both easy to access and not too confusing. I expect that students would need a few minutes to figure out the what they were looking at, but once you get comfortable with it then the program is very easy to use. The program is flexible enough to do a most evolution experiments you could think of doing with a two alleles at a single locus. The manual is clear and well written, and includes exercises to get students started. This program should be useful from introductory through advanced undergraduate genetics and evolution courses, especially in courses which plan to make somewhat extensive use of computer simulations (say more than one or two hours). Computer: Macintosh Source: BioQuest asdg@umdd.umd.edu or see address above under Resources. Cost: Low (single user) / High (site license) (3d) PopGen This is a simple population genetics simulation. There are two modes, one a simulation of evolution at a single locus, and one a quantitative simulation mode. In each mode, the program puts up two windows, one containing a graph and the other with a series of slide bars controlling the parameters of the model. For the single locus mode, the graph shows the percentage of the alleles which are of type A (there are only two alleles) over time. Parameters include the size of the starting population, the initial percentage of A alleles, the selective fitness of each allele combination, the mutation rates between alleles, and various types of migration between populations (up to eight populations can be run simultaneously). The quantitative mode shows the changes in mean values of two quantitative characters over time, also with a set of parameters that you can change. This program is simple and straightforward to use. The only complaints I had were that the slide bars are a little clumsier than most macintosh slide bars, and the parameters are sometimes not erased and redrawn properly. You should also know some population genetics before sitting down with this program, as there is no help onscreen and the manual is very short and doesnÕt provide any sort of tutorial. But these are not fatal flaws, and this program should be quite useful for students to play with these simple population genetics models and see how changing different parameters changes the outcome. You might also look at Evolve, which has similar goals but is a little more extensive (though it doesnÕt include the quantitative mode). Computer: Macintosh Source: evolution.genetics.washington.edu (128.95.12.41), in /pub/popgen Cost: Free (3e) Energy Flow Stella Stack This program puts you in charge of managing Silver Springs, an ecosystem which includes primary producers, herbivores, predators, top predators and decomposers, as well as tourists which throw scraps of bread to the herbivores. Your job is to keep the population of top predators at a certain value for 5 years, by regulating the number of tourists who are allowed in per year. You are first introduced to the model by watching it get built on the screen. You are then told your goal of regulating top predators, and asked to make a predication about the population size of the top predators over the next five years (you both draw a graph of what you think population size / time will look like, and write down how you intend to accomplish this). You can adjust the starting populations of each component in the ecosystem, and the number of tourists. As the model runs, it gives you feedback about how well youÕre doing, and you can continually adjust the number of tourists to try to regulate the population. At the end, you get plots of population size over time for each component of the model, and the top predator plot is overlayed on your prediction, so you can see both how well you did and how well you predicted what would happen. This program was designed to be simple to use, and takes students step-by step through the exercise. It shares a common interface with all of KeslerÕs programs (see Enzyme Kinetics for a more complete description). It has the problem of running a little too fast on a fast computer, but other than that works quite well. The exercise is a little simplistic, and will not challenge more advanced students. However, for introductory ecology or conservation biology classes, this program should be quite useful, and should easily work in a one hour lab or discussion period. Computer: Macintosh, also needs Hypercard 2.2 (wonÕt work with Hypercard player). Source: David Kesler, Rhodes College. email: KESLER@ns.rhodes.edu Cost: Free (3f) Island Biogeography StellaStack This is a simple demonstration of the theory of island biogeography. It gives a short introduction to the theory with the requisite three graphs showing effects of distance from mainland and size of islands, then lets the student play with a simple model of species colonization and extinction, where you can adjust the distance of an island from the mainland and the size of the island, let the model run for some preset amount of time, then look at graphs of number of species, colonization, extinction and turnover rates over time. At the end are a series of questions about the results from the model, with the option to go back and rerun the model to check your answers. This program is very simple to use, and takes you step-by-step through the whole exercise. It shares a common interface with all of KeslerÕs programs (see Enzyme Kinetics for a more complete description). The program does not contain a full description of island biogeography and its implications, and so would be most useful as a supplement to a lecture or reading on the topic. In addition, it is very simplistic, and would not be useful as more than a reinforcement of the concept. for introductory students. Computer: Macintosh, also needs Hypercard 2.2 (wonÕt work with Hypercard player). Source: David Kesler, Rhodes College. email: KESLER@ns.rhodes.edu Cost: Free (3g) Max. Sustainable Yield Stella Stack This program lets students try to harvest fish using two different harvesting strategies, fixed quotas, and variable effort, using a very simplistic model. There are several screens of introductory material which discuss fixed quota and variable effort harvesting strategies, using graphs of population size vs. recruitment to show how each of these work. You can then try each of these strategies out on a model of a fish population. The model is of logistic growth, with the parameters of the growth fixed. Before running the model, you can set the initial population size, and either the amount harvested per year (fixed quota) or the rate of harvesting (variable effort). You are asked to make a graphical prediction of the population size over time, given your initial conditions. After running the model, you can see the simulated population size over time superimposed on top of your prediction. When you are done playing with the model, you can read several questions about the resource management strategies you just played with. This program would work best after students have been introduced to some theory on population growth (ie. what a population size vs. recruitment rate graph shows) and harvesting strategies. The program itself is simple to use, and shares a common interface with KeslerÕs other programs (see Enzyme Kinetics for a description). One problem with this program is that the model has no probabalistic elements in it, and so if you pick the right values, both harvesting strategies work just as well. Without chance, you have to play around and imagine for yourself that chance was acting to see the greater risk inherant in harvesting by quota than by a variable effort strategy. There is also no graph of amount harvested per year, so you cannot look at how efficient your harvesting strategy is. However, the program works as a very basic introduction to these concepts, and may be useful in introductory ecology or conservation biology classes which discuss management. Computer: Macintosh, also needs Hypercard 2.2 (wonÕt work with Hypercard player). Source: David Kesler, Rhodes College. email: KESLER@ns.rhodes.edu Cost: Free (3h) Carbon Cycle Stella Stack This program demonstrates the basic parts of the global carbon cycle through the use of a simple model. The model includes five sources, and two sinks of carbon. The sources are burning fossil fuels, decomposing of organic matter, respiration, net destruction of vegetation, and carbon escaping from the oceans. The sinks are gross primary productivity and the oceans. The student is introduced to these through a picture of all the sources and sinks, with small explanations of each. The student is given the mission of keeping global atmospheric carbon dioxide below 720 e15 grams, by adjusting each of the sinks and sources. Before running the model, you are asked to make a graphical description of what you think the CO2 level will be over the 5 years that the model is run. You can then run the model, and at the end of each run look at a graph of the CO2 level over time in the simulation, and see how this compares to your prediction. There are also a series of short explanation of the effects of changing each of the variables. This program works nicely as a simple introduction to the sources and sinks of carbon dioxide in the world, and their relative magnitudes. It is also a nice introduction to how modelling of this sort is done. The user is guided through the steps in the exercise using an easy to understand interface that is the same as that in KeslerÕs other programs (see Enzyme kinetics for description). Since these C02 models are in the news a lot as part of the debate on the greenhouse effect, the content of the program should be interesting to students in a variety of introductory classes. I see a potential problem, however, if the teacher does not make it clear that this is only a caricature of how the real world works (especially since the model is so simple, and doesnÕt include connections even between the variables which exist such as vegetation destruction and GPP), and would also want to make clear that while you can change things in the model such as CO2 flux into and out of the oceans, GPP, etc., in real life there are no slide bars on these things. Still, if the teacher makes these points, the program should serve as a good integrater and solidifier of both how a nutrient cycles on a global basis, and some of the variables involved in the debate on the greenhouse effect. Computer: Macintosh, also needs Hypercard 2.2 (wonÕt work with Hypercard player). Source: David Kesler, Rhodes College. email: KESLER@ns.rhodes.edu Cost: Free (3i) Population Momentum Stella Stack This program explores how the worldÕs human population grows. After a short introduction on population growth and U.N. predictions of this growth, the program presents you with a model of an age-structured population. The population has 11 categories, including three pre-reproductive ages, four reproductive ages, and four post-reproductive ages. You can set the number of individuals in each class, and an overall reproductive rate for the population. You are asked to predict how the population will grow over time by drawing a graph of this growth, which you can then compare to the output you get after running the model. As you run the model the population structure is shown changing in a horizontal bar graph (the classical representation of population structure). At the end are several questions about the results of the model, with the option of going back and rerunning the simulation to answer them. The thrust of the introductory text and the questions is that even with just a replacement rate of reproduction, the human population can grow quite a bit before reaching equilibrium. The program is very simple to use, and takes you step-by-step through the exercise. The interface is similar to the other programs by this author (see Enzyme Kinetics for a description), and works well. This program would make a good one hour lab in an introductory course which talks about human population growth. You may, however, want to look at the BioQuest program Demography, which is a more flexible program also looking at human population dynamics. Computer: Macintosh, also needs Hypercard 2.2 (wonÕt work with Hypercard player). Source: David Kesler, Rhodes College. email: KESLER@ns.rhodes.edu Cost: Free Eli Meir Dept of Zoology, Univ of Washington meir@zoology.washington.edu From owner-software@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.sprintlink.net!nntp.earthlink.net!michaelb.earthlink.net!user From: michaelb@earthlink.net (Michael B) Newsgroups: de.comm.modem,zer.z-netz.telecom.modem.highspeed,zer.z-netz.telecom.telefon,bionet.software,tw.bbs.comp.software Subject: Phone Commutations Date: Mon, 01 May 1995 19:28:17 +0000 Organization: Peanut Zero Lines: 54 Message-ID: NNTP-Posting-Host: michaelb.earthlink.net I need to setup a system for my clients to send data to me via phone lines. I just had ISDN installed and I am running 4-Sight hardware and software. I also have high speed modems running Telafinder software for the BBS. I need info regarding, Hardware, Software, Scripting, or Programming to do the following. At the sending site. File(s) for transmission are put into a hot folder. A transmission document is automatically opened, and the name of the file(s) is stripped off the actual files submitted. The sender is forced to fill in certain fields of the transmission document. ( The document cannot be closed before the information is complete). The transmission document will comprise a unique three letter mnemonic for the sender, and the date and time stamp (in the form DDMMhhmm) for the time that the transmission document was completed. Once the transmission document is closed, all the files, including the transmission document, are compressed into a single, self-decompressable file. The name of the file will be th same as the transmission document plus a period followed by a three letter mnemonic for the destination sight. The transmission is initiated. This should be possible over phone, ISDN and Internet transmission. A copy of the uncompressed transmission is left in a designated folder on the senders computer. At the receiving site. The compressed file is received and placed into a folder which is date and time stamped with the senders three letter mnemonic. The file is automatically decompressed. If the receiving site is at my company, the transmission document is automatically copied into pre-specified E-mail accounts ( including the clients, if appropriate) plus as printed out on any specified laser printer or fax output. This automated distributed of information should be optional if the client requires it at their site. If the receiving site is a client site where they have not opted to automatically disseminate the transmission document, the transmission document will reside in a pre-specified folder on the clients computer. An alert should be fired when a new file arrives in that folder. The alert should be in a form as a menu bar warning, or a dialogue box in which is self-cancelling after thirty seconds ( or can be cancelled by operator intervention). Please send any info or questions to: Michael Beulke michaelb@earthlink.net Thank you# From owner-software@net.bio.net Mon May 01 23:00:00 1995 Newsgroups: bionet.software Path: biosci!daresbury!trane.uninett.no!sunic!sunic.sunet.se!seunet!news2.swip.net!doc.news.pipex.net!pipex!uknet!gdt!bsspak From: bsspak@bath.ac.uk (P A Keller) Subject: Re: NCBI Entrez for MS Windows Message-ID: Reply-To: P.A.Keller@bath.ac.uk Organization: Department of Biology and Biochemistry, University of Bath, UK References: <3ntt3d$51j@rzsun02.rrz.uni-hamburg.de> Date: Tue, 2 May 1995 09:34:09 GMT Lines: 26 In the referenced article, ruppert@rrz.uni-hamburg.de (Jvrg Ruppert) writes: >Dear netters, > >for a couple of days now have I tried to get the NCBI Entrez network >distribution for MS windows. It is located at their ftp server: >ncbi.nlm.nih.gov. This location is either terribly slow or permanently > [snip] You seem to have a network browser available - why not try using Entrez over the Web, and forget about the software? The URL is: http://atlas.nlm.nih.gov:5700/Entrez/index.html Hope that this helps, Peter. ======================================================================== Peter Keller. \ Dept. of Biology and \ "It is a pity that people are being killed Biochemistry, \ by my guns" University of Bath, \ Bath, BA2 7AY, UK. \ --- Mikhail Kalashnikov ------------------------------\----------------------------------------- Tel. (+44/0)1225 826826 x 4302 | Email: P.A.Keller@bath.ac.uk (Internet) Fax. (+44/0)1225 826449 | P.A.Keller%bath.ac.uk@UKACRL (BITNET) ======================================================================== From owner-software@net.bio.net Tue May 02 23:00:00 1995 Path: biosci!rutgers!gatech!swrinde!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!ubaclu.unibas.ch!schoenbaechl From: schoenbaechl@ubaclu.unibas.ch (Mark Schoenbaechler) Newsgroups: bionet.software Subject: Plasmid design prg's for DOS/Windoze Message-ID: <1995May3.104854.44751@yogi.urz.unibas.ch> Date: 3 May 95 10:48:54 MET Organization: University of Basel, Switzerland Lines: 11 Hi netters, In our lab we are thinking of getting a program for plasmid/vector design. It should read sequence files (e.g. EMBL, GENBANK or so) and we should be able to display it graphically. Also, we should be able to implement additional information, like author, size etc. It would be great if there were some choice of export formats. The platform is DOS/Windoze. I would really appreciate some suggestions and comments. Thanks in advance, Mark. From owner-software@net.bio.net Tue May 02 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!msunews!harbinger.cc.monash.edu.au!news.cs.su.oz.au!metro!unsw.edu.au!aix01.csd.unsw.OZ.AU!s9300078 From: s9300078@aix01.csd.unsw.OZ.AU (Weiguang Huang) Newsgroups: bionet.software Subject: Re: Free graphical software for IBM-pCs? Date: 3 May 1995 12:57:59 GMT Organization: University of New South Wales, Sydney Australia. Lines: 113 Message-ID: <3o7ukn$8a6@mirv.unsw.edu.au> References: <3o1tvc$39r@service1.uky.edu> NNTP-Posting-Host: aix01.csd.unsw.oz.au In article <3o1tvc$39r@service1.uky.edu> Venkat Rajagopal writes: >Hi, > > O would like to know if there are any graphical software there out >on the internet. I am looking for software that would aid in drawing >figures. Somethink like Xfig would be nice. ANy info will be appreciated You can try Symbmath that can draw figures. A new version 3.3 is just available on the internet. SymbMath:: Type: Shareware, student and advanced versions. Machines: PC-DOS, OS/2 Contact: Dr Weiguang Huang, Dept. of Analytical Chemistry University of New South Wales, Sydney, NSW 2052, Australia Phone: [61] (0)2-385-4643, Fax: [61] (0)2-662-2835 w.huang@unsw.edu.au, s9300078@cumulus.csd.unsw.oz.au Version: 3.2, December 1994 Comments: Runs on plain (640k) DOS machines (8086). It is an expert system that is able to learn from user, and a programming language for symbolic, numeric and graphic computation. Its 100+ source code libraries are auto- loaded. FTP: Australia: archie.au /micros/pc/oak/calculcat/sm32a.zip /micros/pc/garbo/math/sm32a.zip plaza.aarnet.edu.au /micros/pc/garbo/pc/math /micros/pc/oak/calculat Czechoslovakia: ftp.vse.cz /pub/msdos/simtel/calculat England: micros.hensa.ac.uk /mirrors/simtel/calculcat/sm32a.zip src.doc.ic.ac.uk /pub/packages/simtel/calculcat/sm32a.zip Finland: ftp.funet.fi /pub/msdos/SimTel/calculcat/sm32a.zip garbo.uwasa.fi /pc/math/sm32a.zip France: ftp.ibp.fr /pub/pc/SimTel/msdos/calculcat/sm32a.zip ftp.jussieu.fr /pub3/pc/SimTel/msdos/calculat Germany: ftp.uni-paderborn.de /SimTel/msdos/calculcat/sm32a.zip ftp.germany.eu.net /pub/comp/msdos/mirror.garbo/math/sm32a.zip athene.uni-paderborn.de /pcsoft/msdos/calculat cranach.rz.tu-ilmenau.de /pub/msdos/comp.binaries/calculator ftp.fu-berlin.de /pc/msdos/math ftp.rrzn.uni-hannover.de /ftp3/msdos-koeln/mathematics rrzs3.rz.uni-regensburg.de /pub/pcsoft/msdos/calculat rs1.rrz.uni-koeln.de /pc/msdos/mathematics sun0.urz.uni-heidelberg.de /pub/msdos/simtel/calculat /pub/simtel/calculat tethys.rz.uni-osnabrueck.de /pub/msdos/math/utk_archive/calculus /pub/msdos/math/utk_archive/diff.equations /pub/msdos/math/utk_archive/linear.algebra ftp.uni-trier.de /pub/pc/msdos-koeln/mathematics harry.informatik.rwth-aachen.de /pub/reze-2.rz.rwth-aachen.de/simtel/msdos/calculat Hong Kong: ftp.cs.cuhk.hk /pub/simtel/msdos/calculcat/sm32a.zip Israel: ftp.technion.ac.il /pub/unsupported/dos/simtel/calculcat/sm32a.zip Italy: cnuce_arch.cnr.it /pub/msdos/garbo.uwasa.fi/math/sm32a.zip ftp.cnr.it /pub/msdos/garbo.uwasa.fi/math /pub/msdos/simtel/calculat Japan: ftp.kuis.kyoto-u.ac.jp /mirrors/simtel20.msdos/calculat Korea: kids.kotel.co.kr /pub/tmp Netherlands: ftp.can.nl /pub/symbmath/sm32a.zip ftp.nic.surfnet.nl /mirror-archive/software/simtel-msdos/calculat Poland: ftp.cyf-kr.edu.pl /pub/mirror/msdos/calculcat/sm32a.zip Singapore: ntuix.ntu.ac.sg /.2/msdos/calculat SK: nic.uakom.sk /pub/dos/simtel/calculat South Africa: ftp.sun.ac.za /pub/simtel/msdos/calculcat/sm32a.zip ftp.mpd.co.za /pub/garbo/math/sm32a.zip Owl.und.ac.za /mirrors/garbo/pc/math/sm32a.zip Sweden: ftp.sunet.se /pub/pc/mirror/SimTel/msdos/calculcat/sm32a.zip Switzerland: ftp.switch.ch /mirror/msdos/calculcat/sm32a.zip nic.switch.ch /mirror/msdos/calculat Taiwan: NCTUCCCA.edu.tw /PC/simtel/calculcat/sm32a.zip /PC/garbo/math/sm32a.zip cc04.ccit.edu.tw /pub2/PC/simtel/calculat ftp.tem.nctu.edu.tw /Msdos/calculat Thailand: ftp.nectec.or.th /pub/mirrors/SimTel/msdos/calculcat/sm32a.zip USA: St. Louis: wuarchive.wustl.edu /systems/ibmpc/msdos/calculcat/sm32a.zip /systems/msdos/garbo.uwasa.fi/math/sm32a.zip Walnut Creek: ftp.cdrom.com /pub/garbo/math/sm32a.zip Corvallis: archive.orst.edu /pub/mirrors/simtel/msdos/calculcat USA: math.berkeley.edu /pub/Software/SymbMath oak.oakland.edu /SimTel/msdos/calculat/sm32a.zip archives.math.utk.edu /software/msdos/sm32a.zip freebsd.cdrom.com /.2/SimTel/msdos/calculat /.3/garbo/pc/math ftp.uga.edu /pub/msdos/mirror/calculat ftp.uoknor.edu /mirrors/SimTel/msdos/calculat Email: /pdget mail /SimTel/msdos/calculat/sm32a.zip to listserv@vm1.nodak.edu, or listserv@ndsuvm1.bitnet WWW: http://www.acs.oakland.edu/SimTel/msdos/calculat ************************************************************************* * Dr. Weiguang Huang * * Dept. of Analytical Chemistry * * University of New South Wales * * Kensington, Sydney, NSW 2033 * * Australia * * * * phone: 61 (0)2-385-4643, fax: 61 (0)2-662-2835 * * email: w.huang@unsw.edu.au, s9300078@cumulus.csd.unsw.oz.au * *-----------------------------------------------------------------------* * SymbMath 3.3: Symbolic Math software with learning * * Get it by ftp ftp.unsw.edu.au in /pub/UNSW/symbmath/sm33a.zip * * Send email SUBSCRIBE SYMBMATH to majordomo@explode.unsw.edu.au for * * adding your name to the mailing list SymbMath@explode.unsw.edu.au * ************************************************************************* From owner-software@net.bio.net Tue May 02 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!osiris.wu-wien.ac.at!dipl1-iwi.uibk.ac.at!robert From: robert@PROBLEM_WITH_INEWS_DOMAIN_FILE (Robert Koechl) Newsgroups: bionet.software Subject: Re: Bio Education Software FAQ (1 of 2) Date: 3 May 1995 19:45:24 GMT Organization: I need to put my ORGANIZATION here. Lines: 676 Message-ID: <3o8mgk$nj0@osiris.wu-wien.ac.at> References: <3o47uc$std@nntp3.u.washington.edu> NNTP-Posting-Host: dipl1-iwi.uibk.ac.at X-Newsreader: TIN [version 1.2 PL2] Eli Meir (meir@zoology.washington.edu) wrote: : Biology Education Software FAQ : Copyright 1995 by Eli Meir and the Biology Education Software Taskforce : of the University of Washington : All Rights Reserved : This document is freely redistributable as long as absolutely no money : is charged and no changes are made to the document. The latest version : of this document is posted at ftp.zoology.washington.edu in /pub/doc : (1) WhatÕs in this FAQ? : (1a) Who is B.E.S.T. ? : (1b) Where to address comments, queries, etc.. : (1c) How we picked software to include here : (1d) What information we include about each piece of software we : review : (1e) How to submit software for inclusion on this list : (2) Resources for information on biology education software : (2a) BioQuest : (2b) CTI Centre for Biology : (2c) NECUSE Biology Software Reviews : (2d) Quarterly Review of Biology : (3) Ecology and Evolution Software : (3a) Biota : (3b) Environmental Decision Making : (3c) Evolve : (3d) PopGen : (3e) Energy Flow Stella Stack : (3f) Island Biogeography StellaStack : (3g) Max. Sustainable Yield Stella Stack : (3h) Carbon Cycle Stella Stack : (3i) Population Momentum Stella Stack : (3j) Blind Watchmaker : (3k) Simlife : (3l) Populus : (3m) PopDyn : (3n) Fish Farm : (4) Physiology and Neurobiology : (4a) Neuro 140 : (4b) Axon : (4c) Isolated Heart Laboratories : (4d) Neurosim II : (4e) Frog Dissection and other dissection tutorials : (4f) NeuroLab : (4g) SymBioSys : (4h) Quantitative Circulatory Physiology : (5) Cell and Molecular Biology : (5a) Genetics Construction Kit : (5b) SequenceIt! : (5c) PurifyIt! : (5d) RateIt! : (5e) Enzyme : (5f) MacMolecule : (5g) Visual Genetics : (5h) Enzyme Kinetics Stella Stack : (6) General purpose software useful in education : (6a) Stella : (6b) Extend : (6c) Mathematica : (6d) Maple : (6e) Matlab : (6f) LabView : (6g) SuperScope : (6h) Spike Studio : (7) Textbooks on CD : (8) Mosaic sites and other random stuff : (8a) Institute for Molecular Virology : (8b) BioCatalog : (8c) Neurosciences on the Internet : (8d) Quantitative Training for Life Sciences : (9) Acknowledments : ----------------------------------------------- : (1a) Who is B.E.S.T. : B.E.S.T. stands for Biology Education Software Taskforce of the : University of Washington. We are not quite as official as that title : makes us sound, but have done quite a bit of work looking at : educational software for use in the biology classes here at UW. The : group is composed of several graduate students and PhDÕs from the : Department of Zoology at the UW. In addition to gathering software, we : have run classes here examining biology education software, have : invited notable people in the field to come and speak at our : departmental seminars, and some of us are authors of educational and : other software. Among the primary people involved in the group are : Adrian Sun, George Gilchrist, Tarif Awad, Creagh Bruener, David : Baldwin, Kevin Obrien, and Eli Meir (the author of this FAQ). : We are not claiming to be especially knowledgable or gifted when it : comes to educational software, nor are we claiming to be teachers who : are speaking from years of experience in using computers in education. : We have provided some references to articles and reviews by people who : are much more knowledgable than we are. Rather, based on our : experience as students, teachers, and authors of materials for : undergraduate education, we aim to present what we think are the most : useful pieces of software for undergraduate education in various : branches of biology. We hope this will provide a starting point for : instructors in other universities who are looking for good software to : use in their classes. : (1b) Where to address comments, queries, etc.. : You can get in touch with us by emailing to : best@zoology.washington.edu, or by emailing the author of this document : at meir@zoology.washington.edu. You can also get us through snail mail : by sending to : Eli Meir : B.E.S.T. : Dept. of Zoology, NJ-15 : University of Washington : Seattle, WA 98195 : (1c) How we picked software to include here : In searching for educational software, we quickly realized that there : is lot of stuff out there which is not very interesting. We did not : want to include all of that in our list, so we have weeded out a lot of : software. This weeding is obviously subjective. What one person : considers junk might be exactly what another person is interested in. : Originally I was going to spell out these biases in this FAQ, but due : to lack of time, hereÕs a quick summary. : First of all, anything that didnÕt work on a reasonably new computer : and operating system was excluded. We also excluded most software : which didnÕt run on a Macintosh or IBM machine, since that is what most : students and teachers have access to. There is some bias towards : Macintosh software, since that is the computer which most of us have : sitting on our desks, but we included any good IBM software we came : across as well, and have also included a small amount of UNIX software. : Secondly, we have a bias against software which puts a textbook or a : study guide onto the computer and claims that just the fact its on a : computer screen makes it somehow superior. We also did not : particularly like most software whose only innovation was a bit of : hypertext capability (ie - click on a word, it gives you a definition : of the word or takes you somewhere else in the document). We do like : software that uses the computer to do things which would be hard or : impossible to do on paper. We especially like simulations and other : programs which let a student perform experiments. : (1d) What information we include about each piece of software we : review : We have tried to write three paragraphs about each piece of software : weÕve seen. The first paragraph gives our description of what the : software does. The second paragraph is a short review of the software. : The third paragraph gives information on how to get the software, and : approximate price range if we know it. In the price range, Free means : free, Low means $100 or less, and High means more than $100. These are : by no means gauranteed to be accurate. : We have NOT class tested most of this software, so the reviews are : based on our impressions as students and teachers. In general, only : one or two people have looked at each piece of software, and most : titles have only been looked at by the author of this FAQ. Because of : this lack of class testing and the small number of reviewers, we have : limited each review to a single short paragraph which states what we : see as the strengths and weaknesses of the package, and our gut feeling : about how useful we think it is. We hope that this short review will : help users of this document to decide what software they are : interesting in looking for on their own, but do not intend it as an : authoritative statement on the value of the software. Also note that : we have in essence given favorable reviews to all software included : here, since quite a bit of software was left off this list (well over : 50% of what we looked at is not on here). : If someone other than the author of this FAQ contributed to a review, : their initials are given next to the software title. : (1e) How to submit software for inclusion on this list : We welcome new software, and will be happy to include it in the list if : it meets our criteria as discussed above in (1c). However, there are a : couple conditions. : (I) We will only accept software for review from the authors or : publishers of the software, or on an original store-bought disk with : the manual. This does not mean that others cannot tell us about : software theyÕve used and liked. We really want to hear about software : from everyone, and if you inform us of a piece of software and tell us : how to get ahold of it, we will do our best to get a copy and look at : it. However, to protect us from copyright problems, virus problems, : etc., we would rather only receive software from the actual authors, or : from anonymous ftp sites if the software is in the public domain. When : cost is a factor, we may review demo versions of software instead of : the full package. : (II) We prefer reviewing real copies of a piece of software, rather : than a demo version, and if we have only seen a demo version then we : will mention this in our review. : (III) We prefer receiving software on a diskette. We also would like : to see a manual, or any other documentation which exists. The : documentation can be included as a file on the disk, if you prefer, in : either ASCII, Microsoft Word, or Wordperfect formats (UNIX software can : have documentation in standard unix formats). If you want to send : software to us via the network, please inform us beforehand that you : plan to send us something. For our protection, we may still request : something in writing stating that you are the author (or at least a : phone number). : (IV) We would also welcome contributions from people outside the group : here at UW. If you would like to submit a review for this FAQ, please : write it in the form of the other descriptions here, and send it to us : with some indication of how you have used the software and what your : qualification is to review it (it doesnÕt have to be very high, but : weÕd like to know). If we are satisfied that it is a fair description : of the program, then weÕll include it in the next release of the FAQ. : We will also try to get ahold of a copy of the program ourselves to : look at. : (2) Resources for information on biology education software : (2a) BioQuest : This is a consortium of software developers and educators which have : gotten together to produce a CD full of really good biology education : software. Many of their programs are described in this document, and : you can get fuller descriptions of their programs by getting their : Intro_to_BioQuest hypercard stack off of the internet. Before putting : a piece of software on their CD, they subject it to a pretty rigorous : peer review process, and make sure its been tested in many classrooms. : I think that this is some of the best stuff out there, and well worth : the price (which is quite cheap - under $100 last time I checked for : all of their programs for a single user, more expensive for a site : license). : In addition to software, the BioQuest group has developed a whole : philosophy of education, which they use to guide their development and : selection of educational software. This philosophy revolves around the : three PÕs - Problem-posing, Problem-solving, and peer-Pursuasion. They : describe this philosophy better than I can here, so IÕll let you get : ahold of it yourself. ItÕs well worth reading their material, even if : you donÕt end up using their software. : To get the Intro_to_BioQuest hypercard stack, look in: : To order the BioQuest CD, send email to asdg@umdd.umd.edu, or write to : Academic Software Development Group : Computer Science Center : University of Maryland : College Park, MD 20742 : For information, you can write to BioQuest@beloit.edu : (2b) CTI Centre for Biology : This is a gopher site which you can access with mosaic that includes : reviews of some 650 pieces of software for teaching biology. The : reviews are pretty short, saying the name of the software, the : distrributor, what types of computer it works on, and giving a short : paragraph of description. There is also a warning at the beginning : that the information has not been kept up to date since 1991, although : there are reviews of software that have come out since then. The big : advantage to this database is that it is the most comprehensive of any : weÕve seen - over 650 products are listed - so it might be a good place : to start a search. : Get there using Mosaic - its at Liverpool University Computer Science : gopher site in the UK. : (2c) NECUSE Biology Software Reviews : This is a book of biology software descriptions and reviews, with more : information than whatÕs included here. The 1994 version covers almost : 50 titles. The reviews are organized by topic, with various indexes in : the back. Along with information such as author, supplier, cost, : computer system, etc., is a short description of the program, a set of : poor/good/excellent grades for a number of criteria, and a synopsis of : the programs strengths and weaknesses. There is also an extensive list : of videodisks in the back, with just one line of description and a : price and supplier. : To get this book, write to Carol Ann Paul at Wellesley College, or : Graham Kent at Smith College (Dept. of Biological Sciences, Smith : College, Northampton, MA 01063). : (2d) Quarterly Review of Biology : The Quarterly Review of Biology is one of the few sources for academic : reviews of software interesting to biologists. Each issue includes a : few software reviews, not all of educational software, but quite a few : are. The reviews are generally written by an expert in the field, and : are pretty good. : (3) Ecology and Evolution Software : (3a) Biota : This program lets you play around with differential equation models in : ecology. It is very different, however, than some of the other ecology : programs listed here in that it lets you mix and match classical : ecological equations with each other to make systems of equations. : This works as follows. You can have up to 10 different species and/or : ecosystem components. Each species has an equation which governs its : growth and death, for instance exponential, logistic, lotka-volterra, : and so on. You may also add in interactions between the species, such : as specifying one of the species as a predator on another one, again : governed by classical differential or differencce equations. Each : equation has a set of parameters that you can set. You then run the : models and watch population sizes over time of each species. You can : also sample the populations using a couple of sampling techniques, and : you can specify that the sampling include error to simulate real life : sampling. : In addition, the program lets you add in a spatial component to the : models, by having separate populations of each species in distinct : spatial areas. You can have up to 200+ spatial areas, and in each one : you can independently specify starting conditions. You can then : specify how migration will occur between each pair of cells for each : species cells. The program will give you separate population size : graphs for each area when you run the model, so you can look at : metapopulation dynamics, island biogeography, etc.. : The user interface for Biota is particularly well-designed, given the : complexity of the program, and lets you easily change equations and : parameters through pop-up menus, dialogs, and maps of the different : areas. Because of the ability to mix and match equations, species, and : areas, you should be able to use this program to design and play with : models demonstrating many concepts, from simple population growth : models to moresophisticated concepts involving space and several : interacting species. Nevertheless, I would be hesitant to use this in : an introductory class, because despite the nice user interface the : level of understanding you need to figure out whatÕs going is still : fairly high. There are a lot of equations and interactions to keep : track of, and you need to understand these at least superficially to be : able to play with parameters, and interpret the graphs of population : size in light of those parameters. Building new models that are stable : is also not trivial. So I think this program would best be used in : more advanced ecology courses, where either you want students to be : able to play with models but donÕt want to use a full-blown modelling : program such as Stella or Mathematica, or you want to be able to play : with spatially-explicit models. : Computer: Macintosh : Source: BioQuest asdg@umdd.umd.edu or see address above under : Resources. : Cost: Low (single user) / High (site license) : (3b) Environmental Decision Making : These are a series of three modules built around a crippled version of : a program called Extend. Extend seems to be a program somewhat like : Stella (see review). Using the version of Extend included, you can run : three different models, one of a grasslands ecosystems with fires, a : second looking at logging, and a third looking at fishing. Each model : has functional blocks representing things like trees, fire, logging : effort, and cash. You are asked to connect the blocks together to make : ecosystems, and then to connect these ecosystems to human management : systems. The manual takes you through this process step-by-step. You : can then play with changing selected parameters of each block, and : running the model to see what happens to population sizes (or the : equivelant variable) in each component of the system over time. The : authors of these models want students to focus on the process of model : building, and how you calibrate and use models, rather than on the : models themselves, so all the parameters for each block are easily : available to be played with, and the equations connecting the blocks : are not shown from within the program. : The models which the authors have developed are nice, and should be : useful in a course looking at the interactions between people and : ecosystems. The software makes it fairly easy to change parameters and : add and remove links between things, though there are a lot of : extraneous tools and commands that could potentially confuse : non-computer literate students. However, in more than an introductory : class, or if the instructor would like to modify these models instead : of using them as is, then I think it would be better to go with a : full-blown modelling program such as Stella, or perhaps the full : version of Extend. : Computer: Macintosh : Source: BioQuest asdg@umdd.umd.edu or see address above under : Resources. : Cost: Low (single user) / High (site license) : (3c) Evolve : This is a population genetics simulator. It simulates evolution in a : two-allele system, with natural selection, genetic drift, and gene : flow. You can set separate survival and reproductive rates for each : genotype per generation, number of immigrants of each genotype, : percentage of each genotype which emigrates, and to simulate : evolutionary bottlenecks and genetic drift you can set a maximum : population size, after which the population crashes down to a lower : population size (by randomly killing individuals of all genotypes). : You can also use one set of parameters for a certain number of : generations, then change the parameters and continue running the model, : simulating environmental variability. The main interface to the : program is a graph window where you can choose to plot the frequencies : of each of the genotypes in the population, the allele frequencies, the : population sizes of each genotype, and/or the total population size. : All of these results and more are also shown in a table at the bottom : of the window. To facilitate comparisons between the results from : different parameters settings, you can run multiple trials and plot one : trial on top of another. All the parameters are set within a single : dialog box. : This program is quite nicely laid out, with a lot of information and : controls put into a single window and a single dialog box in a way that : makes them both easy to access and not too confusing. I expect that : students would need a few minutes to figure out the what they were : looking at, but once you get comfortable with it then the program is : very easy to use. The program is flexible enough to do a most : evolution experiments you could think of doing with a two alleles at a : single locus. The manual is clear and well written, and includes : exercises to get students started. This program should be useful from : introductory through advanced undergraduate genetics and evolution : courses, especially in courses which plan to make somewhat extensive : use of computer simulations (say more than one or two hours). : Computer: Macintosh : Source: BioQuest asdg@umdd.umd.edu or see address above under : Resources. : Cost: Low (single user) / High (site license) : (3d) PopGen : This is a simple population genetics simulation. There are two modes, : one a simulation of evolution at a single locus, and one a quantitative : simulation mode. In each mode, the program puts up two windows, one : containing a graph and the other with a series of slide bars : controlling the parameters of the model. For the single locus mode, : the graph shows the percentage of the alleles which are of type A : (there are only two alleles) over time. Parameters include the size of : the starting population, the initial percentage of A alleles, the : selective fitness of each allele combination, the mutation rates : between alleles, and various types of migration between populations (up : to eight populations can be run simultaneously). The quantitative mode : shows the changes in mean values of two quantitative characters over : time, also with a set of parameters that you can change. : This program is simple and straightforward to use. The only complaints : I had were that the slide bars are a little clumsier than most : macintosh slide bars, and the parameters are sometimes not erased and : redrawn properly. You should also know some population genetics before : sitting down with this program, as there is no help onscreen and the : manual is very short and doesnÕt provide any sort of tutorial. But : these are not fatal flaws, and this program should be quite useful for : students to play with these simple population genetics models and see : how changing different parameters changes the outcome. You might also : look at Evolve, which has similar goals but is a little more extensive : (though it doesnÕt include the quantitative mode). : Computer: Macintosh : Source: evolution.genetics.washington.edu (128.95.12.41), in : /pub/popgen : Cost: Free : (3e) Energy Flow Stella Stack : This program puts you in charge of managing Silver Springs, an : ecosystem which includes primary producers, herbivores, predators, top : predators and decomposers, as well as tourists which throw scraps of : bread to the herbivores. Your job is to keep the population of top : predators at a certain value for 5 years, by regulating the number of : tourists who are allowed in per year. You are first introduced to the : model by watching it get built on the screen. You are then told your : goal of regulating top predators, and asked to make a predication about : the population size of the top predators over the next five years (you : both draw a graph of what you think population size / time will look : like, and write down how you intend to accomplish this). You can : adjust the starting populations of each component in the ecosystem, and : the number of tourists. As the model runs, it gives you feedback about : how well youÕre doing, and you can continually adjust the number of : tourists to try to regulate the population. At the end, you get plots : of population size over time for each component of the model, and the : top predator plot is overlayed on your prediction, so you can see both : how well you did and how well you predicted what would happen. : This program was designed to be simple to use, and takes students : step-by step through the exercise. It shares a common interface with : all of KeslerÕs programs (see Enzyme Kinetics for a more complete : description). It has the problem of running a little too fast on a : fast computer, but other than that works quite well. The exercise is a : little simplistic, and will not challenge more advanced students. : However, for introductory ecology or conservation biology classes, this : program should be quite useful, and should easily work in a one hour : lab or discussion period. : Computer: Macintosh, also needs Hypercard 2.2 (wonÕt work with : Hypercard player). : Source: David Kesler, Rhodes College. email: KESLER@ns.rhodes.edu : Cost: Free : (3f) Island Biogeography StellaStack : This is a simple demonstration of the theory of island biogeography. : It gives a short introduction to the theory with the requisite three : graphs showing effects of distance from mainland and size of islands, : then lets the student play with a simple model of species colonization : and extinction, where you can adjust the distance of an island from the : mainland and the size of the island, let the model run for some preset : amount of time, then look at graphs of number of species, colonization, : extinction and turnover rates over time. At the end are a series of : questions about the results from the model, with the option to go back : and rerun the model to check your answers. : This program is very simple to use, and takes you step-by-step through : the whole exercise. It shares a common interface with all of KeslerÕs : programs (see Enzyme Kinetics for a more complete description). The : program does not contain a full description of island biogeography and : its implications, and so would be most useful as a supplement to a : lecture or reading on the topic. In addition, it is very simplistic, : and would not be useful as more than a reinforcement of the concept. : for introductory students. : Computer: Macintosh, also needs Hypercard 2.2 (wonÕt work with : Hypercard player). : Source: David Kesler, Rhodes College. email: KESLER@ns.rhodes.edu : Cost: Free : (3g) Max. Sustainable Yield Stella Stack : This program lets students try to harvest fish using two different : harvesting strategies, fixed quotas, and variable effort, using a very : simplistic model. There are several screens of introductory material : which discuss fixed quota and variable effort harvesting strategies, : using graphs of population size vs. recruitment to show how each of : these work. You can then try each of these strategies out on a model : of a fish populat