10 March 1998
After a talk with Larry Hurd this morning I've embarked on a project to orchestrate cooperation between Larry, the Library, and the Media Center in Biology 245 (General Ecology) in the Fall term. I'll use this space to keep track of what I find and think.

Here's the catalog description:

An introduction to the study of interactions between organisms and their environments. Topics are arranged hierarchically: Emphasis is on ecology as a scientific process rather than merely a collection of information about natural systems. Laboratory course.

Here's a link to the W&L Biology Dept ==> Ecology and Evolution resources page that I put together quite a while ago.
Some links:

Landscape Ecology and Biogeography (CSU Australia)

Aquatic Ecology Page

What's the role of simulation in the study/teaching of ecology? Is there anything for an interactive interface (Java-based, say) to do in this connection? Are there things that perl could handle?

Ecological Modelling Resource Page


What's needed here is probably $ to pay somebody to write code, once it's clear what the code should attempt to do.

It seems obvious that most of the visual component of the course (overheads, figures, slides) could be put on the web, linking with explanatory text for further elaboration of what's covered orally. It's the links that really add value, though having the possibility to revisit examples is also advantageous.
To realize this what's needed is appropriate scanning hardware and image manipulation software, but it's also necessary to make it easy for the instructor to work with what's there --to add commentary, make links, etc.

Another piece of the puzzle is linking library resources to the course, books and journals and electronic resources. This is partly a matter of calling attention to things that are relevant to what's covered in classes and labs, partly a matter of teaching finding skills in the context of a course (rather than in the abstract, as in Bio182), and partly a matter of inspiring exploratory behavior --in place of the passive attitude that generally accompanies a lecture course.
One model for how this all could work is for the librarian --that's me-- to work as an adjunct to the professor (attending classes and labs, taking responsibility for coordinating media and web, being general factotum). That certainly builds skills for the librarian, but may not contribute all that much to changing how the professor deals with the technologies involved.
It's also necessary to change what students are called upon to do --to somehow involve them more immediately and more thoroughly in every aspect of the course, and thus minimize the opportunities for passivity. It's not necessarily a matter of asking them to do more, but rather to do different sorts of things, and maybe do them more publicly (viz: putting material like lab reports on the web). For this it's necessary to think about what the objectives of assignments really are.
General topics from the syllabus:
20 Mar: some thoughts on Java and some results of a hunt for examples
23 Mar: a new book, just arrived
 TITLE        Software visualization : programming as a multimedia 
                experience /
                edited by John Stasko ... [et al.] ; foreword by Jim Foley.
 PUBLISHER    Cambridge, Mass. : MIT Press, c1998.
 DESCRIPT     xvi, 562 p., [8] p. of plates : ill. (some col.) ; 24 cm.
 SUBJECT      Visual programming (Computer science)
              Multimedia systems.
 1 > Science Library        QA76.65 .S56 1998
(not a book about programming visualizations, but rather about visualizing programming --but still useful to know about as we move in the direction of object oriented programming and empowerment of underpowered users)
It's interesting how laughably out of date books in this realm quickly become, which is to say: how rapidly the frontier advances, and how much effort has to go into scanning incoming traffic.
24 March
Here's a link to the application for Class of '65 funds to support the project.
27 Mar
Another element to think about: macros to make Excel/Quattro an effective analysis tool for lab exercises (and the means to transfer the results to web pages). Larry mentioned that he wasn't pleased with the statistical software he'd tried, and I suggested that we could tame the spreadsheets into being the sort of tools students need --since they (supposedly) already know about spreadsheets in theory, and have them available. This is part of the use-it-to-know-how-to-use-it problem: unless the tool is active, what one knows about it attentuates quickly. Since we teach its use in Bio182 it should actually be in use in lab settings...
So I need to find out about (a) what stats he wants to run and (b) how to create macros [answer: ANOVA (1,2), MANOVA, linear regression, t-tests, unbalanced designs, nonparametrics if possible --not exactly the science of racquets]
It's interesting that amazon.com has a whole lot of how-to macros books listed, but nearly all are out of print, and the search found a couple of titles about Visual Basic. Is there something I should know about going on here?
So it seems... a quick search via AltaVista turns up things like
This course is for users who want to begin automating 
Microsoft Excel tasks. You will use Microsoft's Visual Basic
Language to create macros. You use the Macro Recorder to 
automatically record procedures. You will learn to run and
edit macros and to use the Visual Basic Toolbar. You will 
create buttons and assign macros to them. In addition, you
will create interactive macros using dialog boxes. You should 
be very familiar with Microsoft Excel to benefit from
this course.
(there are many others along these lines...)

SmartTable seems to convert Excel spreadsheets to Java applets (and here's part of the manual). The not-Pro version is $149 list. We should know more about this...

Here's an example from Cal State Stanislaus (and a link to their Biology Lab Online page)

Some general ruminations on numeracy (written in re: scivis):

A basic Problem which afflicts all in the sciences: we have access to vastly more data than used to be the case, and we have tools that let us manipulate and analyze data, and display and distribute the results, much more rapidly than formerly. Students and practitioners must continually learn and then apply new tools (mostly a matter of software, and thus largely of interface), and need to develop presentation skills as well as analytical acumen.

Making visual representations of data and the results of analyses has become an essential professional skill, but is not generally taught in any systematic way --indeed, seems to be seen as a distraction from important traditional elements of scientific curricula. The complexity (and rapid obsolescence) of software packages complicates the pedagogical problem still further: the student may be taught the ins and outs of a particular product, but what's really needed is to learn the general skills that will facilitate use of any product he or she encounters in later years.

It seems to be tacitly assumed that 'everyone' knows how to use a word processor, and that online help files (and Help Desk personnel) can make up for any deficiencies. The same should be true for spreadsheet programs (number processors, in essence), and could be extended to mathematical software like Maple and Mathematica, but the fact is that computer-based quantitative skills are not widespread among students --or faculty, for that matter. In general, people know what they have to know to get by; it's a time-consuming struggle to learn new tools, and hardly worthwhile unless there's some real application for their powers.

31 March
Some preliminary thoughts about slides: database, search utility, forms-based handling.
1 Apr
I'd really like to get some control over just what it takes to realize graphical versions of mathematical models --what the code looks like for examples like Nils Kösters' Java Applets for Population Dynamics, or Rockefeller's logistic curves applet (see their analytical methods bibliography). Another set of applets is at www.jump.net. (And this source from Swarthmore collects a bunch of math applets). (See also Frank Wattenberg's logistic page).
A link to Java Applets for Statistics from Duke -- and see Webster West and his WebStat, and some applets for teaching.

And some by Bryan Lewis, including source code for some.

7 April
It occurred to me to wonder about whiteboard collaboration, and I have a few links to that:

Shared Whiteboard for collaborative computing using Java Multicast and RTP (Evelyn Lai-Tee Cheok and Chi-Hao Li) and program documentation

(This technology seems more suited to distance education and remote meeting applications in realtime, but it's close enough to the 'collaboration' aspect of what we're investigating that it's worth looking into).

And JavaBeans... something that needs more looking into as a means to cratft construction kits for people who don't want/need to write Java code, but should be able to get at Java functionality. A lot of materials at www.javaworld.com , like Building a bevy of beans (see the end of this article for links to others).
Demography from The University of Oregon Biology Software Lab

and Demography: the Java version

JavaStat ("Web Pages that Perform Statistical Calculations!")

22 April

 AUTHOR       Hannon, Bruce M.
 TITLE        Modeling dynamic biological systems / Bruce Hannon, 
                Matthias Ruth
 PUBLISHER    New York : Springer, c1997.
 SERIES       Modeling dynamic systems.
 Science Library        QH324.2 .H36 1997

4 August
Brandeis Biomath --see Rate Equations for a nice example of explanation.

27 Oct
A nice summary of a cemetery exercise re: life tables

3 Nov
Some November thoughts on how it's going