Introduction

Introducing the Workbench

The Virtual Ecology Workbench (VEW) is a computer-aided software engineering tool that makes it easy for you to create and analyse Virtual Ecosystems. It uses the LEI-IBM metamodel (Lagrangian Ensemble Integration of Individual-Based Model). It is global: you can make virtual ecosystems for anywhere in the world ocean. And it is flexible: you can include any chemical and plankton species.

Motivation

The computer codes used to create virtual ecosystems are long and complex. It takes a skilled programmer many days to adapt an existing code to add new species or a different scenario for external forcing. Yet, by its nature, virtual ecology requires frequent updating of the model and scenario. That is the case even while you are investigating a single emergent phenomenon. The workbench was conceived as a tool to accelerate this process by automating generation of code for new virtual ecosystems.

Design criteria

The primary goal was to avoid the need for programming. The VEW was designed for users who are not programmers, but who can run Microsoft Excel. The second goal was that the code that could run on any computer regardless of operating system.

Efficiency tool

Achieving those goals required substantial effort by highly skilled software engineers over many years. That large upfront investment was cost-effective because it eliminated the need for expensive programmers in hundreds of groups using the VEW for research, teaching, and operational oceanography.

Speed

Modelling remains a fringe activity in biological oceanography. That is because it takes too long to confi gure models to address new scientifi c problems. The Workbench eliminates that barrier. Using the latest version (VEW4) you can create a new code in few hours. It takes typically about one hour per simulated year to run the code on a personal computer.

Easy to use

The workbench makes extensive use of pull-down menus to specify each element of a virtual ecosystem. In many cases you will be able to build it from modules stored in the VEW archive. When that is not possible you can easily create new modules by using the VEW equation editor. This makes it easy to introduce equations you have found in the scientifi c literature. The VEW automatically checks the syntax and units before adding new equations to the archive.

Specification file

The specification file buffers the user from the computer code. It comprises fi fty or so elements. The workbench provides a separate graphical user interface (GUI) for each element. Each GUI offers three facilities adapted to the particular element:

1. Select a version of the element from the VEW archive.
2. Create a new version, using a VEW equation editor.(Each new version is automatically added to the archive for future use.)
3. Enter numerical values of parameters or other data using templates supplied by the GUIs.

When you have used each GUI the workbench automatically adds the information to the growing specification file. And it adds data sets for the initial and boundary conditions. The VEW Designer acts as a control panel, guiding you through the sequence of specifications.

Java code

When the specification file is complete, the workbench automatically generates the run-time code in Java. That language was chosen because it can be run on all personal computers, workstations and mainframe computers, regardless of their operating system. The run-time code and associated data sets are not long. They can easily be stored on a CD. You do not need the workbench to run it one your computer.

Data set

Running the code creates the Virtual Ecosystem. It is a large data set. For the simple food-chain model used to illustrate this booklet, the data set includes about one gigabyte per year of fi eld data (environment and demography), plus about one megabyte per year for each audit trail. These are the emergent properties of the virtual ecosystem. In practice you will work with a small sample of the complete virtual ecosystem, which is too large to be stored conveniently on a personal computer. Typically you might select one year out of a simulation lasting twenty years. The selection will normally contain all the environmental and demographic data, plus audit trails for one thousand of the millions of particles.Your selection is part of the specification file. You can store the data on a DVD for analysis.

VEW Analyser

The VEW automatically documents the contents of the virtual ecosystem in the form of an XML fi le attached to the data set. VEW Analyser uses that file to configure its GUIs. The picklists automatically show only those emergent properties that have been logged.