School of Computing

A virtual laboratory notebook for simulation models

A. J. Winfield

In Russ B. Altman, Dunker K. Keith, and Lawren Hunter, editors, Pacific Symposium on Biocomputing '98, volume 3, pages 182-196. World Scientific Pub Co., January 1998 PSB'98 electronic proceedings availiable at http://www.cgl.ucsf.edu/psb/psb98/.

Abstract

In this paper we describe how we have adopted the laboratory notebook as a metaphor for interacting with computer simulation models. This `virtual' notebook stores the simulation output and meta-data (which is used to record the scientist's interactions with the simulation). The meta-data stored consists of annotations (equivalent to marginal notes in a laboratory notebook), a history tree and a log of user interactions. The history tree structure records when in `simulation' time, and from what starting point in the tree changes are made to the parameters by the user. Typically these changes define a new run of the simulation model (which is represented as a new branch of the history tree). The tree shows the structure of the changes made to the simulation and the log is required to keep the order in which the changes occurred. Together they form a record which you would normally find in a laboratory notebook.

The history tree is plotted in simulation parameter space. This shows the scientist's interactions with the simulation visually and allows direct manipulation of the parameter information presented, which in turn is used to directly control the state of the simulation. The interactions with the system are graphical and usually involve directly selecting or dragging data markers and other graphical control devices around in parameter space. If the graphical manipulators do not provide precise enough control then textual manipulation is still available which allows numerical values to be entered by hand. The Virtual Laboratory Notebook, by providing interesting interactions with the visual view of the history tree, provides a mechanism for giving the user complex and novel ways of interacting with biological computer simulation models. Download publication 171 kbytes (PDF)

Bibtex Record

@inproceedings{572,
author = {A. J. Winfield},
title = {A Virtual Laboratory Notebook for Simulation Models},
month = {January},
year = {1998},
pages = {182-196},
keywords = {determinacy analysis, Craig interpolants},
note = {PSB'98 electronic proceedings availiable at http://www.cgl.ucsf.edu/psb/psb98/},
doi = {},
url = {http://www.cs.kent.ac.uk/pubs/1998/572},
    ISBN = {9810232780},
    booktitle = {Pacific Symposium on Biocomputing '98},
    editor = {Russ B. Altman and Dunker K. Keith and Lawren Hunter},
    publisher = {World Scientific Pub Co.},
    refereed = {Yes},
    volume = {3},
}

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