Useful Reading

This page is intended to be a drop off point for papers that people have found useful when pulling a model together or when thinking about modelling in general.

Its starting small, but will hopefully grow through time as people drop more in.

1. Plankton modelling and how using simpler models can help you understand more complex ones
2. Qualitative modelling as a way of thinking about system structure

The following are reports that were important during the development of Atlantis that provide useful information on parts of its internal formulation and structure

1. Port Phillip Bay Integrated Model (PPBIM) technical report and a paper by Murray and Parslow (1999) on the effect of the way mortality is formulated in plankton models.
2. The complete set of papers on the development of ERSEM and ERSEM II
3. Fulton 2001 - Beth’s PhD thesis (where it all began) which was published in a series of papers available here (covering model complexity, representation of morality and functional feeding responses, influence of physiological representations and spatial resolution effects).

Below is a list of papers that provide some useful examples of how Atlantis has been used to date - please add others you have found useful (upload as attachments to the page).

1. Fulton et al 2004 - Testing ecological indicators
2. Fulton et al 2007 - tech report on testing alternative management strategies (AMS) for SE Australia
3. Fulton et al 2014 - paper version of the AMS tech report
4. Fulton et al 2011 - a general lessons learnt about EBM from various Atlantis models
5. Fulton and Gorton 2014 - report on simulating climate effects
6. Link et al 2011 - technical report on the construction and calibration of the NEUS model
7. Kaplan et al. 2014 - study using the Economics submodel
8. Hutton et al. 2010 - AFMA report on bycatch management using Economics submodel
9. Ihde et al. 2016 - Design and parameterization of the Chesapeake Bay Atlantis Model