Nemo -- A stochastic, individual-base, genetically explicit simulation platform
version 2.1.1 - released 4 May 2009
Nemo implements many different life cycle events and genetic traits. It also allows to model species interaction between a parasite and its host. All this is framed within a flexible metapopulation model that allows for patch-specific carrying capacities, dispersal rates, and extinction/harvesting rates, etc. Populations can be dynamically modified during a simulation, allowing for population bottlenecks, patch fusion/fisson, and expansion, etc.
Nemo's interface is a simple text file containing the simulation parameters and their values. Each parameter can have several argument values thus allowing to run many simulations from a single init file. Parameters can also be set with temporal values that will automatically modify the simulation settings during its run.
Main Features:
Traits
- neutral markers
- deleterious mutations
- dispersal
- Wolbachia
- breeding (with promiscuity, polygyny, monogamy, selfing, cloning)
- disperse (migrant pool/propagule pool island model, 1D & 2D lattice models, etc.)
- aging (with ceiling patch regulation)
- viability selection
- extinction/harvesting
- patch fusion/fission
- crossing design
- and more...
Nemo can thus be used to study the joint evolution of dispersal and deleterious mutations in structured populations or the infection dynamics of Wolbachia under various population models. The number of populations, individuals per population or loci to simulate are restricted only by computer physical capacities. Nemo is highly optimized to run in batch mode and a parallel computing version is part of the release thus making it a very flexible and powerful simulation tool.
Releases
04 May 2009: version 2.1.1
02 February 2009: version 2.1.0
10 March 2008: version 2.0.7
06 June 2007: version 2.0.6.
09 April 2007: version 2.0.5.
21 March 2007: version 2.0.4.
Download
Source code, documentation, and binary files are available at the download site. From that site, you can download the following files:
Nemo-2.1.1-doc.tgz : the user manual and the code documentation (in archive html.tgz)
Nemo-2.1.1-src.tgz : the source files and documentation
Nemo-2.1.1-Mac-Intel.tgz : executable for Intel-based Mac, with doc and source
Nemo-2.1.1-Mac-PPC.tgz : executable for non-Intel Mac, with doc and source
Nemo-2.1.1-Win-Binaries.tgz : executable for Windows (XP/2000/Vista), with doc and source
Installing
The installing guidelines are available in the files INSTALL and README that you will find in the Nemo-xyz folder once you expanded one of the archive listed above. These files are Unix files and may not be displayed properly under other operating systems (i.e. don't use Notepad.exe under Windows but use Wordpad.exe instead).
Support
Please register! to the mailing list to get the latest release and bug information and post your comments and questions. This is a very low traffic list (less than a message per month).
You will find most recent news and information about software updates here or on http://sourceforge.net/projects/nemo2. That site also offers a forum, and a bug and request tracker.
Coding support
The present site is dedicated to the code documentation and development guidelines of nemo that you can find below. These guidelines give a rough approach to coding within the Nemo framework. The code documentation presents the whole documented code of Nemo. The documentation of some classes may be brief. This will be corrected in future releases, if time permits.
License
Nemo is released under the GNU Public License version 2, available here.
Nemo is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
Citing Nemo
Please cite Nemo as:
Guillaume, F., and J. Rougemont. 2006. Nemo: an evolutionary and population genetics programming framework. Bioinformatics 22:2556-2557.
PDF copies can be obtained upon request to the first author.
References
Here is a list of published works using Nemo as a research tool.
Guillaume, F., and N. Perrin (2006) Joint evolution of dispersal and inbreeding load. Genetics 173:497--509.
Guillaume, F., and M. C. Whitlock (2007) Effects of migration on the genetic covariance matrix. Evolution 61:2398--2409.
Reuter, M., Lehmann, L., and F. Guillaume (2008) The spread of incompatibility-inducing parasites in sub-divided host populations. BMC Evolutionary Biology 8:134.
Jaquiéry, J., Guillaume, F., and N. Perrin (2009) Predicting the deleterious effects of mutation load in fragmented populations. Conservation Biology 23:207--218.
Note: send us your references and we'll add them here!
Development Guidelines
Nemo's framework has been designed as a programing tool to easily implement new components into the simulation framework. Interfaces are provided to derive new evolvable traits, new life cycle events and their accompanying data handlers. Besides that, the implementer should not worry (or not too much) about how its new components are handled within the population and simulation frameworks. The population framework is designed to give access to the individuals within the different age classes and sub-populations present in the model to the different components, in particular the life cycle events.
4. Adding the stat and file handlers.
5. Building and linking your project with Nemo.
Community
Nemo is currently developed and maintained by Fred Guillaume.
The following persons have contributed to its development at some point:
Jacques Rougemont (MPI version)
Samuel Neuenschwander
Alistair Blachford
Sam Yeaman
Nemo also benefited from development done on EasyPop by François Balloux, and from some improvements brought to quantiNEMO, an off-shoot based on earlier work done in collaboration with Samuel Neuenschwander and Jérôme Goudet.
Many thanks to all those great people!
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