RAMAS® IRM
DESCRIPTION
RAMAS® IRM (Insect Resistance Management) is a software platform for modeling the risk of pest adaptation to Bt crops under a broad range of resistance management strategies. The tool has enough flexibility to address all major insect crop pests through user-defined life histories.
IRM modeling investigates the complex interaction of insect pest population dynamics and population genetics with agricultural technology and farming practices. The total integration of landscape, demography, and evolution places IRM at the cutting edge of landscape genetics and applied evolution.
Our goal is to provide a common platform for IRM modeling that fosters both transparency and innovation in the devlopment and management of transgenic pesticidal crops. A guiding principle in the development of this flexible tool is that it should remove barriers to powerful modeling. That means pushing the limits of what is currently practical in terms of complexity while keeping the software easy to use even for beginning modelers.
We invite input from the IRM community to shape this product as it evolves.
System Requirements
SOFTWARE
Agricultural Landscapes
Infinite Variety: Real agricultural landscapes are mosaics of crops, phenologies, IRM tactics, and environmental conditions. Capture this complexity with RAMAS® IRM by modeling the co occurrence of unlimited user defined cropping strategies, including within and between-year crop rotations. Include conventional and transgenic varieties of the same crop to model the effect of incomplete adoption. Add non-host crops, trap crops, and fallow fields.
Landscape Uncertainty
Every replicate simulation draws a new random landscape that is then varied through time. Control the frequency of crop varieties and their rotations. Choose what refuge configurations to plant. Define spatial and temporal variation in conditions that affect trait expression. Risk results incorporate the significant uncertainty arising from landscape level patterns.
Spatial Dynamics
Tailored Movement: RAMAS® IRM uses an intelligent two-tiered approach to compute baseline rates of dispersal, minimizing artifacts of the interplay between dispersal distance and spatial resolution. Specify the unit of time and number of time steps over which dispersal takes place. Vary retention rates by crop. Allow sex-specific mate attraction. Guarantee a minimum spatial resolution. Movement is stochastic and influences both demographic and genetic drift.
Population Dynamics
Totally Stochastic: Applied Biomathematics has built its reputation on Monte Carlo simulations of finite populations that are used around the world. RAMAS® IRM brings this experience to bear on agricultural pests with stochastic population dynamics structured by stage, sex, genotype, crop, and field.
Build a Pest
The flexible life history constructor allows you to build a uni- or multivoltine pest that encounters different crops in each generation. Vary the order of mating and reproduction by sex. Specify density dependence and thresholds for pesticide application to explore implications for resistance management.
Population Genetics
Recombine: In RAMAS® IRM, recombination is explicit, freeing models from the assumption of Hardy-Weinberg equilibrium. Optional sex specific recombination and gene linkage further help you understand how IRM tactics will affect target species.
Up To Four Genes
Model major genes for up to four toxins or investigate major/minor gene systems for a single trait. Allow selection to vary across multiple crops present in the landscape. Link the strength of selection to environmental variability through a dose-response function. Specify initial gene frequency, mutation rate, dominance, and cross resistance.
Fundamental flexibility
Alter major aspects of model behavior and underlying assumptions with a mouse-click. Toggle between deterministic and stochastic modes, explicit recombination and Hardy-Weinberg, finite population dynamics and frequency-based modeling. Originally intended to address the diversity of common approaches in IRM models, these options have proven to offer powerful insights into the consequences of modeling choices.
Q: What is new in version 2.1?
RAMAS IRM 2.1 now supports up to 4 loci, fitness costs, developmental delays due to sex and genotype, and explicit adult phenology. Under the hood, algorithms used for dispersal have been optimized for faster performance. Information on female natal environment is preserved to properly express maternal effects during dispersal and oviposition in multi-crop landscapes. Refuge location management now has three options: fixed, randomized, or alternating. Density dependence options have been expanded and the user can now set a threshold population density below which survival is density-independent (as in Hibbard et al. 2010).
Q: Does RAMAS IRM use individual-based simulation?
The program uses population-level modeling. The population is structured by genotype, sex, and location. Evolutionary changes are modeled using common population-genetic methods.
While the simulation is population-level, demographic stochasticity is captured through the use of discrete probability distributions for all demographic rates.
Q: Is RAMAS IRM frequency-based?
The program follows the abundance rather than frequency of genotypes. This allows realistic ecological phenomena like extinction and density dependence. However, any IRM 2.1 model can be run in frequency-based mode with the click of the mouse. This feature provides great insight into the role of demographics in resistance evolution.
Q: How many loci can be modeled?
Four. The program currently only includes inheritance via discrete biallelic loci. How to incorporate more genes or more continuous responses to selection is a subject for community discussion as all approaches have both strengths and weaknesses. We welcome all input.
Q: What is the model's spatial resolution?
The user specifies the desired minimum spatial resolution (e.g., 100 m). The program then divides farm fields to guarantee that minimum spatial resolution, although some cells in the landscape may actually be smaller. Changing the spatial resolution is as easy as typing a single number, allowing users to quickly check how the choice of resolution affects model projections.
Q: Does the program allow crop rotations?
Yes. Rotations are defined by the user simply as a list of the order in which crops are planted. The same crop can be planted for any number of years before rotating. The simulation chooses a starting point in the rotation at random for every farm field in the landscape.
Q: What is RAMAS?
Risk Analysis and Management Alternatives Software. The RAMAS software library, developed by Applied Biomathematics, features tools for conservation biology, toxicology, human health, and engineering. You can learn more about our products and research at ramas.com.
Q: What is the time step of the model?
The time interval represented by one step of the model is variable. For larvae, it is a single larval stage. For adults, the user can specify whether a model step represents a day, week, month, or generation. The adult stage is described by one or more substages specifying the timing and duration of mating, dispersal, and oviposition.
Q: Can I enter uncertainty in the parameters?
Currently, RAMAS IRM does not explicitly support parameter uncertainty. We are working on incorporating both one-parameter-at-a-time sensitivity analysis and full parameter uncertainty for a future version of the program. We view this as a fundamental feature and invite any input on desired capabilities or methods. We have had success integrating RAMAS IRM with the R computing environment so that large sensitivity analyses can be automated and run in parallel.
Q: Can I include pesticide application above an IPM threshold?
Yes. Additional mortality can be imposed on any larval stage and it can be conditional upon abundance. However, keep in mind that abundance is monitored only at the end of stages. Hence, if you want to ask whether to spray adults, indicate the final non-adult stage as the basis for action. If you instead select adults as the basis, the program will use LAST YEAR'S adult abundance. Such lags may be interesting as a means of investigating the action of natural enemies but are probably not what you intend for conditional pesticide applications.
Q: Are there eggs in the model?
The number of eggs per female adult, as well as egg survival and its annual variability, is defined in the Demography form. An egg stage, however, does not exist. A soil treatment or other factor that affects egg survival can be directly specified. However, if you want that factor to be conditional upon the abundance of a particular life stage then you will have to shift its effect either to the parental adult stage (fewer adults means fewer eggs) or to the first larval stage (reflecting that fewer eggs survived).
Q: How does mate attraction work?
Areas with high mate density are weighted more heavily in the dispersal matrix. In practice, attraction to mates can either reduce or increase the average displacement of dispersing adults depending on landscape patterns.
Q: Can males and females have different recombination rates?
They can. Currently, recombination in each sex can be turned on or off.
Q: Can males and females have different dispersal rates?
They can. Each sex has its own parameters for dispersal distance and mate attraction.
Q: Is there an option for non-compliance?
Yes. The rate of compliance with structured refuge guidelines is modeled as a random probability of planting the refuge. Slight deviations from refuge guidelines are not modeled.
Currently, there is no autocorrelation in non-compliance. However, if you want to look at the effect of persistent non-compliance, you can create two different "crops" (one with the refuge and one without) and define their frequencies in the landscape. Occasional compliance could be modeled using a long rotation of the two crop types.
Q: What results does the program produce?
RAMAS IRM version 2.1 reports the means and maxima for the density of emerging adults, the frequency of resistance alleles, and fitness on toxic crops. RAMAS IRM also reports durability as the probability of maintaining susceptibility over time. Figures and data tables can be exported.
Q: What happened to the demo program?
We have discontinued the demo program due in part to abuse. But it was great to see people all over the world tyring out RAMAS IRM. You can purchase RAMAS IRM with the confidence of a satisfaction guarantee. Our primary desire is that this tool finds its way to users worldwide. We will consider brief proposals describing your need for the program if the cost of purchase is prohibitive.
Q: Why can't I install the program?
The installer registers your user information with our license server. If you are having trouble installing the program, it may be that your firewall is preventing registration. You can add an exception for RAMAS IRM to your firewall's settings. Another common problem is that you have the program installed on another machine or did not sucessfully un-register the program when uninstalling it from another machine. Contact us if you cannot resolve this issue.
Q: How do I report a bug?
Just send us a quick email describing the problem you encountered. Include any error message you get. Thanks for your help.
FAQ
Recent events concerning RAMAS IRM:
November 2019
Check out our virtual poster presented at the 2019 ESA conference in St. Louis, MO.
June 2019
The next version of RAMAS IRM will have a time-valued planting calendar with support for multiple cohorts and overlapping generations. Our first tests of the new system show it's a rich framework for thinking about how insect management affects the evolutionary process.
November 2018
Our member symposium at ESA in Vancouver, Density Dependence, Community Genetics, and Resistance Evolution, was a great time thanks to all the interesting folks presenting. Talks ranged from empirical measurement of density-dependent survival to theoretical studies of effects on resistance evolution and the consequences of different modeling approaches.
February 2018
Applied Biomathematics' Senior Scientist Nick Friedenberg is helping to organize a symposium at this year's Entomology conference in Vancouver, BC, on density dependence and pesticide resistance evolution.
December 2017
Look for a new study by Jeannette Martinez, Michael Caprio, and Nicholas Friedenberg in the Journal of Economic Entomology featuring models backed by RAMAS IRM.
November 2017
Nick Friedenberg attended the 2017 national conference of the Entomological Society of America and presented results from a collaboration with Jeannette Martinez of EPA and Michael Caprio of Mississippi State University.
April 2017
We participated in the 2017 onRamp Insurance Conference in Chicago, IL. We are exploring whether crop insurers could help promote better resistance management compliance by using RAMAS IRM to price resistance risk.
October 2016
Nick Friedenberg had a great time giving our workshop on IRM at the 2016 Student Conference on Conservation Science, held at the American Museum of Natural History in New York City.
September 2016
Applied Biomathematics welcomes Vincent Keenan, a visiting scholar from the University of Liverpool. Keenan, who's work centers on the dynamics of range expansions and ecological invasions, will help to implement optimized numerical methods for the simulation of dispersal.
June 2016
Applied Biomathematics congratulates Nick Friedenberg for securing a Phase II Small Business Innovation Research award from USDA-NIFA. The grant supports research and development leading to an expansion in the number of genes RAMAS IRM can simulate, along with other additions to the program and validation through reproduction of published models.
NEWS
DOWNLOADS
View a demonstration of RAMAS IRM version 1.0
Download our annual Entomology conference presentations below.
Download the original version 1.0 brochure (PDF)
We have discontinued the demo program due in part to abuse. But it was great to see people all over the world trying out RAMAS IRM. You can purchase RAMAS IRM with the confidence of a satisfaction guarantee. Our primary desire is that this tool finds its way to users worldwide. We will consider brief proposals describing your need for the program if the cost of purchase is prohibitive.
PRICING
RAMAS IRM provides the power to conduct demographically explicit studies of the evolution of resistance to Bt crops. Our newest software product, RAMAS IRM has the potential to enhance or define graduate research.
We want students to be part of RAMAS IRM's community and design. We therefore offer a 6-month license for only $200 (not combinable with other discounts). A student license can be upgraded to a full license at any time by paying the balance of the single-user price.
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Corporate site license price is per seat per year.
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Other site or classroom licenses are annual and allow 25 simultaneous users.
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Technical support is free for colleges, government, and non-profit organizations.
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Technical support for private users is available for an annual fee.