Avida Ed Quick Start User Manual
- Avida Ed Quick Start User Manual 2017
- Avida Ed Quick Start User Manual Download
- Quick Start Sat
- Avida Ed Application
This page contains peer-reviewed model lessons, including in-class, homework and lab exercises, that instructors may download and modify for their own classes under a Creative Commons (Attribution, Non-commercial, Share-Alike) license. For each model exercise, we also have instructor support materials with background information about the lesson, exercise variations and answer keys that are available for registered instructors. We have included a few examples of the instructor support materials (though with the answer key redacted). To find out how instructors can receive these supplemental materials for the other exercises, please contact <pennock5@msu.edu>.
PLEASE NOTE: These exercises were designed for use with the Avida-ED 1.0 and 2.0 application. They have not yet been updated for the new Avida-ED 3.0 web application. They can still be used in Avida-ED 3.0, but screenshots and some interface descriptions will differ slightly (e.g. metabolic rate has been retitled ‘energy acquisition rate’). When we have completed updates, they will be posted here and these earlier versions will be placed in an archive.
The page also includes a section listing some of our publications that specifically deal with curriculum.
MODEL LESSONS
• Avida-ED lab book
Familiarize yourself with the Avida-ED Quick Start User Manual, which can be found at the end of th is Lab Book. Along with a Glossary, this is an invaluable resource on how the Avida-ED program.
User Manuals. The latest Opengear product Quick Start Guide and User Manual may be downloaded here: Opengear Console Server User Manual; Lighthouse User Manual; CDK User Guide; Quick Start Guides. Operations Manager OM2200. Includes: OM2216, OM2248-10G, OM2248-L, OM2248-10G-L, OM2224-24E, OM2224-24E-L, and OM2224-24E-10G-L. Familiarize yourself with the Avida-ED Quick Start User Manual, which can be found in the Lab 1 folder on MBox. Along with its included Glossary, this is an invaluable resource on how the program works.
Wendy Johnson, Cory Kohn, Amy Lark, Louise Mead, Robert T. Pennock, Jim Smith, Michael Wiser
Wondering where to begin? The Avida-ED lab book includes a sequence of three model exercises that have been used together in several courses. They work to introduce students to the mechanics of the software while also teaching some of the evolutionary concepts that many instructors want to include as core learning goals. The lab book also includes a background article about digital evolution, the Avida-ED quick-start user manual, and several additional model exercises.
– Avida-ED lab book – 2018 version
- Exercise 4 – Exploring Population Change without Selection
• Understanding the Introduction of Genetic Variations by Random Mutation
Robert T. Pennock & Amy Lark
This lesson focuses on mutations as a source of genetic variability and what it means to say that mutations occur randomly at some rate. Students will make predictions about and observe the effects of random mutations on the genomes of Avidians
– Student handout
– Instructor support material (answer key redacted)
• From Genotype to Phenotype: Understanding the Introduction of Phenotypic Variations
Robert T. Pennock
Phenotype refers to observable traits of individuals that arise from the causal interaction of their genotype with the environment. In this exercise, students will investigate some simple relationships between genotype and phenotype and observe how changes in the genomes of Avidians lead to changes in their functional traits.
– Student handout
– Instructor support material
• Exploring the Effects of Mutation Rate on Individuals
Amy Lark
This exercise is based on a 2012 study that examined butterflies in the vicinity of the damaged Fukushima nuclear power plant that were exposed to leaked radiation. Students test the study’s conclusion that increased mutation rate likely caused the adverse biological effects. An article on this model lesson was published in American Biology Teacher.
– Student handout
– Organism file: @allfunctions
– Instructor support material (answer key redacted)
• Exploring the Effects of Mutation Rate on Populations
James Smith & Amy Lark
Two important characteristics that we can use to describe a population are the average fitness1 of the individuals that make up that population and the population size. In this exercise you will determine whether these characteristics are affected by mutation rate and, if so, in what ways.
– Student handout
– Instructor support material (answer key redacted)
• Artificial Selection: Evolution in Practice
Rett Weber, Wendy Johnson & Amy Lark
Students are presented with a hypothetical scenario in which they use the mechanism of artificial selection to evolve an organism with a particular trait.
– Student handout
– Instructor support material
• Exploring Selection and Fitness
Avida Ed Quick Start User Manual 2017
Amy Lark & Robert T. Pennock
In this exercise students will perform a series of experiments in order to determine the relationships between variation, selection, and fitness. Drawing from patterns in data they collect, students will then develop a hypothesis regarding how bacteria evolve resistance to antibiotics.
– Student handout
– Instructor support material
• Experimental Evolution Project with Evolving Digital Organisms
Robert T. Pennock & Amy Lark
This is an assignment for an open-ended major project. Students will propose an evolutionary hypothesis that can be tested with Avida-ED, design and conduct an experiment, analyze their data, and write up a research report.
– Student handout
– Instructor support material
• MORE COMING SOON
PUBLICATIONS about Avida-ED Curricula
James J Smith; Wendy R Johnson; Amy M Lark; Louise S Mead; Michael J Wiser, Robert T. Pennock “An Avida-ED digital evolution curriculum for undergraduate biology“Evolution: Education and Outreach (2016, 9(1), 1-11; DOI 10.1186/s12052-016-0060-0)
Amy Lark, Gail Richmond, Robert T. Pennock. “Modeling Evolution in the Classroom: The Case of the Fukushima Butterflies.” American Biology Teacher (2014, 76(7):450-454)
Elena B. Speth, Tammy Long, Robert T. Pennock and Diane Ebert-May. “Using Avida-ED for teaching and learning about evolution in undergraduate introductory biology courses.” Evolution Education & Outreach. (Vol. 2, No. 3, pp. 415-428, 2009)
Cory Kohn, Robert T. Pennock, Jim Smith, Michael J Wiser, and Louise S Mead. “A Digital Technology-based Introductory Biology Course Designed for Engineering and Other Non-life Science STEM Majors” Computer Applications in Engineering Education. (2018; DOI: 10.1002/cae.21986)
Amy M Lark; Gail Richmond; Louise S Mead; James J Smith; Robert T. Pennock. “Exploring the relationship between experiences with digital evolution and students’ scientific understanding and acceptance of evolution.” American Biology Teacher (2018, 80(2):74-86; DOI 10.1525/abt.2018.80.2.74)
Wendy R. Johnson & Amy Lark “Evolution in Action in the Classroom: Engaging Students in Science Practices to Investigate and Explain Evolution by Natural Selection.” American Biology Teacher (2018, 80(2):92-99)
Are You Ready for a Challenge?
This tournament is a test. A test to see how well you can evolve your Avidian to compete in head to head combat with another Avidian in different conditions. Do you think you’re up to the challenge to see if you can make the Avidian to not only survive but to thrive in many different conditions with changing per site mutation rate, changing available resources, and where the offspring is placed? Not only is this a tournament, it is a great learning opportunity and experience to better understand evolution for everyone.
What is Avida?
A spin-off of the artificial life program Avida, Avida-ED is designed for education through the creation, proliferation, and evolution of digital organisms. Each organism is a little piece of code that performs functions by utilizing resources, reproduces, and randomly mutates, just like a real organism. Avida-ED is not an evolution simulation; it is actual evolution. It was developed at Michigan State University for their undergraduate courses as a learning tool.
“Avida-ED is the educational version of Avida, a software platform created by a group of computer scientists and software engineers interested in the experimental study of digital organisms in order to better understand how biological evolution works. Both Avida and Avida-ED provide an instance of evolution in a model environment. The evolution itself is real; the digital organisms are subject to the same processes as biological organisms, such as reproduction, mutation, and natural selection. Scientists use Avida to study how digital organisms evolve and examine questions related to the evolution of complex features, sex, parasitism, cooperation, and foraging behavior. Avida has even been used to confirm the outcomes of ongoing biological experiments. This is possible because the process of evolution is ‘substrate neutral,’ meaning that when a system possesses three key characteristics –variation, inheritance, and selection –evolution will inevitably result.” -from the Avida-ED Lab Manual
How do I make my organism?
Avida Ed Quick Start User Manual Download
Avida-ED can be found here. In the box on the left, navigate to the link called “Avida-ED”. This page includes both the link to the web version of Avida-ED and links for download.
Here are some useful links and tutorials for how to use Avida-ED
Rules:
Quick Start Sat
The tournament will be performed in a single-elimination bracket format. Each match will have two Avidians placed in the default positions. The winner will be declared as whoever has the majority at 1000 iterations. If no winner is obvious, we will go to overtime in increments of 500 iterations until a winner is declared. Each winner will move on to the next round of the tournament. Subsequent rounds after the first will have resources, offspring placement, and mutation rate randomly decided. The first round will consist of the resources NOT and NAN, offspring placed near the parent, and a 2% mutation rate. Conditions will be the same for all matches in the same round.
Avida Ed Application
The winning Avidian will receive a grand prize donated by Cedar Crest’s Sustainability and Environmental Awareness Club!
All .zip files must be named in the following format:
nickname_firstinitiallastname.zip
Example: whisper_mdammer.zip
To enter, please upload your Avidian to google drive linked below by Thursday, March 28 at 11:59 pm
For any questions, please contact Kassaundra Blodgett ([email protected]) or Magdalena Dammer ([email protected])
If you are having problems clicking the link or the link bringing you to the wrong place, please try to copy and paste it into the URL.