Educational Software

Bringing Systems Biology to the Classroom


The Center is developing computer simulations which will enable students to study and perform systems biology research.

Geniverse

GENIQUEST

The Center helped develop GENIQUEST (NSF, DRL0733264) working with the Maine Mathematics and Science Alliance and the Concord Consortium, in order to bring systems biology to a broad student audience. This three-week computer-based module for high schools uses quantitative trait loci and fictional organisms (dragons and drakes, a model organism for studying dragon diseases) to teach computational biology using real mouse data, but a simplified genome. The genome is complicated enough to be realistic but simple enough for the students to be successful in searching for causal interactions. [ More information ]

Geniverse

Geniverse

The Center for Genome Dynamics, the Concord Consortium, the Maine Mathematics and Science Alliance, BSCS, and TERC teamed up to develop a genetics simulation project. Genetics is poised to revolutionize medicine and society. Geniverse aims to help prepare students for this future. In Geniverse, we’re building a game environment to help students see biology as an active, experiment-driven science. We’re engaging students with the tools and processes of bioinformatics in a collaborative virtual environment. Geniverse will permit students to interact as scientists and build essential skills and understandings in both genetics content and in the nature and process of science. [ More information ]

DrakeQuest

DrakeQuest

Students that complete Geniverse and want additional challenges are given the chance to work with drakes with a realistic metabolism. We incorporated data from a metabolism simulator into the model and provide the students with the ability to breed drakes, feed them different diets and subsequently test them for a wide spectrum of metabolic parameters. The breeding is simplified by having the drakes always lay exactly 20 eggs, thus making the discovery of lethal genetic combinations much easier for the students. DrakeQuest is a web application that was developed using a Java backend and a Google Web Toolkit front end. DrakeQuest provides teachers and students with a rich genetic environment to explore that spans from simple genetics to codominance, sex reversal, lethal traits, and metabolic disorders. [ More information ]

GenetIF

GenetIF: Interactive Fiction

Middle school students may not have sufficient background knowledge to work with Geniverse and we wanted to provide a program to help get them started. A survey of teacher and student needs revealed that teachers were concerned that the program should concentrate on reading, record keeping, and problem solving. We met these needs through Interactive Fiction (IF). Interactive Fiction is a perfect development engine to provide a captivating story and is much more than just a mindless computer game. Students must read and interact with the program to progress through the story and solve problems. In GenetIF the students are new members of a research team working with drakes in order to solve biological problems and uncover the genetics of complex traits. Students navigate by reading the information provided on the screen and entering commands at prompts (>), which allows them to proceed to the next step or perform certain tasks. They are guided through the challenge by notes from an unseen mentor, Dr. McClintock. They breed drakes, collect data about the characteristics of the offspring, and use this data (in conjunction with prior knowledge of inheritance) to explain the inheritance pattern of eye color in drakes. Students are challenged to solve the genetics of eye color, scale color, and ultimately solve a mysterious disease. All of these scenarios are based on real human and mouse genes and at the end of each challenge the students gain access to a “reality room” where they get references to the real world genetics they were just working with. [ More information ]

Antz

ANTz ... *

Stepping away from dragons and drakes, we worked with the University of Maine at Orono’s Computer Science department to find a team of freshman students to create an educational simulation game for middle school students. Their project simulates an ant colony trying to find food. Ants move randomly and when they find food they return to the nest leaving a pheromone trail. Other ants smell this trail and follow it to the food. In our simulation the students can control many of the parameters of the simulation: how much pheromone, how fast it evaporates, how sensitive the ants are to the pheromone, how likely they are to follow the trail, how much food, how far away it is, how many ants, etc. The students are encouraged to make hypothesis and test them by altering the parameters. They are guided by questions: if there is no pheromone and you plot time to find food vs. distance the food is away, what does the function look like? What are the optimum parameters to find food and does this vary with distance? In addition to teaching middle school students, this program also provided freshman undergraduate computer scientists with exposure to systems biology through the development of these cyberlearning modules. [ More information ]