Using Cell Phones to Demonstrate Biological Networks

The Idea

● Most high school students have a basic understanding of cell

phones and how they function.● Cell Phone Networks (in this simulation) are similar to biological

networks and can be modeled identically in Cytoscape.● The cell phone simulation teaches students concepts they can use

with more advanced, biologically-oriented networks.

Artificial Constraints

Our simulated network is not exactly like a real cell phone network. It is subject to the following artificial constraints:

● A given phone can only call the phones in its phone book. (There is no Caller ID or other mechanism to add new phone numbers.)● Phone A can only receive calls from phones which have Phone A in their phone books.

A section of the network

● Each phone (node) has a name like “2E”● Arrows indicate who can call who, for example, 2E can call 2A and 2D● Node border colors indicate cellular carriers (Sprint PCS, AT&T, etc.).

The SimulatorThe “Simulation” menu shows what can be done.

Find Shortest PathThis example animates the shortest pathbetween 5C and 7E.

Phone Tree

● Simulates what happens if one phone calls everyone in its phone book, they call everyone in their phone book, etc.● Behaves identically to modeling of genetic signaling pathways.● Framed to students with questions like:

Say that student 5C hears a juicy rumor. If she calls everyone in her phone book, and they calleveryone in their phone book, who will hear about it? Who won't?

And the answer is...

Everyonewill hearabout it!

StatisticsAdditionally, a Statistics dialog box pops up with more information about the phone tree, allowing students to answer questions like: who made/received the most/least calls?

Perturbing the Network

This is all well and good, but in a real biological network, conditions may be such that not every node would be turned on in a “phone tree”-like situation. The simulatormodels this by allowing the user to “knock out” (removethe edges of) nodes based on the following:● Selected nodes● Phone carrier● Presence or absence of the following attributes:

● Email capability● Roaming capability● Picture (camera) capability So what happens if 5C spreads her rumor

via email instead? This means all phones without email capability are knocked out--they can't transmit the message.Who will get the email?

Only a few phones receive it.

Tip of the Iceberg

These are just a few quick examples of what you can dowith the Cell Phone simulator. The same technology (Jython scripting interacting with Java classes) and muchof the same code can be reused to make simulators for many different kinds of networks.

Try it Yourself

To play with the simulator yourself,click on this link:

http://halo.systemsbiology.net/cytoscape/cellphone

Credits

Halobacterium Research Group @ Institute for Systems Biology and Bellevue School District (BSD).

Supported by a grant from the National Science Foundation (0313754) to Drs. Nitin S. Baliga and Leroy Hood as well as

financial support from the BSD.

Contributors:

Simulation model: John Thomson*, Sarah Nehring+, Dan Tenenbaum, Paul Shannon

Laboratory experiments: Gregory Alvardo*, Stephanie Gill*, Megan Meislin^, Claudia Ludwig+, Jeanine Sieler+, and

Marc Facciotti

Handbook: Simin Mirzanian+, Camille Scalise+, Claudia Ludwig+, Jeanine Sieler+, Sarah Nehring+

Outreach: Patrick Ehrman (ISB) and Kathee Terry (BSD)

Project Leader: Nitin S. Baliga

*=High School Student Interns; +=High School Teachers; ^=Undergraduate Student Intern

Disclaimer

Any opinions, findings, and conclusions or recommendations expressed in this material are

those of the author(s) and do not necessarily reflect the views of the National Science Foundation.