Using Cell Phones to Demonstrate Biological Networks

1
Using Cell Phones to Demonstrate Biological
Networks
2
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.

3
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.

4
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, ATT, etc.).

5
The Simulator

• The Simulation menu shows what can be done.

6
Find Shortest Path
This example animates the shortest path between
5C and 7E.
7
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...
8
Everyonewill hearabout it!
9
Statistics

• Additionally, 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?

10
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 rumorvia email
instead? This means all phones without email
capability are knocked out--they can't transmit
the message.Who will get the email?
11
Only a few phones receive it.
12
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.

13
Try it Yourself

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

http//halo.systemsbiology.net/cytoscape/cellphone
14
Credits

• Halobacterium Research Group _at_ 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

15
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.