Unit: Ecological Networks Part 1- Network interactions

Lesson Title: Lesson 2- Cytoscape cell phone network

Instructional Activities:

INTRODUCTION/WARM-UP

1. Warm Up Idea: list at least 2 ways in which your cell phone network from yesterday could be altered or “messed up”. Hint: think of things that might happen that could change who could call who.

   Goal: get students thinking about the cell phone network again, and get the students thinking about how changes in a network will impact how a network will function. The cool thing about Cytoscape is that students will be able to make these big system changes and run simulations to see what the impact is.

   Possible student responses: add a phone number to your phone book, cell phone dies so you can’t call your friends, drop your cell phone and break it, can’t get a signal, lose your friends phone numbers, etc…

   If you did the homework assignment (create your own challenge question), have students pass in 3x5 cards now which have the questions on them. You can shuffle them and re-pass them out to students to answer while they are in the computer lab.

WHAT IS CYTOSCAPE?

1. Show Power Point on Cytoscape and networks to show the program we will be using (Network Examples in Cytoscape.ppt)

   Today the class will be using a computer program that is used in real-life biology research labs in order to study the interactions within networks. It will allow us to answer complex questions about complex networks.

   Slides 2-4 show how food webs, something students are familiar with, can be written in network format with clear nodes and edges. Slides 3 & 4 show networks that have been created by teachers using the Cytoscape program.

   Slide 5 shows the cell phone network which the students made yesterday- it will probably be much more neat and organized and easy to read than what students could come up with on paper.

   Slides 6-7 show some applications of this software and how it is used in research labs. Networks can be REALLY complex! We hope to use this software again when we talk about genes and proteins in this class.

2. Hook up teacher computer to projector in order to demonstrate how to use Cytoscape.

      a. Pass out Cytoscape Instructions.doc and demonstrate the steps involved in opening the program.

   Advice for teachers: you will need to test out these instructions beforehand. The program might open in a slightly different way depending on whether you are using a mobile laptop lab, your own personal computer, or the library computer lab. You should be able to follow the Cytoscape instructions step-by-step with the students following along.

      b. Demonstrate some of the features of the cytoscape program. The most important features for today’s lesson are under the "simulation" menu.

   • It is up to the comfort level of the teacher to decide how much time to spend on the "how-to".
   • Selecting nodes: if you click on a node (remember: each node represents a cell phone), it will turn grey. This indicates that you have "selected" that node.

     

      

   • Knockout and reactivate selected nodes: selecting nodes is useful if you would like to “knock out” that node from your system. In order to do this, select a node (see above) and then under simulation click on knockout selected nodes. The node will still appear on the screen, but all the arrows connecting it to the network will disappear. You have removed the node from the network: it can no longer make or receive phone calls. You can reinstate the node into the network by selecting reactivate selected nodes.

     

      

   • Knockout & Reactivate nodes based on carrier: Remember from day 1 that the cell phone information cards had a bunch of extra information on them about what cell phone carrier you were using, whether or not the phone had email capability, etc… These properties are programmed into the Cytoscape version of the cell phone network. Therefore, we can use this information to knockout groups of cell phones based on their properties.
     • Knockout by carrier: each phone has been assigned to one of seven carriers (note: these correspond to the numbered groups they originally met in while making the network). You can select to knockout a carrier, such as Verizon, and then all of the phones serviced by Verizon will be knocked out of your network.
   • Knockout & Reactivate nodes based on property:
     • Knockout by property: each phone can be put into a category of either phones with or phones without for each of the three properties email, roaming, picture.

     

      

   • Phone Tree. You can use this function to answer questions about how information will be passed through the entire system.
     • A separate window will show up for the phone tree function (see screenshot), and in this window you can select a start node from a list of all of the phones in the network. This represents the origin of the information flow. After selecting a start node, hit the start button and watch as the info flows through your cell phone network!
     • When a person receives a phone call, their node turns red. When 1A is selected as a start node, all everyone except 5C gets a call, so 34 nodes turn red. (see screenshot)
     • After all the calls have been made, a statistics window will pop up. This window gives some great information that they might be able to use to answer their questions. (see screenshot).

     

     

     

      

   • Shortest Path. This feature is useful if you would like to determine the shortest path of information flow (ie least number of phone calls) between person A and person B.

     

      

     

      

   • Reset Graph. This is a very important button because it will reset anything you have done; the knockouts, the phone tree, etc… If students think that they messed up, tell them to hit the reset button and try it again. It is also important to reset in between questions.
   • Help page. This will link you to the ISB cell phone simulator help page (see screenshot), which has helpful links with instructions similar to those given above. May be helpful for students looking for help while on their computers.

     

      

   1. Pass out assignment for today: Cytoscape Cell Phone Questions.doc (also see Cytoscape Questions Teach KEY.doc). We will be answering more complex network questions using the large 35-node cell phone network.

      Important: students should be using the computer tools to answer these questions, rather than just using the screen as a neater paper version of their network. Encourage the students to fool around with the various options in the software. If it seems to get messed up, they can always close the program and re-open it by following the instructions again.

STUDENTS IN COMPUTER LAB

1. Walk to computer lab or pass out computers from mobile laptop lab. Students should work in groups of two on this activity, if possible. Students need to bring with them: Cytoscape instructions, Cytoscape cell phone questions, and a pen or pencil.
2. LOGGING IN: it is very important that you STAGGER THE LOGIN process for all of the students in your class. There are many ways to accomplish this. One suggestion is to split the partners into 4 groups (have them number off 1-4), then tell them “Ones can log in now, Twos can log in now, etc…” Leave a few minutes lag time between each group.

   Whenever you have many students logging on at once, it will slow down the system. In order to avoid this, stagger the timing of students log on… This is VERY IMPORTANT. If the computers freeze or slow down, students will get frustrated with the activity before they even begin!

3. Wander the room and monitor student progress.

Things to look for:

   a. look for the cell phone network screen to be open on their computer. They should NOT have a blank Cytoscape screen- the network should automatically appear if students follow the directions correctly.

   b. If students are using the information flow feature, the nodes in the network should be turning red as information passes from cell phone to cell phone. Looking for the red color is an easy way to determine whether students are actually using the software.

   c. If a student seems to have “screwed up” their network, and if you can’t figure out what they’ve done, DON’T PANIC! Simply close the program and then follow the instructions to restart.

Encourage students to play around with the software. Trying different things is the easiest way to learn how to use a program, and they should not be able to “ruin” the network, because they can always close down the program and re-open it from the website!

If students get done early: encourage them to try to create their own network and try to run the simulation on it. (see extension activities)

Assessment: How will I know they know…

Cytoscape Questions: student should be able to answer questions by manipulating cell phone simulation. Monitor student progress in computer lab: if the simulator is working, you should see nodes changing color from white to red as messages are passed through the network.

Resources:

Cytoscape Instructions.doc

Network Examples in Cytoscape.ppt (power point)
Cytoscape Cell Phone Questions.doc
Cytoscape Questions Teach KEY.doc

Accommodations:

This lesson results in students more thoroughly understanding how and why technology is used to understand complex networks and it also highlights many important aspects of biological networks (importance of redundancy, the variation in node importance, etc.). You can offer biological examples to illustrate this, but you can also encourage students to connect this further to their daily life. The conceptual thinking behind this is what is important, not the specific examples. This may also help when students become confused or intimidated by vocabulary. In this case, the vocabulary words (Cytoscape, simulation, knock out, etc.) are not required to master the needed content and ideas.

Extension Activities:

Have students create their own networks using Cytoscape.
How to make a network in Cytoscape.ppt If more guidance is needed for students to research their own network than given in the above PowerPoint presentation, provide students with possible networks to research, such as the African Savannah, Arctic Tundra, etc.

Also, the Extension Activity document listed in Lesson 1 can be completed after this lesson, instead of after Lesson 1 if more information on Bioinformatics is desired.