Perhaps, the first thing
you should do is check out this brief introduction to NetSim, an iPad app that the CSUN IT department and yours truly developed and launched last year. Then, watch this video tutorial https://www.youtube.com/watch?v=NZ_vbQ-bi1s&feature=youtu.be . on how to use NetSim. By the way, accept my apology for the low quality of the video – this is a work in progress in several ways, and I have not had the time to edit a tutorial video that looks a little more professional. On the flip side, you’re the first humans on Planet Earth to use this app in a real-life scenario. (…Yes, you may tell your friends…)
I can imagine that you’ll have several questions. Let me preemptively answer some:
– What kind of biological network should I create?
It should be a molecular or genetic network. It can be genes and proteins interacting with one another, including protein-protein, protein-DNA, genetic and enzymatic interactions. Please refrain from mapping physiological or ecological networks. Any interactions among biological entities within a cell will work.
– Does it have to be real, or can I make one up?
It has to be based on some sort of evidence. Obviously, you will have to come up with (i.e. make some informed guesstimates about ) specific values for parameters for which no values may exist, or are easy to find. But I do expect the nodes (genes/proteins/molecules) and the interactions between them to be based on real evidence, and that the values that you choose for them are reasonable. In fact, you’ll have to share a reference to the sources that you used to put together your network, and some narrative to explain some of your decisions in compiling the network together.
– Does my network have to have a minimum number of nodes or interactions?
No. The more the merrier, of course. But the simplest of networks with only two nodes and a couple of carefully selected parameters (and one that shows some complex behavior) could earn you several points.
– Do I need an iPad to download / install NetSim?
Yes. The app was developed in the context of the iPad initiative, and it runs only on the iPad. It won’t work on other tablets, laptop/desktop computers or iPhones.
– Do I need to create and share my network all in one sitting?
No! NetSim allows you to save your work in progress. At the very end, you will generate a share code that you will submit as part of your submission. But that’s at the end, when you’re happy with your product. In the meantime, you can open and work on your network as many times as you want/need – the only thing that you need to remember is to save your updated networks (the iPad will save them locally, and you will be able to find them later by date/time).
– How many points will I get for submitting a network?
The maximum number of extra-credit points is 50. Yummy. But, how many points you really get of course depends on a series of grading criteria. Very generally speaking, the more of the items below that you check, the more points that your network will accrue:
-Narrative & References: You need to submit a paragraph or two describing the biology behind your network. Do not assume that I will know any network that you submit, no matter how “famous” or common its nodes and interactions may be. Do not assume that I will immediately understand the regulatory connections within your network based on parameters and configuration. A more complete and eloquent narrative allows me to figure out if you chose reasonable parameters and connections (and note I say “reasonable” not “right” or “correct”; once again, there may not be “right” or “correct” parameters for your network). In your narrative, you will also have to include any references backing up your network. If you cite the book, give me (a) page number(s). If you’re citing something from lecture, give me a lecture date. If your citing any internet source, give me something accurate that I can check (perhaps a valid URL?)
-Originality. I expect a fair share of networks depicting, for instance, the Trp or Lac operon (or any of the other real-life processes that we discussed in class). And that’s fine! But if you can come up with a network that you put together based on material outside of the book or lecture… that’s even better!
-Number of nodes and interactions: the more, the merrier (i.e. the more points).
-Number of feedback loops and autoregulatory connections: the more, the merrier (i.e. the more points).
-Complex behavior: Do the nodes in your network show any complex behavior (dancing up and down, or drastically changing behavior depending on slight changes to initial conditions or key parameters)…? Or does your network show some nodes quickly shooting up and staying up, while others decrease and never come back, regardless of what parameters you choose for your your network …? The closer to more complex behaviors, the better!
-Have you named all of your nodes? Have you?
-Parameter choices. Are your time delays, interaction strengths and signs, start values and detereoration and production constants properly justified (i.e. reasonable) based on the information in your sources?
– Can you give us an example?
You can find an example of a submission here. The text portion of your submission should briefly describe the reason behind your choices for network architecture and parameters. In the example that I provide, I included a graph from the source article on which the network is based – I suggest that you add a visual reference to your source if you can, which could make your job explaining the network a lot easier (a good picture is worth a thousand words). Notice, also, that a simple reference to the source is enough. And most importantly – make sure to include the share code generated by NetSim (and remember that you need to generate the share code only once; after that, all the changes you make will be saved to the same network).
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