Thursday, September 3, 2009

MC Interface Revealed!

Hi Everyone!

I am pleased to post (for the first time) screen shots of our Membrane Computing Agent Base Model. In this post i am focusing on interface mostly. Beside the fact that we want to have an accurate model, we also want a model that is easy to use. So we thought about design issues with our interface. How can we (computer scientists) hide as much code as possible so when a biologist uses our software, they don't freak out.

So lets take a look at our main screen:

If the size of the picture is small and you have a hard time making out the details, you can always click on the photo and see a full size version. Unfortunately this is the largest size that the blog allows for posting images online. Anyways going back to our interface, on the top you see "Quorum Sensing Model - Version 2.0". So this is our QS model and the version 2.0 is our latest release. We initially started with version 1.0 and gone through 1.1, 1.2, 1.3, ... , 1.7. With versions 1.x we were adding basic functionality to the system. Simply setting up a framework, introducing rules, figuring out how to define rules and so on. In version 2.0 we have build the interface on top of our framework so users can interact with the system without the need of knowing how the code works. You don't need to compile anything, or type a single line of code. This is the beautify of Mathematica. I don't want to get into Mathematica and our implementation; however I want to mentioned that all you need to know to run our program is a shift+enter and that will do the trick. We have also worked on improving run-time speed of our simulation and I am happy to say that version 2.0 is about 5x faster than version 1.0!

Going back to our interface, there are three different tabs on the top: Input, Visualization and About. Input tap includes 2 sub-tabs: Simulation parameters and Rule Constants. Under simulation parameters, we have different parameters to set before running the simulation. To get the user started, each parameter is set to a default value. User is able to modify each value before running the program. We will go over each parameter on our next post. For now lets focus on interface. We have different parameters for the simulation in general (population size and simulation step). Cytoplasm, Periplasmic space and environment also get their own list of parameters. At bottom of the interface we have a check box which allows user to introduce division into the mix. So there are two different way of running the simulation. When division check box is not selected, starting with 20 individual cells, the simulation ends with 20 cells and outputs a set of results. However when division checkbox is selected, user might start with 20 cells and based on how many steps is specified by the user, the system might end up with 40 or 80 cells. Results of the simulation also reflect the division. Next blow the checkbox we have a button for running the simulation and then the current status of simulation is shown below ("Ready!"). In order to give user an idea about current status of the simulation we have added a progress bar which only appears when the program is running. This progress bar gives the user a status update on how long will the simulation take before completion. Here is a screenshot of a simulation in progress:

In this example the simulation is 69% completed. Next is looking at rule constants. Each rule in our simulation has a constant associated with it. This constant is used for calculating probability of a reaction. The system is loaded with default values for each constant. However one can modify each value before running the simualtion. Here is an screen shot of rule constants:

Because it is hard to remember which constant belongs to which rule, we have enabled a tool-tip option so when a user moves the mouse pointer over each constant, its corresponding interaction rule is displayed (as shown above). This should help out the user in associating each constant value with an interaction rule in the system.

We are going to skip visualization section for now (still under development). Lets go to About tab.

Here under about tab we plan to include copy rights, information about developers and other related information. There is also another aspect of our modeling project which is on hold for now due to time constraints. That is, ability of exporting results. Lets take a look at what we are planning to have maybe by end of this year:

Yes, we are planning to integrate the ability of exporting results from the simulation to HTML (for posting online), SBML (Systems Biology Markup Language - for visualizing metabolic pathways and importing to popular biological modeling tools such as Cell Designer) and PDF (for sharing as well as printing). This is part of our future work for expanding the model and making it even more useful.

If you have been wondering about results, well our model is also able to produce nice and clean graph visualizations. Lets take a look at sample AI2 concentration over 1000 steps:

I am gong to present only this graph for our result section just to demonstrate that our model is able to not only simulate by also analyze the results and visualize them.

Ok. This should do it for now. Consider this post as a sneak preview of what hopefully will be a complete Quorum Sensing Model. We hope to have our completed model posted on UCalgary wiki by end of september.

Thanks for following our progress!


Friday, August 21, 2009

Hiatus...Or not.

As summer winds to a close, and fall classes loom closer and closer, we recognize that it will be difficult for us to post by our regular schedule (as in, a greater deviation than usual).

However, rest assured that updates from all subteams will still be completed on a regular basis! Right, guys?

:D Enjoy the rest of the summer, and see you in September!


Thursday, August 20, 2009

Labbing it up!

Hello virtual world of synthetic biologists, engineers and the rest of the cool kids floating around in cyber space!

Jamie is back with a short and sweet update from the lab side of things.

This past week Emily (with a little Vicki-probably about 0.1 of her to be exact) alongside with Kevin proceeded to test the reporter circuit with the mutant circuits. This involved a quick plasmid switch of the mutant Vicki, I mean OD47A into psB1AC3 simply due to antibiotic resistance and selection pressure. Overnights were grown and tested in the plate reader Synergy HT.

Jeremy and myself (Jeremy did most if not all of the pipetting; I might have plated one or two transformations here and there) just finished up the signalling pathway in pCS26. Sequencing results were analyzed with tools available over at (i.e. BLAST) and the signalling cascade is now officially completed with glycerol stocks, plasmid DNA and restreaks ready to go!

I (sort of) lied when I said the luxPQ-luxOU construct was done. Just a tad. Carol's project involving the synthetic sigma70 promoter is currently on hold as not only is Carol off in Vancouver on a well deserved holiday but new primers need to be made with the degenerate bases. We hope to resume progress on this after next week.

Meanwhile, I myself am fiddling around with mineral oil, plate reader, 96 well microplates,Vibrio harveyiSalmonella typhimurium, Escherichia coli, centrifuges in hopes of isolating AI-2. Please note this is all done without the handy dandiness of multi-channel pipettes or access to a VICTOR; nevertheless learning to pipette effectively and how to calibrate a different model of plate is useful and exciting!

Without further ado, on behalf of the lab team I will like to sign off (not permanently though ;) - can't get rid of us THAT easily) for the summer. Thank you everyone for following us throughout the sunny (and rainy) summer days and I look forward to blogging again once the school year rolls around. So until next next week a.k.a. September, see you later :D!

FM 707.1 Marketing Update for the Week of August 17th 2009

Hello everyone,
My name is Fahd Mirza and you are reading my FM 707.1 marketing update for the week of August 17th. This week was rather slow for marketing because our marketing team was either busy with lab or ethics work. However we still managed to get a lot of stuff done for marketing,
1) Last Thursday, we were interviewed by the CJSW 90.9 Radio station. CJSW is the University of Calgary Community Radio station whose aim is to promote the activities of the University of Calgary students in Calgary and surrounding areas. We were interviewed by Joe Burima, who is the current program director for CJSW. On behalf of the University of Calgary iGEM team, we would like to sincerely thank CJSW for their support to iGEM and hope that they would continue to support our team in the future.
2) This week, Prima and I continued to contact Syn-Bio and Oil & Gas Companies for potential sponsorship/partnership. We hope to wrap up the sponsorship agenda by the end of August.
3) The biggest news of this week is that we have surpassed the amount of funds that we needed for this year. All the funds generated from now on will be contributed towards our next year’s iGEM fund for recruitment and other purposes.
4) We have also been working on our August newsletter which will be out soon.

We have also been working on our August newsletter which will be out soon. Also Prima has contacted the company that will be responsible for making our University of Calgary 2009 iGEM team shirts. We will also be working on attracting the media’s attention for our aGEM and iGEM jamborees.

Tuesday, August 18, 2009

Letter from one island to another

Dear Mandy,

Due to finals early this week and you having left for Hawaii, second life team members have been sparse. I wanted to stay in touch and keep you up to date somehow.

As you are aware, since scripting and equipment in the lab has been completed, last week we began the base of the Biobrick spiral where some of the fundamentals of molecular biology, including the central dogma will be located. You will be happy to know I have completed the DNA replication animation that avatars will be able to click on in order to learn what is required to happen for successful replication as well as a initiation point/button to begin the activity as well as reset it. All that is left is make it user friendly since everything that can be touched will perform some action and these actions just need to be explained and secured so that order is important. This may also be done with the help of a notecard that has been made. The only reason this went so slowly is the fact that I am attempting to complete wiki notebook updates in parallel and believe me, it has been a painful experience decrypting the notes that I have. Now, transcription and translation will have to be added and will most likely be tackled by either you or myself in the near future. I have started the initial framework for transcription, but most likely will not be able to complete it before this week is finished.

As I understand it, the biobrick simulator is basically completed and now the levels have to be organized and the textures for the buttons of the biobrick simulator interface. Thank you for completing the buttons Patrick required for the HUD he has made. They look great and I’m sure he really appreciates it.

I see the area avatars first enter the island has been expanded by you and Stefan and now includes a map (including teleportation areas) and directive tubing into synthetic kingdom. To ignore the big red X’s and arrows would have to be intentional and pathway stones litter the landscape throughout. Stefan has been working on his eukaryotic cell and finishing up his disease hunting bacteria within it. Also, I would like to thank you for allocating an area for previous iGEM projects and I see that the logo now decorates the outer walls of the virtual lab. A section of the island will now be filled with worthy iGEM projects, which may be done in the fall with enough linden dollars.

Hoping you are able to locate a bobtail squid,


Monday, August 17, 2009

Sensitivity analysis: Models... have feelings too!

Vicki and Chinee has put quite an amout of time into tracking down those sensitive ones in our system. Vicki is currently working with the Sensitivity analysis tool in Matlab commandline in order to find the sensitive parameters that influence the GFP output the most. The following graph is the result her sensitivity analysis model has generated so far: (click to enlarge)

The closer the graph gets to 0, the lower the influence this parameter has on the GFP output, and vice versa. According to this graph, the kForward (reaction rates)values 1, 3, and 4 seems the most influential parameters relative to 2 and 5; thus these parameters will be looked at further.

From these results, Vicki performed parameter optimization on them. In parameter optimization function, she was able to play with the individual parameter values in order to come up with a best fit line model to the predicted levels of GFP output. The following is the graphical result of the above function.

Here, the circles represent the made up predicted data, and the colored lines represent each optimized parameters. The optimized rate constants for kForward1, 3, and 4 fit nicely to the pattern of the predicted data; however, the optimized rate constants for kForward 2 and 5 do not, meaning that these parameters do not play a big role in determining the GFP output values.

From these two functions, Vicki would be able to, once we get some lab results, optimize our significant rate constants to fit the behavior of our AI-2 system.

Along with Vicki, Chinee was also working on the parameter sensitivity; however, with a different tool. In Simbiology, Chinee was able to outline the key difference between the initial amount and the reaction rates of the parameter. The following is the graph when all the parameters have a reaction rate value of 1:

The following is the graph when all the parameters have a reaction rate value of 10:

The only difference between the above two graphs are that the lines in the second graph are much more steep than the lines in the first graph. This means that the reaction rate only influences how immediate the reactions happen.

And finally, the graph when all the parameters have an initial amount of 10:

The above graph is very different from the ones above. From this, one can see how initial amounts of parameter play a much bigger role than the rate constants of each parameters.

I, Kevin, and Carol attempted to fix some biological misunderstandings within the reactions, and produce a graph that displays the pattern of each parameters. The following is the graph:

The patterns observed are reasonable and match what was expected. The lab data is needed to get an accurate model of our system; however, from it we can still test the sensitivity of each parameters by changing them one by one and simulating the results.

We hope to get some lab data by this week.

Thursday, August 13, 2009

FM 707.1 Marketing Update for the Weeks of August 3rd 2009 and August 10th 2009

Hi everyone,
My name is Fahd Mirza and you are reading the FM 707.1 Marketing Update for the week of August 3rd 2009 and August 10th 2009. These past two weeks have been intensely busy and highly productive for our marketing team.
Last week, we had organized a massive bake sale having more than 400 baked items to sell. This event managed to raise a net profit of $500.04 Cdn Dollars. All the funds would be directed towards our research project. We had also managed to get sponsorships from Corning Life Sciences (Thanks to Prima Moinul) and VWR Scientific (Courtesy Fahd Mirza) last week. Our July newsletter was also ready to be sent out to potential/current/future sponsors and to media organizations who gave us media coverage. I want to thank Jamie Feng and Prima Moinul for doing a marvelous job on the newsletter.
Nexen Inc. was declared our Sponsor of the Month for the month of August. It is with Nexen Inc.’s generous donation that iGEM Calgary would be able to achieve its goals.
This week, our iGEM Calgary team toured the Oil Sands in Fort McMurray courtesy of Andrew Hessel and OSLI (Oil Sands Leadership Initiative). The tour was a great learning experience and an exciting opportunity for iGEM Calgary team to work on future potential synthetic biology projects for iGEM. It was also an opportunity for our marketing team to form important partnerships with the Oil and Gas Development companies.
We are still working on getting more sponsorship for our research project and I hope that we are successful in this endeavor. Within the next couple of weeks our marketing team will be working on our August newsletter and getting media coverage for our project, the All Alberta iGEM Jamboree (also called aGEM) and the iGEM competition itself at MIT.