Difference between revisions of "Team:Pretoria UP/Collaborations"
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Revision as of 18:49, 17 October 2016
Collaborating with other teams We collaborated with three different teams in the 2016 iGEM season. We created a documentary for team Aix-Marseille focusing on the socio-economic and political issues facing the current platinum sector, including the Marikana strikes. We assisted team MacQuarie by making a graphical user interface on MatLab showing how the concentration of various intermediates including ALA (Y-axis) changes over time (X-axis) in chlorophyll.
Collaboration with Aix-Marseille University South Africa is regarded as having the largest platinum reserves in the world. The Merensky Reef stretching from southern Zimbabwe through to Rustenburg and Pretoria is the centre of platinum mining in South Africa. AMPLATS is the leader in platinum mining in South Africa, producing 40% of the total group platinum group metals. The Aix-Marseille University iGEM team identified problems faced by the mining sector which include limited sources, the use of hazardous chemicals to eliminate impurities, the disregard of safety measures and the lack of methods to recycle platinum next to highways.The solutions they came up with are to concentrate the platinum accumulated from roadside soil by phytoremediation plants and to transform it into nanoparticles. We assisted them by creating a documentary focusing on the socio-economic and political issues facing the current platinum sector, including the Marikana strikes. We also looked at the possible implications of their 2016 project.
Interview with Dr Meyer at the University of Pretoria for team Aix-Marseille.
Interview with Mr Henwood at the University of Pretoria for team Aix-Marseille.
Collaboration with Macquarie University We assisted the team MacQuarie by making a graphical user interface (GUI) on MatLab. The GUI that was made is a graph which shows how the concentration of various intermediates including ALA (on the Y-axis) changes over time (X-axis) in chlorophyll. Team MacQuarie provided a list of specifications for the interactive graph they wanted. These specifications include:
1. Creating an interactive display that plots the Chlorophyll concentration as a function of time.
The GUI was created using Matlab’s built in app, GUIDE (GUI development environment). GUIDE was ideal for this problem as it allowed for complete customisation of the of the interactive graph according to the specifications of team MacQuarie.
The GUIDE interface allows the programmer to easily place plots, sliders, texts and buttons, amongst other handles, in the exact position that is needed. Figure 1 shows the GUIDE interface as well as the layout that was designed for MacQuarie according to their team’s specifications. These included allowing the user to enter the initial total enzyme concentration as well as the ALA concentration. The user can also set the number of days using the slider. The plot is then generated automatically upon each input.
Figure 1: GUIDE interface with layout of GUI handles, including a set of axes, two "edit text" boxes, a "slider" and eight "static text" boxes. Saving this layout generates a skeleton code.
Once the desired layout was achieved, Matlab generates a skeleton code upon saving which can then be used to assign the various functions to the various handles. Attached is the code as well as the GUIDE layout structure that was used to generate the interactive graph. Three additional functions were added to the code. The first function, “plotter”, was used to generate the actual graph. This function requires three inputs, the total duration of time (in days), the total enzyme concentration as well as the ALA concentration. The second and third functions were required to model the actual concentration changes as a function of time and were provided by team MacQuarie.
The two “edit text” handles were then programmed to allow the user to enter their desired enzyme and ALA concentrations. The slider was also programmed to extend or reduce the time duration (X-axis) of the plot. Lastly one of the “static text” handles was programmed to inform the user of the position of the slider, namely a value between 1 and 16 days. A zooming toolbar was also added to the GUI to allow the user to zoom into sections of the plot.
Running the code starts the newly programmed GUI with which the user can now change the various variables and see the effect it has on the concentrations. Figure 2 is a few screenshots of the GUI in action. Due to the nature of MacQuarie`s experiments the graph was crucial to make an accurate conclusion about their results. We also helped them to solve coding problems on MatLab.
Figure 2-4: Screen shots of the GUI showing the plotter in action.
2. Increase or decrease the time duration with the help of a slider.
3. The maximum duration of time should be 16 days.
4. Users should be able to zoom in and out of plot.
Collaboration with Heidelberg University
