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| - | <div class="boxOuter full" style="padding: 0px; border: 1px solid black; background-color: black;">
| + | |
| - | <h3><img src="https://static.igem.org/mediawiki/2012/b/b2/Lazyscientist2header.png"></h3>
| + | |
| - | <div class="boxInner centre clearfix">
| + | |
| - | <div class="pic" style="border-color: transparent; float:right; margin: 5px 20px 5px 30px;">
| + | |
| - | <a href="https://static.igem.org/mediawiki/igem.org/a/ae/Dundee12lazy.gif">
| + | |
| - | <img src="https://static.igem.org/mediawiki/igem.org/a/ae/Dundee12lazy.gif" width="150px"
| + | |
| - | alt="Lazy Scientist II screenshot" />
| + | |
| - | </a>
| + | |
| | </div> | | </div> |
| | The Dundee iGEM team of 2011 created an Android application named the Lazy Scientist, and this | | The Dundee iGEM team of 2011 created an Android application named the Lazy Scientist, and this |
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| | free to <a href="#dl">download</a>, and the full source code is provided. | | free to <a href="#dl">download</a>, and the full source code is provided. |
| | <br /><br /> | | <br /><br /> |
| - | The application currently contains the following tools:
| |
| - | <br /><br />
| |
| - | <ul style="padding-left: 4%;">
| |
| - | <li>Ratio to Percentage/ Percentage to Ratio Convertor</li>
| |
| - | <li>OD660 to Cell Count Estimator</li>
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| - | <li>Simple Dilution Calculator</li>
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| - | <li>Serial Dilution Checker</li>
| |
| - | </ul>
| |
| - | <br />
| |
| - | <div class="caption" style="width: 80%;">
| |
| - | (** Note: The OD660 calculator is based on a single sample set of data that, for obvious reasons,
| |
| - | can only provide an estimate of cell count.<br />
| |
| - | For more accurate OD calculations, in-situ, calibrated laboratory equipment should be used.)
| |
| - | </div>
| |
| - | </div>
| |
| - | </div>
| |
| - |
| |
| - |
| |
| - | <div class="boxOuter full" style="padding: 0px; border: 1px solid black; background-color: black;">
| |
| - | <h3><img src="https://static.igem.org/mediawiki/2012/1/1c/Splicerheader.png"></h3>
| |
| - | <div class="boxInner centre clearfix">
| |
| | | | |
| - | <br />
| |
| - | <div class="pic" style="border-color: transparent; margin: 5px 20px 5px 20px;">
| |
| - | <a href="https://static.igem.org/mediawiki/igem.org/3/37/Dundee12splicer.png">
| |
| - | <img src="https://static.igem.org/mediawiki/igem.org/3/37/Dundee12splicer.png" width="400px"
| |
| - | alt="Splicer Screenshot" />
| |
| - | </a>
| |
| - | </div>
| |
| - | Splicer is a short game of six test levels developed for the Windows desktop. The premise is
| |
| - | simple - from a selection of Biobricks, you are tasked with the creation of biological solutions
| |
| - | to given problems. By selecting each Biobrick, you insert it into the plasmid in the centre. Once
| |
| - | you think you have a viable solution, you click on the 'Transcribe & Translate' button to see if
| |
| - | you were right. If you are comfortable with C#, the full source code is included so that you may
| |
| - | add more Biobricks and more levels.
| |
| - | <br /><br />
| |
| - | The game was developed in Visual Studio using the XNA libraries, and full source code is provided
| |
| - | in the <a href="#dl">download</a> section, along with a full installable version of the game, which
| |
| - | can be removed via the Windows control panel as normal.
| |
| - | </div>
| |
| - | </div>
| |
| - |
| |
| - | <div class="boxOuter full" style="padding: 0px; border: 1px solid black; background-color: black;">
| |
| - | <h3><img src="https://static.igem.org/mediawiki/2012/c/ce/Cellsimheader.png"></h3>
| |
| - | <div class="boxInner centre clearfix">
| |
| - | From the onset of the project, the modelling team had to carry out investigative research to
| |
| - | understand the biological processes that were involved in the project to ascertain appropriate
| |
| - | modelling methodologies to adopt. Due to the unique combination of factors involved in the project,
| |
| - | it became evident that there were considerable quantities of mathematical variables that defined the
| |
| - | behaviour of the cellular interaction. From a software development perspective, it was attractive
| |
| - | to take the mathematical axioms of behaviour, and to wrap them within a bespoke modelling solution
| |
| - | to provide a visual representation of the project.
| |
| - | <br /><br />
| |
| - | <div class="pic" style="border-color: transparent; margin: 5px 20px 5px 20px;">
| |
| - | <a href="https://static.igem.org/mediawiki/igem.org/3/32/Dundee12cellsimanimsmall.gif">
| |
| - | <img src="https://static.igem.org/mediawiki/igem.org/3/32/Dundee12cellsimanimsmall.gif" width="400px"
| |
| - | alt="CellSim Animation" />
| |
| - | </a>
| |
| - | </div>
| |
| - | CellSim is a cross-platform, 2D, cellular automata
| |
| - | <a href="https://2012.igem.org/Team:Dundee/References" target="_blank">[4]</a> (CA) modelling
| |
| - | tool that was developed
| |
| - | to demonstrate, in a graphical manner, how the synthetically modified E-coli and C.diff cells
| |
| - | could interact in a simulated environment. The application was designed to simulate the cellular
| |
| - | interactions whilst also providing a customisable simulation environment that could enable the tool
| |
| - | to be used in other, similar projects. CellSim was developed to enable it to be executed on either
| |
| - | Linux or Windows based systems, and is released under the GNU GPL 3 license that permits copying,
| |
| - | modification and redistribution of the program. The source code and full class diagram is provided
| |
| - | within the download archives for educational purposes as well as encouraging others to build upon
| |
| - | the initial release.
| |
| - | <div class="clearfix"></div>
| |
| - | <br />
| |
| - | CellSim initialises the environment by parsing the text data file 'settings.dat' which must
| |
| - | be located within the same folder as the program. The download archive contains an example of the
| |
| - | settings file which provides all the parameters that are available for user modification.
| |
| - | The current development version (1.0) provides an environment in which the following aspects
| |
| - | can be simulated and defined by the user:
| |
| - | <br />
| |
| - | <ul style="padding-left: 4%;">
| |
| - | <li>Cellular Mitosis Rates</li>
| |
| - | <li>Strains</li>
| |
| - | <li>Colony Size, Initial Positioning & Colouration</li>
| |
| - | <li>Medium Flow Effects</li>
| |
| - | <li>Mucus Wall Effects</li>
| |
| - | <li>Time Calibrated Rendering</li>
| |
| - | <li>Nutrient Availability, Supply & Absorption</li>
| |
| - | <li>Low Nutrient Mitosis Suppression</li>
| |
| - | </ul>
| |
| - | <br />
| |
| - | <div class="pic" style="border-color: transparent; float:right; margin: 5px 20px 5px 20px;">
| |
| - | <a href="https://static.igem.org/mediawiki/igem.org/1/10/Dundee12cellsimcd.png">
| |
| - | <img src="https://static.igem.org/mediawiki/igem.org/1/10/Dundee12cellsimcd.png" width="400px"
| |
| - | alt="CellSim Class Diagram" />
| |
| - | </a>
| |
| - | </div>
| |
| - | The program was developed around an MVC structural design pattern
| |
| - | <a href="https://2012.igem.org/Team:Dundee/References" target="_blank">[3]</a>
| |
| - | with a subtle modification.
| |
| - | The initial design adopted a classic MVC
| |
| - | <a href="https://2012.igem.org/Team:Dundee/References" target="_blank">[3]</a>
| |
| - | architecture, whereby for each generation, each cell
| |
| - | was updated within the model classes, and subsequently rendered within the view classes. Due to
| |
| - | the large number of cells that the program is required to simulate, code profiling highlighted
| |
| - | the inefficiency if iterating through all cells twice. Furthermore, the status of each cell is
| |
| - | partly determined by neighbouring cells, and therefore a method was required to detect the presence
| |
| - | of neighbouring cells and their status. To accomplish this through data provided solely within the
| |
| - | model, for each cell, all other cells would require iteration and interrogation leading to a time
| |
| - | complexity of at least O(n<sup>2</sup>). Due to the mitosis behaviour of cells, the source number of cells
| |
| - | also increases in a quadratic manner. The quadratic mitosis behaviour cannot be alleviated, as it
| |
| - | represents the real-world scenario, so a solution was sought to alleviate the compound quadratic
| |
| - | time complexity that arose from the classic MVC
| |
| - | <a href="https://2012.igem.org/Team:Dundee/References" target="_blank">[3]</a>
| |
| - | implementation.
| |
| - | <br /><br />
| |
| - | The solution adopted was to carry out cell interrogation, cell update and rendering in a single
| |
| - | pass, and establishing the presence of neighbouring cells by direct interrogation of the graphics
| |
| - | memory as opposed to model data interrogation. By calculating the base address of the graphics
| |
| - | memory in conjunction with the co-ordinates of the current cell, a direct memory address could be
| |
| - | calculated and accessed to establish the presence of neighbouring cells, alleviating the need to
| |
| - | iterate through all cells. By adopting these measures, the time complexity of the 'cell evolution'
| |
| - | section of code was reduced to a constant, greatly improving the speed and number of cells that
| |
| - | the program could comfortably emulate.
| |
| - | <br /><br />
| |
| - | Cellular movement emulates fluid flow by imposing a circular pressure front that is circular in
| |
| - | nature. This provides a simple model that affects each cell's horizontal position by exerting
| |
| - | a greater force on those nearest to the centre of fluid flow. To enable variable flow rates to be
| |
| - | simulated, a normalised force was calculated from the cell's co-ordinates (x, y) relative to the
| |
| - | display screens height (Ymax), multiplied by a user adjustable force factor (f) and utilised to
| |
| - | modify the horizontal position of the cell. By carrying out this calculation on each cell, a
| |
| - | realistic, circular flow pressure is simulated. The new horizontal cell position is calculated
| |
| - | from the following formula:
| |
| - | <br /><br />
| |
| - | <div class="pic clearfix" style="border-color: transparent; padding-left: 150px;">
| |
| - | <a href="https://static.igem.org/mediawiki/igem.org/b/bb/Dundee12flowformula.png">
| |
| - | <img src="https://static.igem.org/mediawiki/igem.org/b/bb/Dundee12flowformula.png" width="600px"
| |
| - | alt="CellSim Flow Formula" />
| |
| - | </a>
| |
| - | </div>
| |
| - | <div class="clearfix"></div>
| |
| - | To provide a realistic and accurate movement of cells within CA environment, each cell contains
| |
| - | co-ordinate members for the respective 'x' and 'y' position. These class members are defined as
| |
| - | float data types as opposed to integers to permit gradual movements to be achieved. To render each
| |
| - | cell, the co-ordinates are simply cast to integer types before being passed to the graphics
| |
| - | interface. This permits cell movements to be calculable to fractions of a pixel, and provides an
| |
| - | accurate representation of the behaviour required.
| |
| - | <br /><br />
| |
| - | The application adopts the SDL (Simple Directmedia Layer) graphics API that was chosen primarily
| |
| - | due to its flexibility, and is licensed under GNU LGPL version 2
| |
| - | <a href="https://2012.igem.org/Team:Dundee/References" target="_blank">[2]. </a>
| |
| - | Furthermore, the library
| |
| - | provides binary compilations for a wide variety of operating systems including Windows, Linux
| |
| - | and MacOS. To encourage development of the program, pre-developed Eclipse and Visual Studio 11
| |
| - | project files have been created, and are free to download and explore. Alternatively, the packages
| |
| - | also include the pre-compiled binary versions of the application within the 'Release' folder of
| |
| - | the download archive (ZIP) files.
| |
| - | <br />
| |
| - | </div>
| |
| - | </div>
| |
| - |
| |
| - |
| |
| - | <div class="boxOuter full" style="padding: 0px; border: 1px solid black; background-color: black;">
| |
| - | <h3><img src="https://static.igem.org/mediawiki/2012/8/86/Downloadsheader.png"></h3>
| |
| - | <div class="boxInner centre clearfix">
| |
| - | <a name = "dl"></a>
| |
| - | NOTE: To run 'CellSim' under Windows, the Visual C++ Redistributable Package must be installed.
| |
| - | This is free, and can be downloaded from
| |
| - | <a href="https://www.microsoft.com/en-us/download/details.aspx?id=30679" target="_blank">
| |
| - | https://www.microsoft.com/en-us/download/details.aspx?id=30679
| |
| - | </a>
| |
| - | Select the file named 'vcredist_x86.exe' (6.2MB), and once downloaded, run the program to install
| |
| - | the Visual C++ libraries required prior to running the 'CellSim' program.
| |
| - | <br /><br />
| |
| - | <strong>Download Links:</strong><br />
| |
| - | Lysis To Kill - Android Package [
| |
| - | <a href="https://dl.dropbox.com/u/52338078/iGEM/Lysis%20To%20Kill.apk">Lysis To Kill.apk</a>
| |
| - | ]<br />
| |
| - | Lysis To Kill Eclipse Project - Full Source [
| |
| - | <a href="https://dl.dropbox.com/u/52338078/iGEM/Lysis%20To%20Kill.zip">Lysis To Kill.zip</a>
| |
| - | ]<br />
| |
| - | Lazy Scientist II - Android Package [
| |
| - | <a href="https://dl.dropbox.com/u/52338078/iGEM/Lazy%20Scientist%20II.apk">Lazy Scientist II.apk</a>
| |
| - | ]<br />
| |
| - | Lazy Scientist II Eclipse Project - Full Source [
| |
| - | <a href="https://dl.dropbox.com/u/52338078/iGEM/Lazy%20Scientist%20II.zip">Lazy Scientist II.zip</a>
| |
| - | ]<br />
| |
| - | CellSim Linux x86 Eclipse Project - Full Program & Source [
| |
| - | <a href="https://dl.dropbox.com/u/52338078/iGEM/CellSim%20Linux%20x86.zip">CellSim Linux x86.zip</a>
| |
| - | ]<br />
| |
| - | CellSim Windows x86 Visual Studio 11 Project - Full Program & Source [
| |
| - | <a href="https://dl.dropbox.com/u/52338078/iGEM/CellSim%20Windows%20x86.zip">CellSim Windows x86.zip</a>
| |
| - | ]<br />
| |
| - | Splicer Source - Visual Studio 10 XNA Project - Full Program & Source [
| |
| - | <a href="https://dl.dropbox.com/u/52338078/iGEM/Splicer%20Source.zip">Splicer Source.zip</a>
| |
| - | <br />
| |
| - | Splicer Installer - Windows x86 Installer - Full Program [
| |
| - | <a href="https://dl.dropbox.com/u/52338078/iGEM/Splicer%20Installer.zip">Splicer Installer.zip</a>
| |
| - | <br /><br />
| |
| - | <div class="caption" style="width: 100%; color: #DD0000;">
| |
| - | All software is provided under the GNU GPL 3 license terms (
| |
| - | <a href="https://www.gnu.org/licenses/gpl-3.0.txt" target="_blank">full text here</a>), and is
| |
| - | provided 'as-is' without warranty of any kind.<br />By downloading any of the software provided, you
| |
| - | are confirming your agreement to the terms of the license in full.
| |
| - | </div>
| |
| - | <br />
| |
| - | Some or all of the software provided may see further development by the author. Due to the
| |
| - | Wiki freeze at the end of the competition, future versions will be released through the
| |
| - | author's Blog at <a href="http://nibblesbytes.blogspot.co.uk/">http://nibblesbytes.blogspot.co.uk</a>
| |
| - | <br /><br />
| |
| - | </div>
| |
| - | </div>
| |
| - |
| |
| - | <div class="clearfix">
| |
| - | <div class="footerbox">
| |
| - | <br>
| |
| - | <center>
| |
| - | <img src="https://static.igem.org/mediawiki/2012/0/04/Sponsorbar2.jpg">
| |
| - | <center>
| |
| - | </div>
| |
| - | </div>
| |
| - |
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| - |
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"
