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Latest revision as of 10:19, 18 September 2015
Introduction
Synthetic Biology is a creative work, but now its design process is facing lots of challenge. BioBrick retrieving process and information collection process have always been a pain point for every Synthetic Biologist, so as the test of design’s efficiency. Our aim is to simplify the design process of synthetic biology and let it become a pleasant work. So here we introduce BioDesigner, a smart Synthetic Biology design assistant. By providing comprehensive solutions for current design problems, BioDesigner could make users concentrate more on the design itself.
BioDesigner integrates incredible functions and features, among which, search, recommendation, and simulation are three vital ones. 1) Search function is used to help users find their needs based on what they describe, besides the related information will also be presented together, including basic information, parts quality evaluation score, as well as parts' related papers. 2) Recommendation function is used to recommend users what they might use during the design process, this could narrow down users’ search scope and shorten the design process. 3) Simulation function is used to simulate the reaction process of the designed device, since using experimental method to test the device is much more time consuming. The detained description of these function are introduced as follows.
Functions
Search
Searching parts and finding parts that might be useful is a frequent process for Synthetic Biology for there are tons of parts. BioDesigner provides a powerful search tool. The search function is based on the search engine elasticsearch, which have a great efficiency and is used by lots of company. We also adjust the search result with users’ current design’s function. User can add a function tag to their design, like “water pollution”, and the parts that related to water pollution will have a higher score, which means they will be ranked on top in the result. Just finding a part is not enough for users, so that we also provide lots of useful information to the user. The information contains part basic information, related registry page, and also related papers, so that the user can learn about the parts’ detail information. By using DNA sequence alignment algorithm, we aligned each part in NCBI database and presented alignment score to the user, which can be quality evaluations of parts.
Recommendation
Recommendation should be some thing that can tell what the user might need, and also provide users candidates to let the user choose, which also means reduce the decision time. BioDesigner analyze the user’s design and then, give recommendations about parts they may need. With Aprior algorithm, the program can find all the parts that are related to the parts in user’s design. With Markov algorithm, the program can find the part sequence that may follows the part the user just add to the design. Together with those two algorithm, BioDesigner provides all the useful parts to the user. Besides, what BioDesigner can do is more than that, with the analysis of pathway data, we find related proteins, compounds and genes, which are things that the user might be interested. By showing those datas in a graph, BioDesigner can help user have a clear thought about what should do in the next step.
Simulator
Traditionally, the test of Synthetic Biology design is by experiments, which is a time consuming process. There are already lots of Biology reaction simulators to help researchers to learn how the gene will express or how the reactions performed. BioDesigner also integrated a simulator. Different from mostly used ODE method, we choose to use stochastic simulation, which provides a view of how reaction will take place, and also can point problems that cannot be determined by ODE.
User Guide
Project Page
Here is the project page for BioDesigner. In this page, you can check all your projects, devices, you can also go to the design page, simulation page and system recommendation page. By click the buttons on top of the page (Simulator, System Recommendation), you can access those two pages. All your projects are placed on the left side. By unfolding project tag, you can check the devices. A thumbnail image for the device will be presented in the center of the page. Clicking the “Design” button on the right, you can design this device in a new page.
Design Page
The design in BioDesigner is based on drag and drop. Dragging a part and drop it in where you want it be, the design is done.
Search for a part can be done on the left side. By typing keywords, you can search parts and find things you may need. Once you find a part you are interested, click it and all the information will be presented on the right side. Dragging the useful one to the center area, the part will be added to your design.
Once a part is added, the recommendation will be presented automatically. Related parts will be presented on the left side. The part sequences are all presented on the bottom side.
System Recommend Page
In system recommendation page, you can get compound / gene relation graph.
By typing a compound name in the left search area, you can search compounds. Each compound is followed with a add button (move the mouse over it), click it to add it to compounds you are interested. Click the “run” button, you can get the result graph. By click the gene node or compound, you can get their informations.
Simulator Page
In the simulator, you can get simulation result for reactions. Reaction defining area is placed on the left side. The parent material area are the initial compounds you added to you reaction. Reaction equation area is where you define the reaction equation.
Here is a example. For reaction a + a = c and a + b = d, compound a amount is 100 and b is 50. In the parent material, add a X 100 and b X 50. In the reaction equation area, first is a + a = c, second is a + b = d, click Simulate, the result will be presented in this page.