Proof And Demonstration
Our project aims to design a metabolic platform that simulates changes in the metabolic network to provide comprehensive results for the researcher. You can take the data from our platform, search the pathways between molecules, and perform the metabolic simulations mentioned above.
These functions, which are hosted on the web, are divided into three main modules: Synthetic Bay (DB), Pathway Finder (PF), and Deep Metabolic Simulation (DMS). Through ‘/Home’, we can enter the Home page of the project. On this page, users can get our project's leading content and the manual (Handbook) of the software. At the same time, they can enter the three functional pages by clicking the navigation bar.
(You can see some simple operation in this video. If you want to get more details, please read our handbook.)
Click the navigation bar from the home page or input ‘/database’ to enter the database module. Here, you will know the basic framework of our data and download the data. Our data provides four downloadable files, named "reaction.csv", "compound.csv", "enzyme.csv" and "Synthetic Bay.db", respectively.
Click the navigation bar on the home page or ‘/PF’ to enter the Pathway Finder module. Pathway Finder includes two functions: forward pathway search and reverse pathway search. In the first function, you can input a start compound and an end compound; we will search for pathways from the start compound to the end compound. According to the length of the path (energy score of reactions) and weighted score, our Pathway Finder will calculate scores and sort all the pathways between the start and end compound to output the better pathways (TOP10). We will finally return a result (PDF) to you.
Meanwhile, users can input the five parameters (KM, KKM, Toxicity, PH, temperature), which means the weight ratio of the their influence. You can assign value to the five parameters according to their importance in the experimental environment or your prior knowledge. A weight matrix will be created based on the value you input and the content of data, and then a score will be given to these pathways. In the reverse pathway search, users input the target molecule and the number of the steps (steps, no more than four). Then you will get some pathways that can produce the target molecule. Our output will be available to download in PDF format. For detailed PDF introduction documents and operation steps, please read the Handbook.
Deep Metabolic Simulation
Click the navigation bar on the home page or ‘/HMS’ to enter the Deep Metabolic Simulation module. DMS aims to provide simulations of metabolism in a computational environment. Users input the default value of common compounds and the special values of particular compounds, which are hypothetical parameters that refer to the number of molecules or the molecular level. Then, we construct an environment that contains all reactions and all molecules (compounds), giving these reactants initial states with the user-defined values; You can also eliminate some reaction (the reaction_deficient_list) according to the demand; these reactions may be which you want to block or have inhibited in gene level. Eliminated reactions will no longer provide the molecules’ transformation on both sides of the reaction. Then we simulate the process of metabolic reactions, let these molecules randomly transform to others until it reaches an equilibrium state. Users can adjust the times of metabolic simulations through epochs. The larger the epochs, the more times DMS functions iterate, and the more stable DMS results are. For users' convenience, we’ve provided an observation list for the compounds that you want to observe (get the change of these compounds), and we’re going to put them first on the top in PDF with red color. Finally, users will get two results: the visible result in PDF format, and the other is the data form result in CSV format. Users can download the data according to their own needs. For detailed PDF and CSV documentation and procedures, please read the Handbook.
Our three modules are inter-related. Users can not only analyze the metabolic system with these modules but also cooperate with other software to form a more standard pipeline. First, you can see the correlation between the reactants from DMS. In DMS, that changes of one molecule will result in other compounds’ changes dramatically. Then you can go to Pathway Finder and search for the pathways between these two reactants. Second, users can search pathways between two compounds, and the reactions in these pathways can be deleted in DMS. as a result, you will find some unexpected results when you use DMS. Third, when you use other IGEM modules for project operation, such as eliminating a particular gene of one reaction or making part of the molecular level changes, you can input the changed level as the initial value into our DMS module, obtain a more comprehensive molecules change within the metabolic system.
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