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Team:USTC-Software/Project/Software
From 2013.igem.org
As an experimenter, have you ever confused about getting no result when all experimental conditions are well enough? Or have you ever been tired of repeating the experiment over and over again without knowing whether your pay is futile? Or have you ever dreamed of choosing an imported gene by global regulation instead of only direct interaction? If yes, take a gNAP before wearing lab gloves!
gNAP, genetic Network Analyze and Predict, is a software analyze the infection of exogenous gene to engineered bacteria’s Genetic Regulatory Network(GRN) and introduce a predicted imported gene satisfying your needs!
To reach the best user experience, we designed four succinct User Interfaces on which you just need to click some buttons all the questions above will be solved.
Starter
“Starter” has only one button which could lead users input all information needed for the next simulation and get ready to start. It is an easy-to-use interface guiding users complete the operation according to the prompts. The exogenous transcription unit’s promoter and gene sequence should be put into gNAP in this part. If not, users could not use analyze function, yet predict module can function well. All the database files will be integrated in this part and genetic information will be stored in an external file, “all_info”, eventually. The original GRN is built in “Starter” with a matrix of regulation in file “old_GRN”.
Now, it’s time to start taking a gNAP!
Monitor
This shows the function of forward analysis.
This shows the function of reverse analysis.
"Monitor" is one of the main module of our software as a monitor keeping watch on running. The command lines in "Monitor" intuitively shows the detail in the process of software running. There are two main functions in this part. One of which is analysis function that simulate the infection of new gene's importing before and the simple evaluation of new GRN. The new GRN matrix is output into a file called “new_GRN”. This function may cost about 3 minutes, so taking a nap will be a good choice. The procession running and command lines' showing are synchronous. Prediction function is another one which can be operated with adding the desired target expression instead of inputting the exogenous gene sequence. The running time of this part is determined by the precision and the number of iteration time in prediction algorithms. "Monitor" is very easy to operate through some simple action buttons and intelligent gene selection mode. The result of this monitor can be found in "Result" and "Display".
Result
"Result" uses simply words to show the results of all functions of gNAP intuitively. There are two parts in the interface showing different results about the modules of analyze and predict.
In the part of analysis, the stability has been scored into five degrees and users can choose a specific gene showing its information. All the information can generate an SBOL file as well as searching genetic information in RegulonDB. In the other part of prediction, target expression and predicted interactions are shown in a table. Users could pick out the significant regulation as a reference of genetic choice.
The most succinct words have been used in this part for giving users the most intuitive and clear results. The graphs and vivid network structure have been put into "Display" with JAVA's rich GUI library.
Display
“Display” is the data visualization part of our software. To reach a better impression, it had been written in JAVA language. There are three parts in “Display” module: show regulation, show gene change and show network. The prediction of interaction between new gene and original genes can be seen in “show regulation” part with both regulated and regulating. “Show gene change” part shows the changing of all genes with the time changing. What’s more, users could see the interactions of whole network in “show network” part. Dragging, choosing, picking out the genes in GUI is available. When choosing one gene in a giant network, all genes which have interactions with that one will be picked out and shown in a small network.
Tutorial
The tutorial of gNAP contains 3 parts: Help Document, Quick Start, and Instruction Video.
Help Document is a PDF document which collects all of the information and operation details of the application. It will be helpful for users who want to carefully understand our software because it contains all details about gNAP using. If you are interested in gNAP and hope to start in a minute, Quick Start is the best choice.
Quick Start is designed for the first-time users especially for those who need to know the basic operation of gNAP. With no doubt, it is brief and will help the users starting using gNAP and doing his work in a convenient and swift way by several pictures with short instructive sentences.
Instruction Video uploaded on YouTube is also tailored for novices. It shows the operation in a dynamic status, which makes the operation vividly and easy-to-learn.
Code
All source code of our software have been pushed up to Github and there is a help document generated by Doxygen based on our notations in the command lines. You can download the PDF file [here] which contains the introductions about all Classes and Functions used in our software.
The command line source files are written in C++ language and visualization part are written in Java language. Both of them can be complied across platforms. The GUI source files are also written in C++ language with Qt Creator, it can also be compiled across various platforms using Qt 5.1.0, which can be downloaded here.
Download
You can download the ZIP files including Executable Program build on Windows, Linux and MacOS here:
gNAP_3.0_linux_32bitgNAP_3.0_windows_32bit/64bitgNAP_3.0_Mac_OS
PDF Download
*QucikStart*Tutorial
Summary
In general, most mathematical models were used for analyze the experimental results. GNA also analyze the GRN but just focus on regulation in original network. However, our software focuses on the infection of imported gene which is quite usual in synthetic biology instead of analyze the GRN only. In the same time, gNAP uses various algorithms and methotheir lab gloves will be really useful to researchers and save them a lot of time.
gFinder: Gene Finder
gFinder is a website software which you can visit from here(http://www.stlover.org/gFinder). It could be used to find the specific gene with target regulations. For example, if users need to find a gene which can enhance geneA’s expression, depress geneB’s expression, enhance..., gFinder can find a gene whose function is similar most from the database. So, with the help of gFinder, the reverse analysis result of gNAP, our main software, can step forward. We could get the specific gene for target expression instead of some interactions. Users could also input the known regulation to get the specific gene from database.
About our database, it is a pity that there is still not have an integral database containing such giant gene regulatory network. So in our software, we use some specific gene sequence segments to create a network. In fact, all genes there is virtual gene. For future development, we also left a file input entrance from which you could input real GRN. What’s more, gFinder is written as a website and it will be really convenient for using. The source code of gFinder is written in C++ language. All source code has been push up to our github.
gRNA: gene regulatory network analysts
Introduction
This little app is a gaming program for children who are interested in network analysis. Through this game they can cultivate the interest of biology and have a visual image of complex regulatory network. The calculation module is as same as the modeling of GRN in our major software “gNAP”. To make the app more interesting, we reduced the difficulty of analysis and investigate the analytical thinking ability of complex network regulation.
Tutorial
• Press ‘start’ to begin the game,
• After you enter the game interface, you can press the gene (those colorful circles) with right button to find out how other gene change if you remove the gene you choose.
• Then you should judge the relationship among the genes. There are two kinds of relationships, suppression and promotion. Attention, not all genes have relationship with other genes, and every two genes can only have one relationship. For example, gene1 suppresses gene2, then they can’t have other relationship such as gene1 promotes gene2 or gene2 suppresses gene1 etc.
• When you have already judged all genes, you can make you own regulatory network. Press the suppression button and the you can draw a red arrow between two genes. If gene1 points to gene2, it means gene1 suppresses gene2. In the similar way, you can draw green arrows with promotion button.
• If you what to undo the last operation, press the cancel button.
• When you have finished you operation, press finish button.
• The bar on the left is control by time and the quality of your job. When this bar disappears, the game is over.
• If you press the finish button, the answer button and next button will available. Press the answer button to check the answer (the answer may not be unique, so even if your answer is different with the answer that computer shows you, you may also get a high score).Press the next button to next level.
• In the next level, you can see how much score you have got in forward level.
• If you want to quit game, press back button in the right-up corner.
• There are 10 levels waiting for you! Good luck!
