Team:SYSU-Software

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 ProjectSoftware ProjctModels Models&AlgorithmTutorialGuidance book and videosTeamInstructor and membersNotebookSchedule of this projectTipsHuman practice safety  creative ideas best solutions OverviewGenomeBrowserBiobrickRiboswitchMetaNewtworkSimulatorG-Circle     Synthetic Biology, depending on interdisplinary knowledge and experience , cooperate wet and dry experiments to create artificial biological systems . Our team has developed a novel software system, BiArkit, to facilitate the design and engineering of specially functional systems. For visualization of genomic data and expression level of functional genes, we develop GenomeBrowser and G-Circle which has been added to the Clotho frame for researchers. Besides, Biobrick is localized and transformed into searching kit for users to get comprehensive information conveniently. Further, Riboswitch and SiRNA are designed to compute out potential regulatory parts for engineering systems. For processing data from system level, MetaNetwork can illustrate information of various biological pathways on the graphical and user-friendly interface. And Simulator is intended for modificating and simulating genome-scale metabolic models, which involves many kinds of analysis to predict possible results of conditional changes in experiments. read more
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      With this Genome Browser, users are able to search Biobricks, plasmids and genomes of model microorganisms; at the same time, gene annotations and information of GenBank are presented. The primary protein sequence is also presented according to the DNA sequences. Aside from searching sequences, users can also input or modify the sequences, insert annotation and build target plasmids they need.
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<title>Team:SYSU-Software</title>
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read more      This is the section for parts information. It can facilitate researchers to search features and functions of Biobricks documented in the Registry of Standard Biological Parts. All of the relevant operations can be completed without connecting with the Internet.
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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read more       This is the section for generating parts information. It can assist researchers to design the sequences and structures of potential riboswitches according to their inputs and choices of aptamers. Both of the up-regulation and down-regulation riboswiches can be provided by this kit.
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<meta http-equiv="Content-Style-Type" content="text/css" />
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read more       This is the section for generating parts information. It can design another regulator in engineering biological systems – siRNA. According to the input sequences, it can figure out the potential siRNA automatically.
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read more       This is the section for system information. Given the friendly interface, researchers can explore and acquire their interested gene’s relevant pathways and networks in one map. Users can even drag every graphic element in the maps to check the information conveniently and effectively.
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<script src="https://2012.igem.org/Team:SYSU-Software/js/jquery-1.4.2.min.js?action=raw&ctype=text/javascript" type="text/javascript"></script>
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read more       This is the section for generating system information. Based on the reconstruction of genome-scale models, researcher can use this kit to edit the existent models according to their needs. Then, they can choose different combination of analysis to predict effect from a intended loss-of –function mutation, find necessary and basic genes maintaining the whole system, predict phenotypic behavior under the given environmental conditions and interpret the coupled reaction activities.
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<script src="https://2012.igem.org/Team:SYSU-Software/js/jquery.faded.js?action=raw&ctype=text/javascript" type="text/javascript"></script>
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read more       This is the section for sequence information. It can illustrate the given genome and the expression level of genes within it under different environment in one graph. In addition, we have developed it as one app and integrated it into Clotho.
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Models <span>Models&Algorithm</span></a></li>
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            <li class="first"><a href="#tab0">Overview</a></li>
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              <li ><a href="#tab1">GenomeBrowser</a></li>
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              <li><a href="#tab2">Biobrick</a></li>
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              <li><a href="#tab3">Riboswitch</a></li>
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              <li><a href="#tab6">Simulator</a></li>
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                <p><img class="img-indent" src="https://static.igem.org/mediawiki/igem.org/7/7c/Cvvxx.png" alt="" width="300px" height="230px" style="float: left ;"/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Synthetic Biology, depending on interdisplinary knowledge and experience , cooperate wet and dry experiments to create artificial biological systems . Our team has developed a novel software system,  
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<a href="https://2012.igem.org/Team:SYSU-Software/Project">BiArkit</a>, to facilitate the design and engineering of specially functional systems. For visualization of genomic data and expression level of functional genes, we develop  
+
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r2">GenomeBrowser</a> and  
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r8">G-Circle</a> which has been added to the Clotho frame for researchers. Besides,  
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r3">Biobrick</a> is localized and transformed into searching kit for users to get comprehensive information conveniently. Further,  
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r4">Riboswitch</a> and  
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r5">SiRNA</a> are designed to compute out potential regulatory parts for engineering systems. For processing data from system level,
+
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r6">MetaNetwork</a> can illustrate information of various biological pathways on the graphical and user-friendly interface. And  
+
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<a href="https://2012.igem.org/Team:SYSU-Software/Project#r7">Simulator</a> is intended for modificating and simulating genome-scale metabolic models, which involves many kinds of analysis to predict possible results of conditional changes in experiments.
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<a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"  style="float: right ;""><b>read more</b></a></p>
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                <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; With this Genome Browser, users are able to search Biobricks, plasmids and genomes of model microorganisms; at the same time, gene annotations and information of GenBank are presented. The primary protein sequence is also presented according to the DNA sequences. Aside from searching sequences, users can also input or modify the sequences, insert annotation and build target plasmids they need.</p>
+
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                  <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
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                <div class="extra-wrap">
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                <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This is the section for parts information. It can facilitate researchers to search features and functions of Biobricks documented in the Registry of Standard Biological Parts. All of the relevant operations can be completed without connecting with the Internet.</p>                 
+
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                  <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
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                <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
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<span lang="EN-US">This is the section for generating parts  
+
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information. It can assist researchers to design the  
+
-
sequences and structures of potential riboswitches according  
+
-
to their inputs and choices of aptamers. Both of the  
+
-
up-regulation and down-regulation riboswiches can be  
+
-
provided by this kit.</span></p>
+
-
                                    <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
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                <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
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<span lang="EN-US">This is the section for generating parts  
+
-
information. It can design another regulator in engineering  
+
-
biological systems – siRNA. According to the input  
+
-
sequences, it can figure out the potential siRNA  
+
-
automatically.</span></p>
+
-
                                    <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
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                <div class="extra-wrap">
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                <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
+
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<span lang="EN-US">This is the section for system information. Given the friendly interface, researchers can explore and acquire their interested gene’s relevant pathways and networks in one map. Users can even drag every graphic element in the maps to check the information conveniently and effectively.</span></p>
+
-
                                    <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
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                <div class="extra-wrap">
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                <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
+
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<span lang="EN-US">This is the section for generating system  
+
-
information. Based on the reconstruction of genome-scale  
+
-
models, researcher can use this kit to edit the existent  
+
-
models according to their needs. Then, they can choose  
+
-
different combination of analysis to predict effect from a  
+
-
intended loss-of –function mutation, find necessary and  
+
-
basic genes maintaining the whole system, predict phenotypic  
+
-
behavior under the given environmental conditions and  
+
-
interpret the coupled reaction activities.</span></p>
+
-
                                    <div class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></div>
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              <p><span lang="zh-cn">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>
+
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<span lang="EN-US">This is the section for sequence information.  
+
-
It can illustrate the given genome and the expression level of  
+
-
genes within it under different environment in one graph. In  
+
-
addition, we have developed it as one app and integrated it into
+
-
<i>Clotho</i>.</span></p>
+
-
                <p class="wrapper"><a href="https://2012.igem.org/Team:SYSU-Software/Project" class="link1"><b>read more</b></a></p>
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Revision as of 18:58, 26 September 2012

Team:SYSU-Software  ProjectSoftware ProjctModels Models&AlgorithmTutorialGuidance book and videosTeamInstructor and membersNotebookSchedule of this projectTipsHuman practice safety creative ideas best solutions OverviewGenomeBrowserBiobrickRiboswitchMetaNewtworkSimulatorG-Circle Synthetic Biology, depending on interdisplinary knowledge and experience , cooperate wet and dry experiments to create artificial biological systems . Our team has developed a novel software system, BiArkit, to facilitate the design and engineering of specially functional systems. For visualization of genomic data and expression level of functional genes, we develop GenomeBrowser and G-Circle which has been added to the Clotho frame for researchers. Besides, Biobrick is localized and transformed into searching kit for users to get comprehensive information conveniently. Further, Riboswitch and SiRNA are designed to compute out potential regulatory parts for engineering systems. For processing data from system level, MetaNetwork can illustrate information of various biological pathways on the graphical and user-friendly interface. And Simulator is intended for modificating and simulating genome-scale metabolic models, which involves many kinds of analysis to predict possible results of conditional changes in experiments. read more 

      With this Genome Browser, users are able to search Biobricks, plasmids and genomes of model microorganisms; at the same time, gene annotations and information of GenBank are presented. The primary protein sequence is also presented according to the DNA sequences. Aside from searching sequences, users can also input or modify the sequences, insert annotation and build target plasmids they need.

read more      This is the section for parts information. It can facilitate researchers to search features and functions of Biobricks documented in the Registry of Standard Biological Parts. All of the relevant operations can be completed without connecting with the Internet. read more This is the section for generating parts information. It can assist researchers to design the sequences and structures of potential riboswitches according to their inputs and choices of aptamers. Both of the up-regulation and down-regulation riboswiches can be provided by this kit. read more This is the section for generating parts information. It can design another regulator in engineering biological systems – siRNA. According to the input sequences, it can figure out the potential siRNA automatically. read more This is the section for system information. Given the friendly interface, researchers can explore and acquire their interested gene’s relevant pathways and networks in one map. Users can even drag every graphic element in the maps to check the information conveniently and effectively. read more This is the section for generating system information. Based on the reconstruction of genome-scale models, researcher can use this kit to edit the existent models according to their needs. Then, they can choose different combination of analysis to predict effect from a intended loss-of –function mutation, find necessary and basic genes maintaining the whole system, predict phenotypic behavior under the given environmental conditions and interpret the coupled reaction activities. read more This is the section for sequence information. It can illustrate the given genome and the expression level of genes within it under different environment in one graph. In addition, we have developed it as one app and integrated it into Clotho. read more 

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