Difference between revisions of "Team:USTC-Software/Project"
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| − | <div class="ar2 | + | <div class="row ar2"> |
| − | + | <div class="column ar0 show-for-large large-3"> | |
| − | + | <div id="navigation-bar"> | |
| − | + | <ul class="menu vertical" data-magellan> | |
| − | + | <li> | |
| − | + | <a href="#Overview">Overview</a> | |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="#Module_Pano">Pano</a> | |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="#Module_Pathway_finder">Pathway_finder</a> | |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="#Module_Forum">Forum</a> | |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="#Module_Simulation">Simulation</a> | |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="#Module_BLAST">BLAST</a> | |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="#Module_ABACUS">ABACUS</a> | |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="#Module_Biobrick_manager">Biobrick_manager</a> | |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="#Plugins_and_Dockers">Plugins & Dockers</a> | |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="#Outlook">Outlook</a> | |
| − | + | </li> | |
| − | + | </ul> | |
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</div> | </div> | ||
</div> | </div> | ||
| − | <div class=" | + | <div class="column ar1 small-12 large-9"> |
| − | + | <div class="row ar0" id="Overview" data-magellan-target="Overview"> | |
| − | + | <hr /> | |
| − | + | <div class="column small-12 large-12 ar0 textcontainer"> | |
| − | < | + | <h1><a href="#Overview">Overview</a></h1> |
| − | + | </div> | |
| − | + | <div class="column small-12 large-6 large-offset-3 end ar1 imgcontainer"> | |
| − | + | <img src="https://static.igem.org/mediawiki/2016/b/bc/T--USTC-Software--project00.png" /> | |
| − | + | </div> | |
| − | + | <div class="column small-12 large-12 ar2 textcontainer"> | |
| + | <p> | ||
| + | Welcome to Biohub! This is a open and fantastic platform with practical functions for synthetic biologists. For scientists whose goal is to make discoveries in biology, steps using bioinformatics can be seen as the most basic but rather troublesome part. To solve this, our team created Biohub. | ||
| + | </p> | ||
| + | <p> | ||
| + | Biohub is a platform with several plug-ins, which means that users can not only employ the functions we provide, but also develop new and useful ones which can meet their special needs, without caring for servers and network transmission.Others include Pathway_finder, which means find the correlation among genes, Pano, meaning designing genetic circuits like an artist, Simulation, which can imitate real experimental circumstances, and other splendid functions. | ||
| + | </p> | ||
| + | </div> | ||
</div> | </div> | ||
| − | + | ||
| − | + | <div class="row ar1" id="Module_Pano" data-magellan-target="Module_Pano"> | |
| − | + | <hr /> | |
| − | + | <div class="column small-12 large-12 ar0 textcontainer"> | |
| − | + | <h1><a href="#Module_Pano">Module:Pano</a></h1> | |
| − | + | <p> | |
| − | + | Pano is a visualized editing interface which is designed to arrange the relationship between genes and to find paths between genes and simulate related substances according to known data. | |
| − | + | </p> | |
| − | + | <p> | |
| − | + | The relationships of genes are represented by graphs, which include nodes and edges. Each node represents a gene while each edge represents a relationship. Users shall build up a graph in order to input a relationship network among genes. Users will be capable to process the network further such as operating a simulation and so on. | |
| − | + | </p> | |
| − | + | </div> | |
</div> | </div> | ||
| − | + | ||
| − | + | <div class="row ar2" id="Module_Pathway_finder" data-magellan-target="Module_Pathway_finder"> | |
| − | + | <hr /> | |
| − | + | <div class="column small-12 large-12 ar0 textcontainer"> | |
| − | + | <h1><a href="#Module_Pathway_finder">Module:Pathway_finder</a></h1> | |
| − | + | <p> | |
| − | + | Pathway_finder is one of the most powerful plug-ins of Biohub. In traditional circumstances, searching for the relationships among components in the genetic circuit can be rather arduous, so users must read plenty of papers and inquire several databases. To rescue biologists from this, Pathway_finder is born now. Select any two components in genetic circuit, and by searching the database of gene routes in the server we can rapidly know whether they have strong relationship, and whether the feature is of interest. | |
| − | + | </p> | |
| − | + | <p> | |
| − | + | Pathway_finder combines metabolic network databases, cell signaling pathway databases and gene interaction databases, and the path between components means produce, combine, influence activation, promote degradation or others. | |
| − | + | </p> | |
| − | + | </div> | |
</div> | </div> | ||
| − | + | ||
| − | + | <div class="row ar3" id="Module_Forum" data-magellan-target="Module_Forum"> | |
| − | + | <hr /> | |
| − | + | <div class="column small-12 large-12 ar0 textcontainer"> | |
| − | + | <h1><a href="#Module_Forum">Module:Forum</a></h1> | |
| − | + | <p> | |
| − | + | In order to make communication in Biohub easier, we designed the 'Forum' feature to provide users an area to communicate, view others' projects and write comments on them. They are also able to share different ideas and generate new thoughts. | |
| − | + | </p> | |
| − | + | <p> | |
| − | + | In Forum, users can write, edit and remove his comments freely just like operating on any other forums. They will harvest enlightenment as well as fun. | |
| − | + | </p> | |
| − | </ | + | </div> |
</div> | </div> | ||
| − | + | ||
| − | + | <div class="row ar4" id="Module_Simulation" data-magellan-target="Module_Simulation"> | |
| − | + | <hr /> | |
| − | + | <div class="column small-12 large-12 ar0 textcontainer"> | |
| − | + | <h1><a href="#Module_Simulation">Module:Simulation</a></h1> | |
| − | + | <p> | |
| − | + | After you have run the module 'Pathway_finder', you may get some nodes. Here you can use this module to simulate the concentration of the substances involved in this reaction. | |
| − | + | </p> | |
| − | + | <p> | |
| − | + | Simulation is a simulator designed to solve the concentration function with respect to time based on the differential equations given by the user. After the user has submitted control functions, this module will upload relative data to a high performance server, which will be able to return results in minutes or hours, based on the quantity of control functions and the width of time domain. The concentration of all nodes will be displayed visualized, meanwhile a proper notice will pop up if an instability is detected in order to warn the user to be cautious about the result after the critical point. | |
| − | + | </p> | |
| − | + | </div> | |
</div> | </div> | ||
| − | + | ||
| − | + | <div class="row ar5" id="Module_BLAST" data-magellan-target="Module_BLAST"> | |
| − | + | <hr /> | |
| − | + | <div class="column small-12 large-12 ar0 textcontainer"> | |
| − | + | <h1><a href="#Module_BLAST">Module:BLAST</a></h1> | |
| − | + | <p> | |
| − | + | Biohub provide users with convenient one-key BLAST. In graphical interface,the user select the components which he or she wants to align the sequence, and by just pressing one build-in button, Biohub will read the sequence and align it with sequences in online databases using BLAST interface provided by NCBI, and show the outcome simply and elegantly to the users. | |
| − | + | </p> | |
| − | + | <p> | |
| + | Tips: BLAST is available only online. When using NCBI BLAST API, any user should obey their usage guidelines. | ||
| + | </p> | ||
| + | </div> | ||
</div> | </div> | ||
| − | + | ||
| − | + | <div class="row ar6" id="Module_ABACUS" data-magellan-target="Module_ABACUS"> | |
| − | + | <hr /> | |
| − | + | <div class="column small-12 large-12 ar0 textcontainer"> | |
| − | + | <h1><a href="#Module_ABACUS">Module:ABACUS</a></h1> | |
| − | + | <p> | |
| − | + | A plugin design to design amino acid sequence from the .pdb file provided by user. The uploaded .pdb file will be evaluated by several progress, with support of simulated annealing algorithm, then the server will generate a .zip file containing several .pdb files and .fasta files for user to download. It’s recommended to run this plugin on a high performance server, because the plugin will invoke computationally intensive programs. So please be patient while this plugin is running, it may take several hours to get results on a high performance server. You can press get status button to check if the calculation is done. | |
| − | + | </p> | |
| − | + | </div> | |
</div> | </div> | ||
| − | + | ||
| − | + | <div class="row ar7" id="Module_Biobrick_manager" data-magellan-target="Module_Biobrick_manager"> | |
| − | + | <hr /> | |
| − | + | <div class="column small-12 large-12 ar0 textcontainer"> | |
| − | + | <h1><a href="#Module_Biobrick_manager">Module:Biobrick_manager</a></h1> | |
| − | + | <p> | |
| − | + | The iGEM Registry has over 20,000 documented parts organized by type, chassis, function and more. Recognizing that this is a great asset in the field of synthetic biology, we believe that it is necessary to let users explore Biobricks on BioHub. As a result, this function was implemented as an official plugin for BioHub. Users can search for Biobricks they desire and easily browse all the information about the searching results. | |
| − | + | </p> | |
| − | + | </div> | |
| − | + | ||
| − | + | ||
| − | </ | + | |
</div> | </div> | ||
| − | + | ||
| − | + | <div class="row ar8" id="Plugins_and_Dockers" data-magellan-target="Plugins_and_Dockers"> | |
| − | + | <hr /> | |
| − | + | <div class="column small-12 large-12 ar0 textcontainer"> | |
| − | + | <h1><a href="#Plugins_and_Dockers">Plugins and Dockers</a></h1> | |
| − | + | <p> | |
| − | + | The great thing about BioHub is that we have designed a unified, extensible plugin platform, which not only have the powerful tools provided by the development team, but also is easy to learn and use by other developers to provide better features. Each specific feature of BioHub is provided by a plugin, whose developer do not need to care about details such as server and network requests. Plugins can just focus on performing their own tasks and manage user's design results. With BioHub's plugin platform, once any of the latest tools or algorithms in the field of synthetic biology got programmed, developers can easily transform it into a BioHub plugin by studying the sample files we provide, making it a new blade of the powerful Swiss Saber - BioHub. | |
| − | + | </p> | |
| − | + | <p> | |
| + | In order to make BioHub easy to install, configure and use, we carefully selected the program architecture and package format. The use of server - client architecture makes it possible for labs to run the server on a high-performance computer, and easily access it from any device. Also, we use Docker to package the program, which makes the server very easy to start, update and shutdown. Normally, users may never encounter any compatibility issues. What's more, we also released a virtual machine image file for non-Linux platforms. | ||
| + | </p> | ||
| + | </div> | ||
| + | </div> | ||
| + | |||
| + | <div class="row ar9" id="Outlook" data-magellan-target="Outlook"> | ||
| + | <hr /> | ||
| + | <div class="column small-12 large-12 ar0 textcontainer"> | ||
| + | <h1><a href="#Outlook">Outlook</a></h1> | ||
| + | <p> | ||
| + | Since our project is a software designed for synthetic biologists to simplify their work as well as give them effective auxiliary, there are undoubtedly dozens of chances of this software to be improved, just like the previous work 'Biopano'. In the future, we will upgrade our program in order to implement more functions as well as enhance the current ones. For example, we may enable the 'Pathway_finder' module to find the strength of the connection between genes, which our software cannot do this at present. Meanwhile, we will introduce our software and its background to our juniors to attract them to join us and to participate in the following iGEM competitions. | ||
| + | </p> | ||
| + | </div> | ||
</div> | </div> | ||
</div> | </div> | ||
Revision as of 21:40, 17 October 2016
Welcome to Biohub! This is a open and fantastic platform with practical functions for synthetic biologists. For scientists whose goal is to make discoveries in biology, steps using bioinformatics can be seen as the most basic but rather troublesome part. To solve this, our team created Biohub.
Biohub is a platform with several plug-ins, which means that users can not only employ the functions we provide, but also develop new and useful ones which can meet their special needs, without caring for servers and network transmission.Others include Pathway_finder, which means find the correlation among genes, Pano, meaning designing genetic circuits like an artist, Simulation, which can imitate real experimental circumstances, and other splendid functions.
Module:Pano
Pano is a visualized editing interface which is designed to arrange the relationship between genes and to find paths between genes and simulate related substances according to known data.
The relationships of genes are represented by graphs, which include nodes and edges. Each node represents a gene while each edge represents a relationship. Users shall build up a graph in order to input a relationship network among genes. Users will be capable to process the network further such as operating a simulation and so on.
Module:Pathway_finder
Pathway_finder is one of the most powerful plug-ins of Biohub. In traditional circumstances, searching for the relationships among components in the genetic circuit can be rather arduous, so users must read plenty of papers and inquire several databases. To rescue biologists from this, Pathway_finder is born now. Select any two components in genetic circuit, and by searching the database of gene routes in the server we can rapidly know whether they have strong relationship, and whether the feature is of interest.
Pathway_finder combines metabolic network databases, cell signaling pathway databases and gene interaction databases, and the path between components means produce, combine, influence activation, promote degradation or others.
Module:Forum
In order to make communication in Biohub easier, we designed the 'Forum' feature to provide users an area to communicate, view others' projects and write comments on them. They are also able to share different ideas and generate new thoughts.
In Forum, users can write, edit and remove his comments freely just like operating on any other forums. They will harvest enlightenment as well as fun.
Module:Simulation
After you have run the module 'Pathway_finder', you may get some nodes. Here you can use this module to simulate the concentration of the substances involved in this reaction.
Simulation is a simulator designed to solve the concentration function with respect to time based on the differential equations given by the user. After the user has submitted control functions, this module will upload relative data to a high performance server, which will be able to return results in minutes or hours, based on the quantity of control functions and the width of time domain. The concentration of all nodes will be displayed visualized, meanwhile a proper notice will pop up if an instability is detected in order to warn the user to be cautious about the result after the critical point.
Module:BLAST
Biohub provide users with convenient one-key BLAST. In graphical interface,the user select the components which he or she wants to align the sequence, and by just pressing one build-in button, Biohub will read the sequence and align it with sequences in online databases using BLAST interface provided by NCBI, and show the outcome simply and elegantly to the users.
Tips: BLAST is available only online. When using NCBI BLAST API, any user should obey their usage guidelines.
Module:ABACUS
A plugin design to design amino acid sequence from the .pdb file provided by user. The uploaded .pdb file will be evaluated by several progress, with support of simulated annealing algorithm, then the server will generate a .zip file containing several .pdb files and .fasta files for user to download. It’s recommended to run this plugin on a high performance server, because the plugin will invoke computationally intensive programs. So please be patient while this plugin is running, it may take several hours to get results on a high performance server. You can press get status button to check if the calculation is done.
Module:Biobrick_manager
The iGEM Registry has over 20,000 documented parts organized by type, chassis, function and more. Recognizing that this is a great asset in the field of synthetic biology, we believe that it is necessary to let users explore Biobricks on BioHub. As a result, this function was implemented as an official plugin for BioHub. Users can search for Biobricks they desire and easily browse all the information about the searching results.
Plugins and Dockers
The great thing about BioHub is that we have designed a unified, extensible plugin platform, which not only have the powerful tools provided by the development team, but also is easy to learn and use by other developers to provide better features. Each specific feature of BioHub is provided by a plugin, whose developer do not need to care about details such as server and network requests. Plugins can just focus on performing their own tasks and manage user's design results. With BioHub's plugin platform, once any of the latest tools or algorithms in the field of synthetic biology got programmed, developers can easily transform it into a BioHub plugin by studying the sample files we provide, making it a new blade of the powerful Swiss Saber - BioHub.
In order to make BioHub easy to install, configure and use, we carefully selected the program architecture and package format. The use of server - client architecture makes it possible for labs to run the server on a high-performance computer, and easily access it from any device. Also, we use Docker to package the program, which makes the server very easy to start, update and shutdown. Normally, users may never encounter any compatibility issues. What's more, we also released a virtual machine image file for non-Linux platforms.
Outlook
Since our project is a software designed for synthetic biologists to simplify their work as well as give them effective auxiliary, there are undoubtedly dozens of chances of this software to be improved, just like the previous work 'Biopano'. In the future, we will upgrade our program in order to implement more functions as well as enhance the current ones. For example, we may enable the 'Pathway_finder' module to find the strength of the connection between genes, which our software cannot do this at present. Meanwhile, we will introduce our software and its background to our juniors to attract them to join us and to participate in the following iGEM competitions.
