Team:USTC-Software/Project
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 Path_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
Gay!
Module:Path_finder
Path_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, Path_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.
Path_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
Gay!
Module:Simulation
Gay!
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 surpport 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.
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 studing 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 undoubtly 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 "Path_finder" module to find the strongness 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.
