Team:USTC-Software
USTC-Software
Welcome to USTC-Software iGEM 2017!
Project Description
Welcome to BioHub 2.0! This is an 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 the most basic but rather troublesome part. To solve this, our team created BioHub in 2016, and we improved it this year. BioHub 2.0 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 iGemer forum, in which teams participating in the competition can communicate with each other, abacus 2.0, which could design amino acid sequence from the .pdb file provided by user, image processing, which can analyze the experimental results by the RGB of image, and other splendid functions. The following is the introduction to some project module:
1. 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.
2. 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.
3. 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.
4. Image processing
In order to help wet students to complete the image processing work quickly, we created the image processing module. In this module, the user can get a series of information, including chemical element, which is converted from the experimental image.
5. Plugins
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.
