Team:USTC-Software/Project.html
Project
Description
Overview
What is BioHub 3.0?
BioHub 3.0 is a synthetic biology community, integrated Intelligent Search Engine and the online report editor. It brings you a new way to edit your reports and search whatever you need only in one step.
The Editor
We established a standardized description of experimental steps. The editor can help you complete high-quality lab reports quickly just by choosing steps and filling in the blanks. Custom steps and protocols are also supported. And in our report editor, biologists could use a number of practical tools such as drawing, tabulation and writing articles, which improve the efficiency of completing the experiment report.
Intelligent Search Engine
We developed our search engine on the base of 2017's project. Our engine has a better command of language recognition. It supports semantic recognition, like "reports today", "reports by ana", "reports this year" and edc.. Meanwhile, we listened to the opinions of the judges. This year we added advanced search and we can now sort the results by time, labels, etc.. It is easier for synthetic biologists to find what they need without many input's instructions. Additionally, we have added many useful databases and academic websites to our search engine, so biologists could search information more quickly.
The community
In this community, bio workers can record their experimental process and release those reports. Meanwhile, they could also read and comment on other scholar's reports. In this way, we make the academic discussion more convinent. We provide both site search and off-site search to provide better user experience.
Motivation
After consulting with several synthetic biology workers, we found that they would inevitably suffer from the need to spend a lot of time to complete the experimental report during the experiment. Therefore, there is an urgent need for a editor that provides a number of practical tools such as drawing, tabulation, writing articles by dragging steps or protocols to improve the efficiency. So it can replace the original Pages or Microsoft Office for its convenience.
As we all know, too programmer-style search engine is very unfriendly to synthetic biologists, so we reidesigned functions of search engines. Researchers can easily find reports written by others after inputting some key words. They could also search information in some databases and websites directly though this engine.
For most synthetic biology workers, it is difficult for them to conduct effective communication on experimental content, so we established a synthetic biology community based on search engine and report editor. In this community, bio workers can use this to record their experimental process and comment on other scholar's reports, thereby reducing the blindness of the research.
In the future
As the advanced architecture and plugin system designed in our Biohub 3.0. It's pretty easy to improve our existed functions and provide new function by activating new plugins. Here are what we want to do in the future.
Improvements
It is super easy to accomplish your report rapidly by useing our editor. But we can make it better.
- We believe it is possible to share your
protocolsandstepswith anyone freely. - It is great significant to make it more efficient to build a new step or protocol.
- Our editor takes too much memories and will be slow down when the report goes long.
The Search Engine at the moment supports searching by nature language thanks to the new nature language processing technology. The intelligence can be improved in understanding what users want and reacting more smartly. On the other hand, we can integrate more databases which are most used by biologists.
The society is still growing. That is why chatting and communication could be considered as an important facility in our society.
New features
Several Interface has been implemented to make it easy to improve Biohub in the future without refactoring core codes. New codes can be considered as a module or plugin.
In the next generation of Biohub, We want to strengthen our society and build a society like Quora where biologists can post their ideas, ask questions, sale their e-books, have a free chat or find partners who share interest in a certain area.
If there is a matching hardware port, it could complete the experiment automatically according to the given steps and protocols. We could match the steps or protocols to the manipulator's operating instructions accurately. For this, we hope BioHub can help achieve experiment automation.
Backend Part
Technology
Django
Django is a free and open-source web framework, written in Python, which follows the model-view-template (MVT) architectural pattern.
Django makes it easier to build better Web apps more quickly and with less code, it emphasizes reusability and "pluggability" of components, less code, low coupling, rapid development, and the principle of don't repeat yourself. It also provides an optional administrative create, read, update and delete interface, which is generated dynamically through introspection and configured via admin models.
Python 3
Python is an interpreted high-level programming language for general-purpose programming. Python has a design philosophy that emphasizes code readability, notably using significant whitespace. It provides constructs that enable clear programming on both small and large scales.
Python features a dynamic type system and automatic memory management. It supports multiple programming paradigms, including object-oriented, imperative, functional and procedural, and has a large and comprehensive standard library. It is cross-platform and it interpreters are available for many operating systems.
Nginx
Nginx is a web server which can also be used as a reverse proxy, load balancer, mail proxy, and HTTP cache. Nginx can be deployed to serve dynamic HTTP content on the network using FastCGI, SCGI handlers for scripts, WSGI application servers or Phusion Passenger modules, and it can serve as a software load balancer.
Nginx uses an asynchronous event-driven approach, rather than threads, to handle requests. Nginx's modular event-driven architecture can provide more predictable performance under high loads.
Standford CoreNLP
CoreNLP is a program of natural language processing, it provides a set of human language technology tools. It can give the base forms of words, their parts of speech, whether they are names of companies, people, etc.
It makes it very easy to apply a bunch of linguistic analysis tools to a piece of text. A tool pipeline can be run on a piece of plain text with just two lines of code. CoreNLP is designed to be highly flexible and extensible. With a single option, you can change which tools should be enabled and disabled.
Django-rest-framework
Django REST framework is a powerful and flexible toolkit for building Web APIs.
REST framework use packages for OAuth1a and OAuth2 in Authentication policies, its serialization that supports both ORM and non-ORM data sources. It customizable all the way down, and it has extensive documentation and great community support.