-
+
-
+
-
+
-
+
-
+
-
+ 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 etc. 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 convenient. We provide both site search and off-site search to provide a 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 an editor that provides a number of practical tools such as drawing, tabulation, writing articles by dragging steps or protocols to improve efficiency. So it can replace the original Pages or Microsoft Office for its convenience.
-As we all know, a too programmer-style search engine is very unfriendly to synthetic biologists, so we redesigned functions of search engines. Researchers can easily find reports written by others after inputting some keywords. They could also search information in some databases and websites directly through 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.
-To be improved（暂缺）
-The interface design of the editor is not yet fully finalized. We also need to further refine the design and implementation based on the features we want to implement. At the same time, we will add and debug more new features. The communication platform we will build will also begin testing.
-Video(暂缺)
-Model（暂缺）
-Implementation
-Server Part
-The server of Bioeditor is written in Python 3.6, which is a flexible and cross-platform language and can reduce the learning costs we develop. Django allows fast prototyping and large-scale deployment, that's why we choose Django to be the basic framework.
-About the Bricks Data(暂缺)
-About Data Organizing
-The initial data will be imported into a separate database. Bioeditor will link to it by creating virtual tables using MySQL's database view technology. Using database views may lower the speed of querying, but it also has a lot of benefits. On one hand, it's easy to get started. Users don't need to care about the complex structure behind. On the other hand, it's easy for beginners, users who use views can only access the result set they are allowed to query.
-About search engine
-We followed last year's filtering of initial data to reduce the impact of unwanted bricks on search efficiency.We used natural language processing during the search process. After the language model is established, the extraction of text keywords is realized by processing such as statistical features such as TF and IDF. So that our search results are more in line with the needs of the user.
-At the same time, we have made the search conditions more diversified. Users can find the bricks they need more conveniently under more query conditions.
-We will recalculate the ranking weights at regular intervals. The reason for not evaluating them in real time is that the task may update the whole table and become time-consuming.
-Frontend Part
-In most templating systems, any changes that the user makes to the view are not reflected in the model. This means that the developer has to write code that constantly synchronize the view with the model and the model with the view.
-So we chose the Angular template, which works differently. Any changes to the view are immediately reflected in the model, and any changes in the model are propagated to the view. You can think of the view as simply an instant projection of your model.
-About UI
-We choose NG-ZORRA as our basic framework. NG-ZORRA is a UI framework developed by Alibaba Group based on Angular template.NG-ZORRA provides us with multiple elegant components and comfortable visual experience. In addition, we also added many wonderful customized components and styles to improve the user experience.
-About sortable
-When a researcher writes an academic report, he/she could click and drag the element of the experimental process from the list to a new location in the report. Obviously, it is convenient for them to write experimental reports.
-Improve(暂缺)
-NLP, deep learning
-Installation(暂缺)
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.
+From 5fd28a5209ed1130ca2f0b47d38cdd67850723aa Mon Sep 17 00:00:00 2001 From: heliyang <596136894@qq.com> Date: Thu, 18 Oct 2018 02:29:40 +0800 Subject: [PATCH 5/6] emmm --- .DS_Store | Bin 10244 -> 10244 bytes wiki_pages/.DS_Store | Bin 10244 -> 10244 bytes wiki_pages/Collaboration/Collaboration.html | 55 +++++------ wiki_pages/HumanPractice/Human_Practices.html | 87 +++++------------- .../ValidatedContribution.html | 4 +- 5 files changed, 44 insertions(+), 102 deletions(-) diff --git a/.DS_Store b/.DS_Store index 64caecce15771cd2c3013b733566e48b94ad6ad8..56b85daa86928dc5f022caef6bc2091f27940713 100644 GIT binary patch delta 234 zcmZn(XbIS`LQKTW!ca%S(9*0{N1@u>+(1Xc)Wmf19
Collaborations
-SJTU
- We have always maintained a good relationship with SJTU. We met at Taiwan and shared our thoughts about - the development of Biohub with them. They think highly of the feature of experiment record.
- "Your experiment recording provides a simple and quick method for routine experiment. It could save a - lot of time for us experimenters. They create the template of the experiment process which could record - each experiment clearly and show the experiment to others easily. It is very convenient to sharing the - ideas of experiment and communicate with each other. However, there are also some things which need to - be improved. Some experiments may do two or more things in the same time, for example, when - experimenters centrifuge something and they need to operate supernatant and precipitate separately so - that it may be better to improve the function at these situations. Also, you could add visualization - function in the editor which makes the showing process more clearly."
- We really appreciate their suggestions and now we are doing our best to improve our project.
- ++
SJTU-Software
+We have always maintained a good relationship with SJTU. We met at Taiwan and shared our thoughts about the development of Biohub with them. They think highly of the feature of experiment record.
+"Your experiment recording provides a simple and quick method for routine experiment. It could save a lot of time for us experimenters. They create the template of the experiment process which could record each experiment clearly and show the experiment to others easily. It is very convenient to sharing the ideas of experiment and communicate with each other. However, there are also some things which need to be improved. Some experiments may do two or more things in the same time, for example, when experimenters centrifuge something and they need to operate supernatant and precipitate separately so that it may be better to improve the function at these situations. Also, you could add visualization function in the editor which makes the showing process more clearly."
+We really appreciate their suggestions and now we are doing our best to improve our project.
+
UESTC
- We invited USETC to experience Biohub and they gave us useful feedback. "Biohub’s UI is awesome and has - a sense of science and technology. Also, Biohub can respond fast and smoothly. However, there are also - some places need to be improved. For example, there is no introduction to the function of Biohub at its - homepage. Besides, it would be better to add the user guide to editor which could be very important for - green hands."
- We have learned a lot from their feedback and now we are improving our function and making our project - better.
- +We invited UESTC to experience Biohub and they gave us useful feedback. "Biohub’s UI is awesome and has a sense of science and technology. Also, Biohub can respond fast and smoothly. However, there are also some places need to be improved. For example, there is no introduction to the function of Biohub at its homepage. Besides, it would be better to add the user guide to editor which could be very important for green hands."
+We have got a lot from their feedback and now we have improved our function and made our project better.
+
USTC
- We had communicated with Team USTC frequently and realized that writing the experiment reports may be a - difficult and duplicated thing. We got the inspiration from them and decided to develop our project now. - During the process of developing, they helped us to build a professional and easy-to-use editor and a - powerful search engine to help experimenters work effectively. They provide the knowledge we need and - experience the functions and help us improving our project.
We had communicated with Team USTC frequently and realized that writing the experiment reports may be a difficult and duplicated thing. We got the inspiration from them and decided to develop our project now. During the process of developing, they helped us to build a professional and easy-to-use editor and a powerful search engine to help experimenters work effectively. They provide the knowledge we need and experience the functions and help us improving our project.
+
