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Revision as of 16:15, 6 October 2019

Tongji Software | Pathlab

PROJECT
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Education & Engagement







TONGJI iGEM PUBLIC NUMBER

We created the tongji iGEM public number and regularly posted relevant pushes on iGEM in the public number.










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THE FIRST PUSH: PROGRAMMER (BALD) iGEMER IS ONLINE



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Main content: Introduce igem from the perspective of software, including the teams participating in the calendar year, the main content of the project, etc., so that readers have a general understanding of igem and software.

THE SECOND PUSH: 6th CCIC IN SHENZHEN

second push 1 second push 2

Main content: It mainly introduces the tongji software team's participation in ccic in Shenzhen, and the harvest of our team. In the process of participating in ccic, we not only listened to the presentation of many teams, but also learned from the experience of other teams. We also listened to many lectures by biological experts and valuable suggestions from the judges on our projects. This was before the official igem competition. Very good exchange opportunities in China.

THE THIRD PUSH: SUBVERSIVE DISCIPLINE - SYNTHETIC BIOLOGY

Original intention: Since our project is closely related to synthetic biology, we hope that our readers will have a certain understanding of synthetic biology before we formally introduce our project, so that we can better understand pathlab.
Main content: As an emerging discipline in the field of biology in the 21st century, synthetic biology is the product of multidisciplinary intersections of molecular and cellular biology, evolutionary systematics, biochemistry, informatics, mathematics, computer and engineering. So far, it has made remarkable achievements in many fields such as bioenergy, biomaterials, medical technology and exploring the laws of life. In 2014, the US Department of Defense listed it as one of the six major disruptive technologies for priority development in the 21st century; in the third technical forecast completed in 2014, China listed synthetic biotechnology as one of the top ten breakthrough technologies. . Moreover, in the “13th Five-Year Plan” for scientific and technological innovation strategic planning, synthetic biotechnology has been listed as a strategic forward-looking key development direction.

THE FOURTH PUSH: EFFICIENT PATH SEARCHER - ALPHA ANT

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Original intention: Our project pathlab was inspired by the previous tongji software project alpha ant. Before introducing pathlab, we wanted the reader to first understand the alpha ant and related path search knowledge.
Main content: Alpha Ant is essentially a computational tool for pathway design and reconstruction. Allowing users to turn on Alpha Ant's effective and powerful path design guide in the face of the vast passages will clarify their choice. Alpha Ant represents an efficient and convenient path building tool. Alpha means "origination." In fact, Alpha Ant is the first software to be equipped with an integrated ranking standard. Alpha Ant means that it can find the most effective metabolic pathway connecting two molecules, just like the biological wisdom of an ant colony. Once food is discovered by scouts, it can be quickly organized to find the most effective source of food. So use ants to represent efficient signal detectors and path searchers.

THE FIFTH PUSH: PATH SEARCH 2.0 - INTEGRATED SERVICE PLATFORM PATHLAB

Main content: Pathlab is a comprehensive platform for channel design, which is mainly used for brainstorming in the early stage of determining the topic. When the user knows the product he wants or the substrate he can use, Path search, enzyme selection, and component search can be performed through Pathlab. In addition to the functions of these backbones, we also have functions such as word cloud, data update, and data upload to assist users in their use.
&nbsp&nbsp&nbsp&nbspCharming points:

1. Optimize on the basis of dfs algorithm, adopt greedy (greedy) algorithm, and make a selection in each step, which is optimal.

2. codon optimization, improve the efficiency of enzyme expression in the plasmid

3. modular design, each part can be split and used separately

4. depth information, to provide users with newer research progress of each enzyme