Overview

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  • Introduction
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  • MoDeL
  • Algorithm
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• MoDeL
  • One-Minute Introduction
  • Features
  • Standardization
  • Future Work
• Demo
  • Overview of Demos
  • pLux-LuxR repression system
  • Toggle-Switch
  • Repressilator
• Notebook
• Human Practice
  • The C Project
  • Safety
• Team
  • Overview
  • Students
  • Instructors
  • Collaboration
  • Attribution & Contributions
  • Acknowledgments

One-Minute Introduction

You are about to begin an exciting journey of the main ideas in MoDeL. For each picture, start from the green flag, follow the arrows, and finally you will reach the destination! Read on from the first step or click one of the three steps!

Chain-Node Model -> Template Modeling -> Automatic Modeling Database Language

Chain-Node Model

Back Up

Template Modeling

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Automatic Modeling Database Language

Back Up

Read More on MoDeL Here! Read More on Our Project Here!

Features

• Home
• Project
  • Introduction
  • User Interface Design
  • MoDeL
  • Algorithm
  • Resources
• MoDeL
  • One-Minute Introduction
  • Features
  • Standardization
  • Future Work
• Demo
  • Overview of Demos
  • pLux-LuxR repression system
  • Toggle-Switch
  • Repressilator
• Notebook
• Human Practice
  • The C Project
  • Safety
• Team
  • Overview
  • Students
  • Instructors
  • Collaboration
  • Attribution & Contributions
  • Acknowledgments

Features

Chain-Node Model

Figure 1: Logo of Chain-Node Model

In most manual modeling, complex is treated as a whole entity in reactions. Plenty of synthetic biology automatic modeling software treats complex the same way. However, there is a big difference between manual and automatic modeling, that is: Model constructors always know which detail of complex needs to be ignored or preserved, but software does not. So in most software, detailed structure has to be specified by modelers, otherwise will be ignored. In most cases, this requires plenty of manual operations and thus making the software not so automatic. Knowing this, MoDeL chooses to preserve detailed structure in complex and present Chain-Node Model, which view complex as a construction of its parts throughout the modeling process. With chain and nodes, describing large biological complex with a great number of basic units and binding sites becomes possible. It also offers great flexibility in modeling. Detailed concepts are explained below.

Abstract Concept of Chain

When it comes to biobrick assembly, DNA of plasmid is often considered as an abstract straight line where biobricks can be placed on and connected together. It actually acts as the basic frame of biobrick assembly. Inspired by this, we present the abstract concept of chain, which also acts as the basic frame of part assembly. Chain is an abstract straight line where different parts can be placed on and connected together. Part is the basic unit of chain, and chain can have as many parts as possible.

To go beyond DNA, and to unify the data structure of Species, we extend the concept of chain in MoDeL to include all the parts we can describe, including RNA, protein, and even compartment, compound and substituent, etc. Parts of DNA, RNA and protein, are all originated from DNA, and they are considered as “Sequence”. Sequence can be connected to other parts of sequence on a chain. On the contrary, parts of compartment and compound are considered as “Non-sequence”. Parts of non-sequence cannot be connected to any other part on a chain, which means, they can only exist on a One-Part-Chain. Substituent is used as a substitution of any other part, so it can be either sequence or non-sequence.

It is important here to mention that the Sequence/Non-sequence division is only a rule guide the modeling. It is not a constraint to Chain-Node model. Actually, we choose to maximally preserve the flexibility and leave all the freedom of constructing a species to users. Users are allowed to construct ANY species they can using Chain-Node Model. For example, one can create a strange species with compartment, compound, and DNA parts on the same chain, which makes little sense in biology. So, it is really up to the users to decide how to use Chain-Node Model in modeling.

Abstract Concept of Node

Node is used to characterize binding structure in biological complex. Node is an abstract concept of binding site or site that can be bond. Links always exist between a binding site and the sites it binds together, indicating the relationship between them. We use trees to represent the binding structure in complex. The parent node represents the binding site, and the child node represents the bond sites. For example the binding structure of TetR dimer is considered as a TetR2 node with two TetR nodes as its children. There is one exception though, the ROOT node. ROOT node is used as the top node in a tree. It can only have one child and no parent. The function of ROOT is to indicate that its child is the last binding site in this tree, and it binds to nothing any more.

In the reactions of promoter repression and activation, the promoter is repressed or activated after binding with repressor or inducer. So its properties are changed, and it is not the original promoter any more. This is an example where binding changes the properties of node. Since we do not store all the possible property alterations within one part, the solution is to replace the old part with a new part that stores the correct properties.

Available nodes can be both a part on a chain or a node of binding site, which leaves a lot of possibilities in constructing complicated binding structure. Again, there are no restrictions, but parts of compartments are not suggested to appear in a binding structure.

The Basic Assumption

The basic assumption of Chain-Node Model is that a part ALWAYS carries its properties wherever it is placed in an instance of Chain-Node Model. This means no matter how complicated the complex is, you can always keep track of the location and properties of every single part. By letting complex inherits its parts’ properties, the assumption saves modelers from rewriting the structure and function of each new complex. However, we should address that the assumption is not suitable for all circumstances. For example, under this assumption, a fusion protein will carry the properties of the fused proteins, which is not true in many cases. A fusion protein may not remain its old properties and even have new properties that none of the original parts have. In this case, our suggestion is to define the fusion protein as a new part. So it is suggested that users choose different strategies of describing the same thing in Chain-Node Model base on different situations, instead of modeling everything in the same way.

Examples

With great power there must come great responsibility. In order to use the powerful Chain-Node Model correctly, please have a look at a few examples we presents.
Example of a species: E.coli cell In MoDeL, the cell of E.coli is described as a species with only one part of E.coli(see Figure 1). Since the concept of part has been extended greatly, living cells can be described in the same way other species. Compartment belongs to “Non-sequence”, so it is suggested that E.coli only exists as a one-part-species.
Figure 1: The Chain-Node Model of a E.coli cell
Example of a species: pLacI*:LacI4 and its tree structure of binding. Here is another example of template species with more complicated structure.(see Figure 2) In biology, LacI tetramer (or LacI4) can bind with promoter pLacI as a repressor. When bond with LacI4, pLacI is repressed and its transcription speed will decrease significantly. In order to express this alteration, as mentioned above, we use another part of pLacI* with decreased transcription speed instead of pLacI in the species.
The structure of binding sites is shown in figure (see Figure 3). The graph indicates that LacI monomers first bind together to form LacI dimer, then LacI dimers forms LacI tetramer, and finally LacI4 binds with pLacI* to form pLacI*:LacI4.
Figure 2: Species of pLacI*:LacI4	Figure 3: Tree structure of binding in pLacI*:LacI4

Modeling with Templates

Manual modeling of biological system is widely used in synthetic biology. However, it requires an overall understanding of the biological network and large amount of data, making it difficult even for professionals. Actually, the data provided manually are redundant because different reactions may occur with a same mechanism. Based on this idea, we introduce the concept of Template, which is the minimal data set for describing biological reaction networks, as a feasible way to implement automatic modeling. The term “automatic” does not mean modeling without providing any information. Instead, we aim at providing minimal amount of data. Similar to C++ programming language, templates allow generic description of species of a certain structural pattern or reactions of a certain reaction mechanism.

Substituent and Template

There are two kinds of templates: Template Species and Template Reactions. They are designed to represent a family of species with similar structure and a family of reactions with similar mechanism respectively. In order to realize this idea, we add the container of Substituent into MoDeL. There are currently six objects in this container, ANY, ANYUB, ONE, ONEUB, NZ and NZUB. Though defined differently, they actually serve the same purpose: representing other parts. Let’s take ANY as an example (see Figure 4). ANY, represents parts on ONE chain and the number of represented parts can range from zero to infinity. For example, a DNA species with structure ANY - pTetR - ANY represents any DNA with part pTetR.

Figure 4: Template DNA species

A reaction with template species as its reactants, modifiers or products is a Template Reaction. A template reaction describes the core structure of reactant that causes the reaction to happen and provides a specification for generating reactions with the same mechanism. This could be understood more clearly by dividing parts in a species into functional groups -- a reaction template describes the interaction mechanism of these functional groups. For example, pTetR promoter is deactivated in presence of TetR dimer. The template species are pTetR DNA template and TetR dimer protein template (see Figure 5) and the functional groups are pTetR promoter and TetR dimer. All the parts of ANY should also be counted as a functional group, though they don’t have functions in this reaction. Any pair of species which partially contain pTetR DNA and TetR protein dimer respectively would bind according to the description of this reaction template. Modeling with templates allows users to define species and reactions only once for one certain family without rewriting them again in database.

Figure 5: Template reaction

We are still looking for more substituents. We are planning to have more detailed substituents that can replace certain number of parts on certain number of chains. Even the arrangement of parts and chains can be specified. We believe it will make our template modeling more powerful.

A Standard Language

MoDeL aims at providing a language and syntax standard for automatic modeling databases used in synthetic biology models. We will discuss a few relevant topics in the following sections.

Standard Biological Part Automatic Modeling Database Language

With plenty of information for automatic modeling needs to be stored, we design our database, and develop a standard language of describing the database. We call the language: MoDeL.

MoDeL (Standard Biological Part Automatic Modeling Database Language) is a database representation format for synthetic biology automatic modeling. This project of MoDeL aims at providing a language and syntax standard for automatic modeling databases used in synthetic biology models on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulations, and so on.

MoDeL is developed as a machine-readable format in XML fashion, programming languages with XML library API (such as libxml2 for C++) are strongly recommended for reading MoDeL database. USTC_Software has been devoted to the standardization of MoDeL. Documents can be found here. Example of database written in MoDeL can be downloaded on our [http://github.com/jkdirac/igame GitHub page].

MoDeL is an attempt to define a universal database markup language for synthetic biology automatic modeling. It supports descriptions of a wide variety of different parts, including biobrick, compound, compartment, substituent, and so on. It can also describe the species constructed by these parts, and reactions happen with the species, such as binding of species, dilution of species, degradation of proteins, amplification of cells, multi-compartment reactions, and so on.

Many traditional methods fail to consider structure of species when trying to markup reactions with only reactants, modifiers, products and kinetic laws. The best part of MoDeL is that it can preserve detailed structure in species and reactions using Chain-Node Model. Based on the model, MoDeL is able to markup almost all kinds of reactions in a detailed and clear way.

Overview of MoDeL

Figure 5 above is an example of a simple network of biochemical reactions(pTetR + TetR2 = pTetR*:TetR2) that can be automatically constructed using MoDeL:

MoDeL supports automatic construction of such network with only the input of its initial conditions and environmental parameters. In order to do this, obviously the data of parts, species, reactions, compartment, units and so on is needed. Besides, relationships between these components are also needed, so we can link to a reaction when we find a species. Data of relationship is stored as references and exists in most MoDeL components.

To define all the needed components in a systematic way, MoDeL organizes them in five component containers at the top level:

:: System: This container contains definitions of units, functions, rules and global parameters. These are all basic elements for other components of MoDeL, and many are mathematical concepts without direct synthetic biology meanings. The name of the container, System, separates this container from others which contains components of biological significance, and indicates this container includes the basic parameters of the whole system.

:: Compartment: This container contains definitions of compartments. Compartment here is considered as a holder of substance with certain volume, so it only stores related data such as units and volume. It also stores a list of compartments that are permitted to be placed inside. For compartments like E.coli that can multiply, a corresponding compartment with the same id will be created in the sub-container of compartment in Part.

:: Part: This container contains definitions of parts. Part includes the basic units that can be inserted in an abstract chain. The container of Part has five sub-containers which are: compartment, biobrick, compound, plasmidBackbone, and substituent. Biobrick contains biobricks from PartsRegistry together with other similar components created by users. Compartment contains cells and other microscopic organisms that can multiply. compound contains small molecules like IPTG and other compounds. PlasmidBackbone contains plasmid backbones come from PartsRegistry or defined by users. Substituent contains substitutes for template modeling.

:: Species: This container contains definitions of various species defined by Chain-Node Model. Each component stores the cnModel structure of chains and trees. Related reactions are also stored. It is suggested that the constructor of a database stores template species instead of real species in this container. Only in this way can he make use of the power feature of template modeling of MoDeL.

:: Reactions: This container contains definitions of various reactions. Each component has its own compartments, reactants, modifiers, products, substituent transfers, and kinetic law. This forms a detailed description of reactions. Again, constructor of a database is suggested to store template reactions instead of real reactions.

The organizational structure of components in MoDeL is shown in the following figure.

Figure 6: Structrue of MoDeL components

As mentioned above, reference relationships are stored in most components. The following figure shows the relationship between different components, the pointer pointing to a component indicates referencing to that component.

Figure 7: Reference relationship of MoDeL components

It is worth noting that MoDeL does not attempt to include all information about each component. In PartsRegistry, a long list of data in XML format is provided including part author, status, sequence, and even group access information. Such data are redundant for our database since they are not necessary elements needed to construct reaction network. Only the useful data is retained.

Relationship with SBML

SBML(The Systems Biology Markup Language) is a machine-readable language in XML fashion. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time. As a widely used model exchange standard, SBML is chosen to be the output of our auto-modeling module.

Generally speaking, MoDeL needs not to be conformed to any constraints set by SBML. However, since SBML is a widely used standard, it is better for MoDeL to share common concepts and components with SBML as many as possible. For example, MoDeL still uses rules, function definitions and unit definitions in SBML. By doing so, it will be easier for software tools to change formats between MoDeL and SBML.

Language Specifications

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Standardization of MoDeL

MoDeL aims at providing a language and syntax standard for automatic modeling databases used in synthetic biology models. Knowing the importance, USTC_Software puts a lot of effort on the standardization of MoDeL. We have requested BBF RFC55 for MoDeL, and constructed a beta version of XML schema to describe the XML structure of MoDeL.

BBF RFC55

BBF RFC55: Standard Biological Part Automatic Modeling Database Language (MoDeL) mainly describes the detailed language specifications of MoDeL with concrete examples, which provides enough information for serious database constructors to build up a database on his own. As a highlight of MoDeL, the concept and the syntax of Chain-Node Model are described in detail. The content of document is currently arranged as follows:

Figure 1: Draft document of RFC55 - Table of Contents

The document of RFC55 has already been submitted. You can find it on the webpage of [http://openwetware.org/wiki/The_BioBricks_Foundation:RFC The BioBricks Foundation:RFC]. Following are some more previews at the draft document.

Figure 2: Preview at draft document of RFC55

Figure 3: Preview at draft document of RFC55

XML Schema

XML Schemas express shared vocabularies and allow machines to carry out rules made by people. They provide a means for defining the structure, content and semantics of XML documents. Being written in XML fashion, a Schema is perfect for MoDeL to allow software to perform check on syntax. Following is the preview of the beta version of XML Schema for MoDeL. The Schema can be downloaded at iGaME project page on SourceForge.

Figure 4: Preview at XML Schema of MoDeL

Figure 5: Preview at XML Schema of MoDeL

Monthly Notebook

Daily Notebook

As a tutor game aimed at improving the understanding and facilitating IGEM and synthetic biology, iGAME itself is exactly a great way of human practice. With iGAME, people do not feel any distance to synthetic biology any more. Actually, it is time for everyone to join this trend to be as cool as Sheldon’s new biologist girlfriend. However, we do not stop here. We paid great effort to the safety issue and we have been dedicated to improving the knowledge of synthesis biology from classes and tried to share the part we contribute to the worldwide. We innovatively plot a new way of spreading the spirits of IGEM by starting our own community and we will never stop sharing and communicating. --Luojun Wang, author of USTC_SOFTWARE human practice Human Practice,"the C project" Although we do software, we also keep eyes on promotion of synthetic biology and sharing our own program. Therefore, we started a long term human practice, “the C project”, since this summer.“the C project”, as we call, consists of three parts: Curriculum, Communication and Community. Curriculum As a IGEM team, we try to let people as many as possible to know what synthetic biology is. Therefore, advisors of our team, Haiyan Liu and Jiong Hong, have established a set of synthesis biology curriculum this summer. We have done many works related to human practice on the curriculum. Jiong Hong (in the right picture), advisor of our team, gave lectures introducing safety and ethnics issues of synthetic biology. Luojun Wang (in the head picture), members of our team, gave lectures promoting iGAME. A survey* on how students know about synthetic biology and their interests for tutor game was made.(*the survey statistics comes from a sample of 240 students. Numbers of undergraduates, masters and PhDs are 160, 60 and 20) Analysis of the results of the survey The first chart shows students' favorite game types for iGAME, and the second chart shows their knowledge of IGEM project. The Circos Map We tried many methods to plot our survey more straightforwardly and clearly before we finally chose Circos [http://mkweb.bcgsc.ca/circos mkweb.bcgsc.ca/circos]. Circos is biological software used to plot genome elements and relationship. Here, we innovatively used Circos to demonstrate our survey.(as in the right picture) Circos is somehow like pie chart yet it can present multi information as all the statistics are proportional and clear on the graph. In the graph, there are three circles. The inner circle stands for their knowledge of synthetic biology, and middle circle stands for their interests of iGame. Deeper the color is, the more they know of synthetic biology or the more they are interested in iGame. For example, light pink means they know little about synthetic biology and deep green means they are very interested of the coming tutor games. The outer circle, however, stands for their major;light green for biology major and light orange for other majors. As the graph shows, synthetic biology is still new to them as the majority have little idea of it, for which is what we will continue our project in the future. However, we are delighted to see that their interests of tutor game are fairly strong. Referring to the possible game types, adventure and strategy games are students’ favorite, while some of them prefer stimulation and action games. In our program, we tried our best to listen to their voice and develop a game which is both educational and appealing. Communication We’d like to share what we have achieved with the world, so we did and will do a great deal to communicate with others and learn. For example, we collaborate closely with USTC wet team to learn what biology majors think of iGame and improve. Several seminars have been hold to make sure our program can really help the promotion of both synthesis biology and our tutor game. In addition, further transnational communication is not absent, like we had a deep talk with Dr. Joy Yueyue Zhang*(*BIOS Centre, London School of Economics and Politics Science) on how our program can change the development of both IGEM and make biology a better subject. Yet we do not stop here. We have sent emails to other teams for further communications and asked for their opions on how we can improve iGame. What is more, all our codes are shared on github[http://github.com/jkdirac/igame](in the right picture). With fixes and new features putting forward every day,any one in any corner of the world can learn and keep update of our work, not just from the surface, but from codes and essense of our work. This is really a great way of communication, for we do not have to say too much to put our achieves across to those who really want to know our work, which really works. Great contributions have been given through github and we get a lot of advices and opinions as well. Community To better promote synthesis and the spirit of IGEM, we decided to establish a community together with IGEM USTC team. For the community, we have set regular classes and lectures for both synthesis biology and IGEM. We also open our laboratory to our community members and teach them basic skills of biology experiment(as in the right picture), like PCR. Of course, this is the main field we will update our progress on in the future.

More information of our community and other human practice of USTC IGEM team, please click2010 USTC IGEM humanpractice!

Overview

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• Demo
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  • Toggle-Switch
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• Notebook
• Human Practice
  • The C Project
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• Team
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  • Students
  • Instructors
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  • Attribution & Contributions
  • Acknowledgments

Team

Team

This year 10 students start USTC_Software igem team. Chen Liao, Zheng Wang, Kun Jiang, XiaoMo Yao, Jue Wang, Luojun Wang, Yubo Qi, Zhaoyi Li, Zhengda He, Shangyu Luo. There are only 8 of us in the picture, when the picture was taken the only female team member, Jue Wang was in Beijing for her TOEFL exam. And Shangyu Luo had been to HongKong for studying in The University of Hong Kong as exchange student. What a pity! But they will join us at igem 2010 Jamboree! USTC has two IGEM teams this year, One wet lab team and our software team, all students majoring in biology was attracted to the wet lab team. Our team consists of students of other departments, such as Mathematics, Physics, Computer Science and so on. Thanks to our Instructors, Hao Jiang, Zhaofeng Luo. With their professional instruction, we are guided to decide the project plan, design and implementation.

About iGEM@USTC The iGEM Team of USTC are the combination of the exact tradition of USTC and the exact vitality of the young. Rigorous daily schoolwork has provided the team members with a solid foundation of basic knowledge, and an innovative spirit enables us to stand on the frontier of the modern science. In 2007, Jian Zhan, Bo Ding, Rui Ma, Xiaoyu Ma, Yun Zhao, Ziqing Liu and Xiaofeng Su, guided by Prof. Haiyan Liu, Prof. Jiarui Wu and Prof. Zhonghuai Hou, won the "Best Foundational Technology Prize" and a Gold Medal, with the project "Extensible Logic Circuit in Bacteria". In 2008, Xunyao Wu, He Shen, Genxin Liu, Jia Liu, Binjie Xu, Yanting Xue, Yu Chen, Zhen Xu, Bo Ding and Jian Zhan, guided by Prof. Haiyan Liu, won a Silver Medal, with the project "Artificial Multi-cellular Self-organization System". In 2009, Hao Jiang, Li Xing, Hao Wu, Zongxiao He, Danqian Liu, Chao Li, Jiayi Dou, Hanyu Lu, Hao Zhou and Bing Wu, guided by Zhaofeng Luo, Jian Zhan, Jiong Hong and Xiaoxiao Ma, won a Gold Medal, with the project "E. coli Automatic Directed Evolution Machine (E.ADEM)". In 2009 we also formed a software team for the first time. Wei Pan, Yuwei Cui, Jiahao Li, Yu He and Xiaomo Yao, guided by Bo Ding, also won a Gold Medal, with the Project "Automatic Biological Circuit Design (ABCD)". Since last year we have accumulated some experience from the project of Automatic Biological Circuit Design (ABCD), we expect to develop a synthetic biology game this time. The game aims at teaching non-biologists how to design biological systems so that players can compete to improve their designs in order to help biologists create the best engineered machines! For more information, go to [http://biotech.ustc.edu.cn/forum/forumdisplay.php?fid=26 USTC iGEM Forum].

About USTC Message from the President A university is the important assurance of maintaining belief, developing science and culture. It is a significant symbol of the level of civilization achieved by a nation. USTC Today The University of Science and Technology of China is a new type of university established by the Chinese Academy of Sciences (CAS) after the founding of People's Republic of China. The establishment of the University is aimed at fostering high-level personnel of science and technology absolutely necessary for the development of the national economy, national defense construction, and education in science and technology. The University was founded in Beijing in September of 1958. Mr. Guo Moruo is the first president of the University...... History of USTC "Pooling the entire strength of the CAS for the development of USTC and combining the institutes of the CAS with the departments at USTC" "Studying hard and excelling in both integrity and specialty"USTC was established in Beijing in September, 1958 under the presidential leadership of Guo Moruo. The establishment was hailed as "a major event in the history of Chinese science and education"...... To get more information, please visit [http://en.ustc.edu.cn/ http://en.ustc.edu.cn/] in English and [http://www.ustc.edu.cn/ http://www.ustc.edu.cn/] in Chinese.

Team Cooperation

Helps and acknowledges

Gallery

Students

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Students

Xiaomo Yao	I am soumort! I have nothing to say!!
Chen liao	My Profile: Chen Liao, Room 418, Key Lab of Quantum Information, CAS, East Campus, USTC Hefei, Anhui 230026, China, liaochen@mail.ustc.edu.cn I’ve just began my first year in the Optics and Optical Engineering program as a master candidate at University of Science and Technology of China. I became interested in iGEM because I found it a great chance to learn synthetic biology. Since iGEM is a student-run and student-manage programe which encourages students both to work collectively in a team and work individually to complete one's own task, it is a great experience to exercise my team working ability as well as creative ideas. In the last months, especially the summer, I worked with students from different disciplines to design and implement our project together and have learnt a lot from them. It is rather a wonderful experience to work with all team members. (^▽^) As a student of department of physics, my research area is development of first principle theory and implementation of LCAO (Linear Combination of Atomic Orbitals) algorithms. As a member of [http://lqcc.ustc.edu.cn/helx/ LiXin He's group], I have successfully implemented atomic force calculation in LCAO method and my next project is to modify and develop algorithms under condition of magnetic B field. Besides scientific research, I do sports very often. Basketball is my favorite and my favorite basketball player is Kevin Garnett (K.G.), his professional attitude on the court as well as his individual character in the life impresses me a lot.
Zhen Wang	I am Zhen Wang! Zhen Wang, Room 418, Key Lab of Quantum Information, CAS, East Campus, USTC Hefei, Anhui 230026, China. Email: xqqixp@mail.ustc.edu.cn; wangzhen.ustc@gmail.com; Hi, I'm Zhen Wang, I mainly work on MoDeL and Database of iGAME. As a member of Lixin He's research group, I focus mainly on calculation of quantum information, quantum correlation and entanglement. You might have noticed that my address is same as Liao's. Yes, we are from the same Research Group, and the same department, too. It will be boring if I repeat all the information again, so I am going to write some experience of myself participating iGEM2010. As a student majoring physics, it is hard for me to believe that I can participate in a biology project. Luckily, to my great surprise, these two areas are not so far apart. Modeling and analyzing skills of physics can also be used in biology, and dry project always means a lot of coding task, I can handle that, too. Of course, there is plenty of biology I need to learn, but with the help of our instructor and wet team members, I learn it fast. So I want to tell everyone that there's no limit in iGEM, join in and unleash your power!
Kun Jiang	Email: jkdirac@mail.ustc.edu.cn I am Kun Jiang, the cheif software developer in iGem 2010 USTC_Software team, responsible for designing the global architecture of our software and developing the ODE Solver module, Berkley database interface module and several simple tools for teammates. It is my second year of studying in computer applied technology lab of Institute of Plasma Physics Chinese Academy of Sciences as a master candidate. I am interesting in software engineering and Computer Sicence. Last year I noticed the recruit advertisement of iGem 2010 USTC_Software team in school BBS website. I make the decision to apply immediately. It's really happy for me during those past server months working with our team. I play Ping Pong most during my spare time, because Ping Pong is a sport emphasizes on speed, skill and acting harmony ability rather than brute force. And I go jogging every day, which i think is a good way to relieve pressure and keep me in health! I want to be a brilliant software engineer developing some brilliant works. I gain strong knowledge in software engineering and computer algorithms. IGEM 2010 is one step to my ambitions, it is a important project but not the last project of my engineering life, I wish I would develop more and more softwares in future. If you need help, do not hesitate to contact me please!
Yubo Qi	I am Yubo Qi! Yubo Qi 3005, national labotarory for physical sciences at the microscape I am an undergraduate student in theoretical physics. But I am also interested in chemical physics and biology. In my labotarory, I concentrate on the calculation about transmission in nanostructure. However, biology science is also my favourite. So, I decide to join USTC_Software team of iGem 2010. Now I write database of biology reaction for my team. I love biology, chemistry, physics and decide to devote myself to the research of interdisipline in the future.
Luojun Wang	Luojun Wang(Vic Wong) Dept. of Statistics & Finance, USTC, Hefei, Anhui 230026, China; Lab of Systems Biology of Hefei National Laboratory for Physical Sciences at the Microscale, USTC, Hefei, Anhui 230026, China vicwong@mail.ustc.edu.cn; victorwangluo@gmail.com; Hey, I'm Vic, an undergraduate senior student majoring in mathematical statistics. Yet my research field is biology statistics, and that is why I'm here. For IGEM, I'm mainly responsible for human practice and have been giving lectures as well as other promotions on both synthesis biology and IGAM. It is this special experience that has not only made my college life amazing, but also presented me with a broader view of biology. Besides working for IGEM, I've also been researching biology statistics, including bioinformatics and biology networks. My goal is to be a biostatistician in the future, on which I'm gonna keep putting effort. Now I'm applying for an opportunity to study as a biostatistics PhD. Good luck to me, huh? : )
Jue Wang	I am Jue Wang!:) Dept. of Math, USTC, Hefei, Anhui 230026, China; Email: juewang@mail.ustc.edu.cn Hi,I am Jue, a Math majored senior student. As the boundaries among different disciplines of science are now blurring, I want to handle the ideology of maths to arrive at a higher standpoint to try to understand the principle of life. iGEM provides us with such a good state to learn from utilization. In this group, I am the unique girl among nine boys, and the most frequently spoken of mine is "Oh, it's my duty to get some soy sauce! " Strange, huh? The connotation of it is not words but meanings. Those guys are too gentle to arrange me doing something of coding.So I am more involved in clerical works, I design the team uniform and our logo,arrange the scheduling and get in touch with sponsors and alumni connection. My life is full of unpredictable tasks, who can tell me what is the next?
Zhaoyi Li	My profile: Zhaoyi Li, Hefei National Laboratory for Physical Sciences at Microscale & National Synchrotron Radiation Laboratory, East Campus, USTC Hefei, Anhui 230026, China, lizhaoyi@mail.ustc.edu.cn </p> During my 2 years’ journey in the nano world, I got to know iGEM and joined in USTC Software team with great honor. Just as NEW YORK TIMES says, iGEM is a Do-It-Yourself Genetic Engineering Program. I am strongly attracted by this idea and cannot help imaging the science fiction picture where our daily life is changed by our genetic machine. It is unforgettable to have a brainstorm with talents from different academic background and turn our imagines into reality. Thanks to iGEM, I experienced a new trip in the synthetic biology and benefited a lot from my partners. Also, to compete against more than 1,000 other students from 100 schools, including many top-flight institutions is exciting. I love traveling and always enjoy trips with my friends. I have a dream that one day I can travel around the world to discover the great scenery make new friends and experience different culture. Sports is also my favorite, I am good at playing football and gifted in table tennis.
Zhenda He	I am Zhenda he! Hello , everyone! My name is He Zhengda , a student from Chemical Physics Department in University of Science and Technology of China . To be a member in 2010 USTC_Software is a really great time for me during the boring semester ! I met a lot of interesting people in the IGEM lab , and I wish to meet all you guys during the Jamboree . I have a enormorous interest in math , computer science and designing stuff . I am a Wiki interface designer in our team . So I hope everyone like it . It's a short description of me~ See you in the Jamboree!
Shangyu Luo	I am Shangyu Luo! Introduction: Hi all, I am Shangyu Luo. It is my Chinese name and my English name is Seraph. I am very pleased with attending iGEM competition with my teammates of USTC SOFTWARE. My major is computer science and I am interested in both computer and biology. During this competition, I gain a lot and make many friends. Thanks for my teammates, teachers and School of Computer Science and Technology! Additionally, I favor AI (Artificial Intelligence) in the fields of computer science, if you would like to create some beings together with me and to make them intelligent, please feel free to contact with me! Thanks all! By Seragh lsyurd@gmail.com School of Computer Science and Technology University of Science and Technology of China

Instructors

• Home
• Project
  • Introduction
  • User Interface Design
  • MoDeL
  • Algorithm
  • Resources
• MoDeL
  • One-Minute Introduction
  • Features
  • Standardization
  • Future Work
• Demo
  • Overview of Demos
  • pLux-LuxR repression system
  • Toggle-Switch
  • Repressilator
• Notebook
• Human Practice
  • The C Project
  • Safety
• Team
  • Overview
  • Students
  • Instructors
  • Collaboration
  • Attribution & Contributions
  • Acknowledgments

Instructors

Zhaofeng Luo	Mail: lzf@ustc.edu.cn
Hao Jiang	Mail:haojiang@mail.ustc.edu.cn Major: Cell Biology Research Interests: Synthetic Biology, Directed Evolution E-mail: haojiang@mail.ustc.edu.cn Former 2009 iGem USTC team member