Team:UESTC
From 2013.igem.org
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<p>We registered our team as UESTC, enjoyed ourselves during summer and autumn, and spent most of our | <p>We registered our team as UESTC, enjoyed ourselves during summer and autumn, and spent most of our | ||
time learning, sharing and working in the room 341 of Yifu Building. For more information about our | time learning, sharing and working in the room 341 of Yifu Building. For more information about our | ||
- | team, please visit | + | team, please visit <a href="https://2013.igem.org/Team:UESTC">our wiki</a> or our <a href="https://www.youtube.com/watch?v=TIOIVq4FHkY">team video</a> on YouTube.</p> |
<span>2. Create and share a description of the team's project via the iGEM wiki.</span> | <span>2. Create and share a description of the team's project via the iGEM wiki.</span> | ||
<p>For overview of our projects, please click <a href="#project">here</a>.</p> | <p>For overview of our projects, please click <a href="#project">here</a>.</p> | ||
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<span>3. Provide a demonstration of their software either as a textual or video tutorial made available on their wiki. This tutorial should explain all the features of the tool as well as provide sample input and output as appropriate.</span> | <span>3. Provide a demonstration of their software either as a textual or video tutorial made available on their wiki. This tutorial should explain all the features of the tool as well as provide sample input and output as appropriate.</span> | ||
<p>To see textual tutorial of our projects, please visit our page on github to download tutorial: <a href="https://github.com/igemsoftware/UESTC2013">https://github.com/igemsoftware/UESTC2013</a></p> | <p>To see textual tutorial of our projects, please visit our page on github to download tutorial: <a href="https://github.com/igemsoftware/UESTC2013">https://github.com/igemsoftware/UESTC2013</a></p> | ||
+ | <p>Also video tutorial is available on YouTube.</p> | ||
+ | <p>To see Nebula video tutorial, please click <a href="https://www.youtube.com/watch?v=Afhu50rp3RM" target="_blank">here</a></p> | ||
+ | <p>To see Transpeeder video tutorial, please click <a href="https://www.youtube.com/watch?v=6QfoALDNO0U" target="_blank">here</a></p> | ||
+ | <p>To see iBricks video tutorial, please click <a href="https://www.youtube.com/watch?v=ktqq0XISr8A" target="_blank">here</a></p> | ||
<h3>Gold Medal</h3> | <h3>Gold Medal</h3> | ||
<span>1. Have another team utilize the software developed by your team. You must clearly show how your software was used and the results that were obtained.</span> | <span>1. Have another team utilize the software developed by your team. You must clearly show how your software was used and the results that were obtained.</span> |
Revision as of 14:26, 27 September 2013
Hello,welcome to visit our Wiki, for better view, please use chrome, firefox, safari .etc modern browser.
Hi! We are 2013 iGEM Competition Software Team UESTC
(University of Electronic Science and Technology of China)
Nebula
No matter who you are, a scientist proficient in synthetic biology or a green hand who only cares about the output, Nebula is your best choice. Two modes are provided: Auto Mode & Manual Mode. In Manual Mode, you are free to link any parts we provide to assemble your device. But you have to make sense of the biological mechanism, of course. In Auto Mode, the only thing you need to do is to determine the inducer and the output. Then, you can sit back and wait for the optimized circuit provided by Nebula. Wow!
MoreTranspeeder
The satisfying amino acid or nucleic acid sequences that the user submitted will be compared to the chosen SD sequences by ClustalW, the sequence which has highest similarity with SD sequences are defined as the slow speed sequence, on the contrary, the one which has lowest similarity with SD sequences are defined as the fast speed sequence.
MoreiBricks
iBricks is an iPhone game concerning synthetic biology. In this game, what you need to do is to synthesize protein to protect a cell. You are provided with several basic parts to synthesize protein. Once you accomplish combining these parts into a circuit, you will enter into transcription process, during which phage will continuously attack your circuit. To protect it, you can press on these phages to kill them. You can also utilize several tools to eliminate phages with higher efficiency. After successfully synthesizing the protein, you can get new parts that increase the possibility of successfully synthesizing proteins. With several synthesized proteins, you can accomplish the goal of synthesizing a complete cell.
MoreNebula
Background
When a man is to begin his own journey of biobricks, he probably needs to turn to the parts registry for information of the parts with which he can construct his own genetically engineered machine. The official site of parts registry is really a terrific work and thousands of biobricks parts have been collected from all around the world. What is more, relatively reasonable classifications of parts have been well characterized and this could be of help for us. Several attempts have already been made in order to simplify the process of designing a biobrick machine, some did well in visualization, but few of them combined the excavated information of classification of parts. Nor could they automatically generate optimized biological circuit according to quality of parts. These indeed reined the efficiency when designing. So the question is raised that a well visualized user - computer interactive and automatic tool that could help us to design the desirable device is in great need.
Nebula (Network of Elaborated Biobricks based on User Locating and Automation) is a biological circuit design tool composed of Auto Mode & Manual Mode. It is freely available for devices powered by IOS. We classified the parts released in 2013 and constructed a database for users to choose what they want. We use AHP (Analytic Hierarchy Process) to score parts and edges (passage linking two parts) according to parts quality including availability, usefulness, sample status, part status and sequencing. According to weight of edges, we present “Index of stability” to users. Users can save the circuits designed in Nebula in case they want to check or change it later.
![](https://static.igem.org/mediawiki/2013/a/a8/UESTC-nebula-pic1.jpg)
![](https://static.igem.org/mediawiki/2013/3/3c/UESTC-nebula-pic2.jpg)
Algorithm
Interactive Part:
The general idea is to classify the biobricks more intensively in a view of user needs. And with these well-defined and characterized classifications, users can select the classification and sub-classification step by step and at last find the parts they want to get. The definition of the classifications of the parts in this software is mainly based on their biological functions, characteristics as well as the structures and also the existing classification methods on the official registry. After researching the features of the parts, we classified all parts released in 2013. For example, promoters in the parts can be classified into four categories: constitutive, sensitive, association with CDS experience and source. And further, the sub-category sensitive can be classified into the following two sub-categories: by inducer and by repressor, and further the sub-category by inducer can be classified into IPTG, LasI/LasR, RhII/RhIR, metal ion and other inducible promoters. So long as the user knows a little basic backgrounds of his work, he will find all the IPTG-induced promoters in our classification system, which would save a lot of time. Moreover, in this process, our software can connect the parts that the users have chosen and the visualization module will show the structure of the constructs. So in this way, a new biobricks device will be design efficiently. The specific classifications of all the parts released in 2013 are detailed as follows:
![](https://static.igem.org/mediawiki/2013/6/6b/UESTC-promoter.png)
No classification for RBS.
![](https://static.igem.org/mediawiki/2013/9/94/UESTC-CDS.png)
![](https://static.igem.org/mediawiki/2013/5/53/UESTC-terminator.png)
![](https://static.igem.org/mediawiki/2013/b/b8/UESTC-device.png)
Automatic Part:
In this part, users only need to determine the inducer and the product. Then, our software will offer users the optimized circuit with the input and output that they designate.
To realize this function, we first collect information of parts released in 2013, including (1) the upstream and downstream parts of each part and device according to the standard of “promoter-RBS-CDS-terminator”; (2) the inducer or repressor of each promoter and device with promoters; (3) the product of each CDS or device with CDSs; (4) the assembly standards each part and device fit; (5) quality of parts and devices including: availability, usefulness, sample status, part status and sequencing.
After collecting all the information, we first use AHP (Analytic Hierarchy Process) to analyze quality of parts and then score every part and device. AHP is a method for organizing and analyzing complex decisions and it is advantageous when factors of the decision are difficult to quantify. The detailed method is as follows:
(1) Construct Model of Hierarchy Structure
This structure includes 3 levels. On the top, it is the level of goal, the score of every part. At the bottom, it is the level of alternatives, the candidate parts. In the medial, it is the level of criteria, the quality of parts. The structure is shown below:
![](https://static.igem.org/mediawiki/2013/9/9d/UESTC-part-rank.png)
(2) Construct Pairwise Comparison Matrix
Supposing there are N factors in a certain level, we now need to compare the degree of importance to the upper level of parts with each other and calculate the relative weight of each factor. This comparison is pairwise. Usually we choose 9 scales when comparing these factors.
![](https://static.igem.org/mediawiki/2013/a/aa/UESTC-table-4.jpg)
aij the result of comparison between factor and factor , then we can construct pairwise comparison matrix .
![](https://static.igem.org/mediawiki/2013/3/3e/UESTC-A.png)
Where aij=1/aji
Following this method, we can construct pairwise comparison matrix of criteria level and alternative level.
According to the meaning of quality of parts, we build pairwise comparison matrix of criteria level. The matrix is shown as follows:
![](https://static.igem.org/mediawiki/2013/9/9c/UESTC-table-5.jpg)
Before we construct pairwise comparison matrix of alternative level, we first designate the level of the quality of each part and device, because the original content is described by words. The results are as follows:
![](https://static.igem.org/mediawiki/2013/0/09/UESTC-table-6.jpg)
![](https://static.igem.org/mediawiki/2013/0/05/UESTC-table-7.jpg)
![](https://static.igem.org/mediawiki/2013/0/0d/UESTC-table-8.jpg)
![](https://static.igem.org/mediawiki/2013/b/bd/UESTC-table-9.jpg)
![](https://static.igem.org/mediawiki/2013/7/70/UESTC-table-10.jpg)
According to this result, we construct pairwise comparison matrix of alternative level B1, B2, B3, B4, B5. The scale of these matrixes is too big, so we don’t display them here.
(3) Consistency Check
The definition of index of consistency check is CI=(λ-n)(n-1), λ is the eigenvalue of maximum of pairwise comparison matrix, n is the dimension of matrix.
The value of index of random consistency is as following:
![](https://static.igem.org/mediawiki/2013/4/49/UESTC-table-11.jpg)
We can obtain our desired RI from this table and calculate the ratio of consistency CR=CI/RI. If CR < 0.1, the degree of inconsistency is acceptable, otherwise, we need to reconstruct pairwise comparison matrix. After calculation, all pairwise matrixes accord to consistency checks.
(4) The Calculation of Parts’ Score
Supposing wA is the eigenvalue of maximum of pairwise comparison matrix A, w1 w2 w3 w4 and w5 is the eigenvalue of maximum of pairwise comparison matrix of B1, B2, B3, B4 and B5 respectively. Then the score of No.n part is:
![](https://static.igem.org/mediawiki/2013/9/96/UESTC-B.png)
The score represents the reliability of the part.
Then, according to the standard of “promoter-RBS-CDS-terminator”, we link all the parts together and construct a network, which is saved as adjacency matrix.
The weight of path is the reciprocal of the sum of two parts on the two sides of the path. As a result, when we search for the shortest path between the input and output, the path tends to go through parts with high scores, which indicates high reliability of circuit.
When users input the inducer and product of their desired circuit, we first determine the starting part and ending part according to users’ inputs, and then use Dijkstra algorithm to find out the shortest path between starting part and ending part. During the process of searching for shortest path, we make judgment at every step. The judgment is as follows: (1) the potential part must share at least one assembly standard with existing parts in the circuit, otherwise, the second shortest one is added to the circuit. (2) If there is more than one promoter in the circuit and the inducers and repressors of these promoters intersect, then we don’t choose this path, because the material that induces one promoter can repress the other, which can lower the rate of transcription.
Following the method above, we can calculate and display the circuit according to users’ input and show the score that indicates the reliability of the accomplished circuit. Users can also save the circuits in Nebula in case they want to check or change it later.
Future work
Now users can only share results as pictures, which is rather convenient for edit again. It will support other formats to share your design, for example, SBOL. What’s more, we will improve our interface to optimize the user experience. In version 2.0, all the parts in parts registry will be included in Nebula, which can greatly increase the convenience for users. Now we have realized the online version of Nebula with some basic functions, which is far from perfection. Much improvement will be made to perfect it in the near future and you can visit it on the page: http://cefg.cn/nebula/
Downloads
To download Nebula in Apple App Store, please visit here.
Transpeeder
Background
Codons are the basic principles in the transmission of genetic information. Each amino acid corresponds to at least 1 codon and at most 6 codons. These codons encoding the same amino acid are called synonymous codes. But appearance frequency of synonymous codons is not equivalent in organisms or genes, while instead, one or several specific codon(s) usually tend to be used more often, and the phenomenon is termed codon usage bias(separate codon usages). In 1991, Danchin and his colleagues first found the codon usages separation in E.coli. With the development of genome sequencing,more and more researchers are interested in codon usage bias,and have found there are different codon usage bias in different species.
Studies have shown that the codon usage bias not only has an effect on protein expression levels but also plays a role in the translation regulation of genes. The protein synthesis velocity is under the influence of the translation initiation rate and the peptide chain elongation rate. Moreover, translation initiation rate is determined by the rate of combining the ribosome and mRNA. Thus the concentration of ribosome and mRNA becomes one of the main influencial factors of protein synthesis. In other words, codon usage will directly affect the efficiency of the transcription and determine the concentration of mRNA. Furthermore, the correlation analysis of codon usage bias and the concentration of mRNA and protein length in yeast also showed that the codon usage bias may help to increase the efficiency of the transcription and translation (such as improve accuracy) and reduce consumption in the process of translation. In 2009, Science reported the ribosome profiling technology (Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling), and in 2012, Nature also published a paper of analysis the codon choice with the method of ribosome profiling technology (The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria). Both these two articles reported the choice of codon in gene sequences will avoid the homology of ribosome binding sites (RBS) sequence in order to improve the translation speed.
Learning from the above two articles, we developed a tool for gene translation regulation which was based on Shine-Dalgarno sequence of species, named Transpeeder. This tool provides the reference for scientific researchers in synthetic genes. At the same time,iGEMers can use transpeeder to mutate the component sequences in order to regulate translation speed and adapt to the experiment requirement when they are designing or using the component in iGEM.
We’ve developed two versions of Transpeeder: the online version and the desktop version. Both of them share the same functions. Users can submit an amino acid, a nucleic acid sequence,upload a local file to Transpeeder or choose parts ID of iGEM. And then Transpeeder will output slow speed sequence and fast speed sequence.
![](https://static.igem.org/mediawiki/2013/a/a2/UESTC-transpeeder-online.jpg)
![](https://static.igem.org/mediawiki/2013/2/29/UESTC-transpeeder-desktop.jpg)
Modeling
Based on the background described above, we put forward an algorithm in order to implement the tool, and the details are as follows.
User can submit an amino acid or a nucleic acid sequence. When the sequence conforms to the input rules, the Clustalw is working. And then Transpeeder will choose the sequence sharing highest similarity with SD sequences as slow speed sequence and the one with the lowest similarity as fast speed sequence.
Algorithm is simply described as follows:
A. Determine the input sequence. Users can select the input sequence type: Amino acid/Nucleotide;
a. For amino acids sequence, determine the existence of the amino acids characters, and feedback to the users.
b. For nucleotide sequence, determine the existence of the nucleotide characters, then identify whether the sequence contains gene sequences (ORF identification).
B. Deal with selected SD sequence. Take E.coli for example,SD=AGGAGGT. Reverse the SD sequence, form new SD’ sequence, SD’=AGGTAGG.
C. Gene sequence split. Due to the SD sequences length are 5-7 nucleotides and the space of the ribosome size is about containing 2 codons. We split gene sequence with the length of 6 nucleotides (codon pair) and step length is set to 6. For each split (codon pair) of sequence set as SS.
D. Sequence alignment. Calling Clustalw2 program to align SS with SD and SD’.
E. Choose the corresponding alignment results according to user’s demands.
Experiments
With the preliminary algorithm, we mutated the GFP_ M62653 to a fast and a slow speed sequence. And we calculated the CAI of them : GFP_FAST(M62653) CAI: 0.695,GFP_LOW(M62653) CAI: 0.611. It is in accordance with previous work. Team UESTC_life helped us with experimental verification, and the results showed that the mutative sequences with our algorithm are in consistent with experiments work.
![](https://static.igem.org/mediawiki/2013/6/60/Experiment.png)
Future work
Now Transpeeder only collects one host: E.coli. In our next edition, we will add more species to it. At the same time, it will support more file formats and add sharing function, so that you can share your results via Twitter, Weibo or Facebook.
Downloads
To experience online version of Transpeeder, please visit this page: http://cefg.cn/transpeeder. You can also download desktop version on it.
iBricks
Background
As synthetic biology is a rather new field to many people, to popularize the concept of synthetic biology and encourage more people to involve in it, we design an interesting video game, iBricks.
iBricks is a video game concerning synthetic biology on iPhone. In this game, what you need to do is to synthesize protein to protect a cell. You are provided with several basic parts to synthesize protein. Once you accomplish combining these parts into a circuit, you will enter into transcription process, during which phage will continuously attack your circuit. To protect it, you can press on these phages to kill them. You can also utilize several tools to eliminate phages with higher efficiency. After successfully synthesizing the protein, you can get new parts that increase the possibility of successfully synthesizing proteins.
![](https://static.igem.org/mediawiki/2013/a/a0/UESTC-ibricks-pic1.jpg)
![](https://static.igem.org/mediawiki/2013/f/f9/UESTC-ibricks-pic2.jpg)
![](https://static.igem.org/mediawiki/2013/8/83/UESTC-ibricks-pic3.jpg)
![](https://static.igem.org/mediawiki/2013/f/f7/UESTC-ibricks-pic4.jpg)
Modeling
All parts are classified into 4 categories: promoter, RBS, CDS and terminator, meanwhile each part has 3 attributions: stability which indicates that how many times your circuit can withstand the attack from phages, transcription speed, which implies the time you need to synthesize the protein, and probability of gaining tools that can eliminate phages during process of synthesis. The value of attributions varies from parts. You need to combine 4 different kinds of parts to gain the most stable, low time consuming circuits with higher possibility of gaining tools.
This game aims to popularize the concept of synthetic biology among the public. Users with no biology background can learn basic information of synthetic biology and meanwhile have great fun.
Future work
As this is our first time to program video games, there still exists a lot remaining to be improved. In our next edition, we will provide users with more levels rather than 5. What’s more, there will be more parts for you to choose. And more tools will be accessible to kill phages more efficiently. Last but not least, we will improve some details. For example, when you have done the game, you have to choose level again rather than enter into next level directly, so we will add this function to it. In a word, it is far from perfection now, and we will keep moving.
Downloads
To download iBricks, please visit the here.
Hello
This is the voice from UESTC, Chengdu, China. We are proud to announce that we have achieved two first here: It‘s the first time that our university take part in iGEM. What’s more, we are also the first team from the southwest region of China participating in the software competition. Wow! We come from University of electronic science and technology of China, which is renowned as China's cradle for the national electronic industry. Also, our university is situated in Chengdu, the city of over a thousand-year-old cultural history in 'the land of abundance'. What's more, we are from the hometown of PANDAs!
Student Members
-
Hi, I am the leader of our team and the director of iBricks. As a junior student majoring in Biomedical Engineering, I have a great interest in data mining in social network and programming software on mobile devices. I did all the scoring algorithm of Nebula in our team.
-
Hi, I am a junior student from school of life science and technology, majoring in Biomedical Engineering and minoring in English. For my great organizational capability, I am the director of Nebula. I am in charge of the statistics of parts in the registry and database established for Nebula.
-
Hi, I am a junior student majoring in Biomedical Engineering. I am fond of photography and sports, especially basketball. I did part of parts statistics and the realization of Transpeeder by Java.
-
Hi, I am a junior student majoring in Biomedical Engineering with strong learning ability. I like running, reading and traveling around. I did part of parts statistics and kept the minutes of our discussion in our way to MIT. My life motto is nothing is impossible to a willing heart.
-
Hi, I am a junior student majoring in Biomedical Engineering with great interest in programming. I chose programming on IOS system as the main attack. iBricks is my first experience in video games. Programming Nebula on iPhone is relatively easy to me. My maxim is where there is a will, there is a way.
-
Hi, I am a sophomore majoring in Theoretical Physics from school of physical electronics. I am regarded as a hard-working student with easy-going personality. Making great videos is what I am always pursuing. Besides this, I also participated in parts statistics work for our projects.
-
Hi, I am a freshman from School of Information and Software Engineering, also a fantastic guy with passion and great imagination. Wiki is rather a great challenge for me, but I really enjoy this process of learning and progressing. The realization of online version of Nebula is also my work.
Advisors
-
Hi, I am a postgraduate majoring in biochemistry and molecular biology, responsible for giving advice on some of the arts designing work in our team, including T-shirts and wiki design.
-
Hi, I am a doctoral student in CEFG. Current Research interests: codon usage, bioinformatics database. I did algorithm of visualization of Nebula and Transpeeder.
Instructors
-
Dr. Jian Huang is a professor in the University of Electronic Science and Technology of China. He holds M.D. degree with experience in medicine, basic immunology and bioinformatics from the West China University of Medical Sciences and the Kyoto University. His studies focus on the molecular aspects of antigens, antibodies and peptide aptamers. His work has resulted in the development of a few immunological databases and web programs which have become to be important tools and data resources for both computational biologists and experimental biologists, especially those using phage display technology.
For more information, please visit his homepage http://immunet.cn/hlab
-
Dr. Lin is an associate professor of the Center of Bioinformatics in the School of Life Science and Technology interested in proteomics bioinformatics and system biology.
For more information, please visit http://lin.uestc.edu.cn/
-
Dr. Xianlong Wang is an associate professor of computational chemistry and biology at the Center of Bioinformatics, the University of Electronic Science and Technology of China. He is interested in modelling both small molecules and biological macromolecules and developing new algorithms.
Contact us
Shahe Campus:No.4, Section 2, North Jianshe Road, 610054
Qingshuihe Campus:No.2006, Xiyuan Ave, West Hi-Tech Zone, 611731
Diaries in May
Friday May 3, 2013
The university tryouts which has lasted for nearly a month ended, and the name list of the selected members of the school team has been determined. Launching ceremony of the iGEM event this year was staged today and the people present are Dezhong Yao, Dean of School of Life; Qiong Zhang, vice secretary of the Communist Party Committee of School of Life; Jian Huang, supervisor of the software team; Xuelian Zheng, supervisor of the Wetware team and all members of the UESTC iGEM team. The leaders conveyed the great attention and expectations from the university.
Saturday May 4, 2013
It is the first meeting that was convened by the software team. Apart from the team members, the people who attended were the supervisors and the advisors. We discussed the schedule and main tasks at this stage and the team leader emphasized the discipline required during the preparations for iGEM. In May, we plan to do massive reading of academic papers on synthetic biology and each member is required to share the ideas that he or she has got from reading these papers, and then the team will discuss the ideas and make a decision on a general direction of our project. In June, the team is to do the intensive reading on the major direction and conceive frame of the project and assign tasks to each team member. In July and August, all members are to dedicate their time to the work distributed to him or her. In late August and September, the project will be under optimizing and improving, and the team will make preparations for the presentation to be held in Hong Kong.
Friday May 10, 2013
We shared six papers in this meeting, the paper “Synthetic biology: New engineering rules for an emerging discipline” introduced some new engineering rules on synthetic biology; the paper “Engineering microbial consortia: a new frontier in synthetic biology” discussed the relationships between commensalism, amensalism symbiosis, mutualism, and parasitism from the perspective of synthetic biology; the paper “Protein promiscuity and its implications for biotechnology” introduced the application of protein engineering in synthetic biology; the paper “Synthetic biology: Applications come of age” summarized the challenges and opportunities of synthetic biology; the paper “Synthetic biology projects in vitro” introduced in vitro synthesis of bioengineering and artificial life as well as the idea of minimal gene design method. After the discussion we had a deeper understanding of the idea of synthetic biology.
Sunday May 12, 2013
In this meeting we discussed eight reviews read by the team members during the past several days. The contents of the reviews are in the areas of gene switch which is based on the research of protein isomerism; mammalian cell structure design using the idea of engineering of small molecules; synonymous codon bias; application of catalytic efficiency of light in synthetic biology reactions and RNA functions. The software Notebook done by other team for past competition was also introduced. Considering what we have already discussed before, we decided to focus more on the projects from the past iGEM teams. Now the topic that interests us is codon optimization based on selection bias, but it calls for further discussion.
Friday May 17, 2013
In this meeting we discussed four papers and some software. “SynBioSS: the synthetic biology modeling suite” is a synthetic gene structure modeling and simulation software in which different parts could be set in a complete network, but it highly recommends a wider and more comprehensive knowledge on synthetic biology, molecular biology and computers. Another paper talked about how antibiotics kill bacteria, and what we can learn from it is the possibility to create a piece of software to simulate this process, which, of course, will provide great convenience to synthetic biology researchers. Yang Xue introduced SBOL to the team, which is an open language for synthetic biology. “Engineering of synthetic intercellular communication systems” summarized how to accomplish cell communication systems in cells in synthetic biology. The software Bioguide introduced by Jurong Zhao focused on the categories for pathway generation and database search. After the discussion, we all agreed that the project we plan to do should be fully considered with the user needs and provide convenience to synthetic biology researchers.
Sunday May 19, 2013
This discussion is mainly on software and biobricks as well as the CLOTHO platform. We talked about the ideas of the software finished by the team Wellesley_HCT_2012, UTP_Software_2012 and USTC_Software_2012 and their advantages, disadvantages and use value, which are inspiring to our own projects.
Wednesday May 22, 2013
We talked about the software MGEC finished by the team Edinburgh _2008, which was designed for biologists to establish genetic engineering circuit model more easily based on modeling and data analysis. Another piece of software we discussed is BioBrick Manager_2010 which is mainly designed to connect Biobrick parts, and then to save as XML file. We also analyzed their disadvantages that need to be improved.
Friday May 24, 2013
In this meeting, we discussed some pieces of software of the iGEM competitions before. For examples, Synthetic Biology Simulation Software: measuring the efficiency of the terminator; Digital Synthetic Gene Circuit Software (which can not perform large-scale optimization), then we thought about what we can do about it. USTC 2012 Software: Anti-circuit design was also introduced.. This time, we discussed a relatively new paper on anti-SD sequence, and the question that whether we can create a piece of software on codon optimization. So after the meeting, we should research this literature intensively to understand how to use the anti-SD sequence to achieve codon optimization and whether someone has already done similar software. Then we should study the corresponding data on RBS site, and grasp the information from compared sequences. More details will be finalized in next meeting.
Sunday May 26, 2013
Today, we continued to discuss some software. Such as Tinker Cell which is a synthetic biology CAD software, in which analysis and biological networks are visualized by third-party C or C + + as well as python modules. And CAD tools, databases, a rule of network Design and a language Kera, GenoCAD, and network concepts were also introduced by different team members. Finally, we summarized the software discussed and drew some conclusions for our projects.
Friday May 29, 2013
CLOTHO platform is a way that can be considered for making software. Also we discussed M4B (with its network structures, including a relatively new scoring rules for parts), and Synbioss. And we studied the python scripting language. This time, a new idea was proposed by Xiaonan Guo, which is to make a phone-based game in order to popularize synthetic biology and concept of biobricks. People can learn some knowledge on synthetic biology in their leisure time. The proposal interested us a lot and we need to check more information. Before we began to realize this idea, there are a lot of tasks to be done.
Wednesday May 31, 2013
For the implementation of the idea we discussed last time, we also need to do a lot of work, and in which deep research is essential. We learned a lot from the game--USTC 2010 IGAME, such as the interface design, understanding a good sense from the perspective of a player. We also discussed AMDL (automatic modeling database language), the smallest gene design software. Last but not the least, we made the plan for the refinement of the game idea proposed last Friday, and discussed the direction and so on. Projects are in progress.
Diaries in June
Sunday June 2, 2013
We continued to discuss some software we’ve collected, including Plasmid Automatic Design Software. And from its idea and approaches we can think about how to combine our game and the concept of synthetic biology. Other pieces of software we discussed are BioBricks jtools, which is a small set of utilities; Biomortar, EvoGents, focusing on how to make gene circuits stable based on genetic algorithms; and Agent Based System. Then, we determined agenda for the next meeting. In addition, the coach told us that Gil-- MIT judger -- would come to communicate with us in our college.
Tuesday June 4, 2013
Software we discussed are: Lachesis, a visualization tool based on parametric models. We talked about a literature which introduced how to choose a route from massive biobrick parts by scoring and the feasibility of the parts in the database. Biodesign is a program which automatically connects the selected parts, but it only supports IOS Systems. ABCD which was made by the USTC in 2009 can automatically generate the designed circuit. We also discussed Gil’s trip and our presentations.
Friday June 7, 2013
This main content of the meeting was the discussion on the codon optimization based on anti-SD sequence, then combined with the previous paper, we summarized a lot comments after researching. We confirmed our second project, codon optimization software, and some preliminary concepts have been conceived. Also we discussed the database to be established for the game.
Sunday June 9, 2013
Gil arrived at our college and gave us a good view of his own research and iGEM competition’s concepts as well as its requirements and rules. .All iGEM team members of our university are present on the presentation. During the meeting, we asked a lot of questions and Gil answered all of them patiently.
Monday June 10, 2013
Our team held a meeting with the co-chair of the iGEM software track. We introduced our team and the progress that we have made to Gil, and he gave us some feedbacks and comments which really inspired us. Hope to see him again at MIT!
Friday June 14, 2013
After this term’s preparations, we strongly felt that it’s the right time for us to make our plan a concrete one. So we divided our projects, distributed the work and all of us are being dedicated to learning and working.
Thursday June 20, 2013
More details were settled, mainly focused on the requirements and the programming languages.
Diaries in July
Saturday July 10, 2013
Mr. Lu, who is responsible for the logistical preparations for our team, held a meeting with us. It mainly focused on the disciplinary issues for the coming intensified training during the whole summer. He also pointed out that we need to take note of the deadlines.
Tuesday July 16, 2013
Our head coach, Prof. Huang, held a meeting with some leaders of our college. And then he conveyed their expectations that we should enjoy the competition process and try to make awesome software. At the same time, he also suggested that we can collaborate with the other team of our university and have a better understanding about what is needed in experiments.
Thursday July 18, 2013
Today’s meeting is a plenary one held for the software and Wetware team of our university. Students from two teams gave some presentations on our ongoing projects and we all learned a lot from each other. Also, we focused on how we can reach some consensus on the collaboration issues.
Thursday July 25, 2013
It’s been a week since we last held a meeting and we are indeed confronting some obstacles in collecting parts information. So today it was a great chance for us to solve these problems and set up basic principles and unified standards on how to extract information on the parts registry.
Sunday July 28, 2013
We gathered and made a report on what we’ve done for the whole July. We determined the name of each project, outlined the framework of next month’s work plan and made some arrangements and work distributions.
Diaries in August
Saturday August 10, 2013
In this meeting, each member introduced the work which he/she was mainly responsible for. It contributed to give us a better understanding of the progress of our three projects. And then, we made some comments and suggestions on the projects for our future work.
Wednesday August 21, 2013
For nearly two months’ hard work, our projects have been almost completed by now. Now we are still engaged in improving day by day. So, today, we held this meeting mainly to make some decisions for the competition in Hong Kong. On the one hand, we discussed the project's progress and improvements. On the other hand, we confirmed the name list that who will make presentation for our team in HK.
Thursday August 29, 2013
We were still engaged in improving our software these days after the last meeting. Today, we held this meeting mainly to sum up the progress of work in August. Second, each member introduced the work which he/she was mainly responsible for. And then, we discussed the plan of our next work in September.
Diaries in September
Saturday September 14, 2013
After last meeting, we carried out our projects as planned, such as finished all documents. Today, we are mainly to see how to perfect our software, and we made some arrangements for the iGEM Jamboree in Hong Kong. Then, the leader of our university’s wet team introduced the course of the experiments which used our software, the results and the matters needed to discuss. Finally, we discussed the plan of our next work.
Thursday September 19, 2013
Today, we mainly did some preparations, such as posters, for our competition in Hong Kong while we continued to complete some of the unfinished work in our projects. At the same time, we summarized the progress we had made, so that we can make arrangements for our next work.
Monday September 23, 2013
Up to now, the projects of our team have been substantially completed. Today, we held a plenary meeting with the wetware team of our university which was mainly to make the first practice for the presentation of the coming trip to Hongkong. The people present were Mr. Lu, who is responsible for the logistical preparations for our team, the two teams’ head coaches and all members.
Thursday September 26, 2013
After three days’ practice, today we held a second plenary meeting of the analog presentation for the competition in Hongkong. Compared to last meeting, the two teams had some progress. But there still exists somewhere that we need to improve and enhance. So, we should continue to practice and improve in the coming days before the competition in Hong Kong.
Medal Fulfillment
Bronze Medal
1. Register the team, have a great summer, and have fun attending the Jamboree.We registered our team as UESTC, enjoyed ourselves during summer and autumn, and spent most of our time learning, sharing and working in the room 341 of Yifu Building. For more information about our team, please visit our wiki or our team video on YouTube.
2. Create and share a description of the team's project via the iGEM wiki.For overview of our projects, please click here.
To see details of Nebula, please click here.
To see details of Transpeeder, please click here.
To see details of iBricks, please click here.
3. Present a Poster and Talk at the iGEM Jamboree.We made our Poster and will give a talk at the iGEM Jamboree.
4. Develop and make available via the The Registry of Software Tools an open source software tool that supports synthetic biology based on BioBrick standard biological parts.Our software tools and source code are now available on Github for free downloads, please click here to download.
Silver Medal
1. Provide a detailed, draft specification for the next version of your software tool.For next version of our project, please see our future work page.
For Nebula, please click here.
For Transpeeder, please click here.
For iBricks, please click here.
2. Provide a second, distinct (yet complementary) software tools project.Our second software is Transpeeder, a distinct yet complementary one. For more details, please click here.
3. Provide a demonstration of their software either as a textual or video tutorial made available on their wiki. This tutorial should explain all the features of the tool as well as provide sample input and output as appropriate.To see textual tutorial of our projects, please visit our page on github to download tutorial: https://github.com/igemsoftware/UESTC2013
Also video tutorial is available on YouTube.
To see Nebula video tutorial, please click here
To see Transpeeder video tutorial, please click here
To see iBricks video tutorial, please click here
Gold Medal
1. Have another team utilize the software developed by your team. You must clearly show how your software was used and the results that were obtained.Our software, Nebula, has been used by team UESTC_Life. The project of UESTC_Life is to constitute a device that can clear the pollution of environment. To find out suitable promoters that can be stimulated by arabinose, the proper CDS and other reliable components, like terminator and RBS, they used the Auto Mode of Nebula which can generate reliable devices with the inducer and output that users designate. Although to accomplish the function of their projects, team UESTC_Life used CDS that is not in the official registry, which is not provided in our database, they used other parts that our software, Nebula, provides.
2. Outline and detail how your software effects Human Practices in Synthetic Biology. Such topics include: safety, security, ethics, or ownership, sharing, and innovation.For details about this topic, please visit our human practice page, click here.
3. Develop and document a new technical standard that supports the sharing of BioBrick Parts or Devices, either via physical DNA or as information via the internet.Among our three projects, both iBricks and Nebula provides sharing function for users. In Nebula, once you complete your designs, you can share the information of your devices as pictures with your friends via Twitter. In iBricks, if you like this video game, you can share it with your friends via Twitter or Facebook, you make an effort to popularize the idea of synthetic biology and iGEM as well.
Human Practice
After about two months’ preparations, we had a general idea about synthetic biology and iGEM. As an area of biological research and technology that combines biology andengineering, synthetic biologists approach the creation of new biological systems from different perspectives, focusing on finding how life works (the origin of life) or how to use it to benefit society. During the birth of our projects’ ideas, we propose to popularize the concept of synthetic biology and iGEM to high school students so as to call on more people to be involved in iGEM.
On July 27th we organize some activities with students of the middle school attached to Sichuan university in cooperation with UESTC wet team. For the sake of more accessible, we made good preparations for this human practice. Posters and videos were made in advance; Great presentations were prepared; a deliberate plan was made in brain storm.
First, we gave a lecture named Dating with my college to them. Silong Jiang from wet team made a short introduction of UESTC, and then Shangnian Wang from we software team led us to the world of synthetic biology. Besides gave us a general idea of synthetic biology, he also present us some successful examples from previous iGEM teams. Colorful bacteria, man-made life and synthetic world aroused them great interest in synthetic biology and iGEM.
Second, together with students of the middle school attached to Sichuan university, we were divided into 6 groups for deeper understanding of synthetic biology and iGEM. We shared our experience of synthetic biology and iGEM as well as our ideas of 2013 iGEM. Though our work have not done yet, we show them part of our projects to make a better explanation. Regardless of generation gap, we really enjoyed this short but beautiful period.
At last, we took some photos as permanent mementos.
What matters most in human practice is to make more people familiar with synthetic biology and iGEM, and we made it. At the same time, we got some new ideas about our work, especially iBricks, through this communication activity. It is of great value to us.
Safety
1. Are you using the iGEM Software repository at github.com/igemsoftware? If you have instead stored your code elsewhere, please explain where and why you have put it there. If your code is not in the iGEM repository, are you using any version control system such as Git, CVS, or SVN?Yes, we are using the iGEM Software repository at github.com/igemsoftware.
2. User Dataa. Does your software store any private data supplied by the user? (For example: the user's name and email address, passwords, DNA sequences, circuit designs, etc.) If yes, please describe what kind of data is stored. If no, skip the rest of this question and move on to question 3.
Yes, users can store their circuit designs in our software.
b. What is the URL or IP address where the user's private data is stored? Where is the physical computer or hard drive that contains the user's private data?The users' private data is stored on his own hard drive for example iPhone. The hard drive belongs to the users so he can put it anywhere he likes.
c. Please describe any encryption, password protection, etc. that you use to protect the user's data. (It is not mandatory to have such protections, but if you do, describe them.)No protection is provided.
3. Does your software include any other security features? Please describe them here.No.
4. Does your software let the user create a design by choosing parts/genes from a list/database, such as the Registry? If so, which lists/databases are included? Is there any restriction on which parts/genes the user can choose?Yes, users can choose parts to create a design from our own database. We reorganized the parts of the Registry of Standard Biological Parts released in 2013 and created a database. There is no restriction on choice.
5. Does your software allow users to write new data into any public lists or databases? If so, do you check the new data for errors before allowing it to be written?We do not allow users to write new data.
6. Does your software include any other features that encourage the user to create safe designs? Please describe them here.No other features.
7. Is your team also doing biological work in a wet lab?Yes.
Safety forms were approved on September 17 2013, by Kelly Drinkwater. ---From the iGEM Safety Committee
Downloads:Basic_Safety_Form and Software_form
Parts submission
We have submitted 6 parts from our verification test of Transpeeder to Registry of Standard Biological Parts. Among them, 4 were accepted. The other two were not accepted because of not compatible with RFC10. The results are showed as follows:
![](https://static.igem.org/mediawiki/2013/d/d2/UESTC-parts.png)
For more information about our submission, please visit Registry of Standard Biological Parts: http://parts.igem.org/cgi/dna_transfer/batch_list.cgi