Team:UESTC/notebook

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.