Team:USTC-Software/vacation

The first training for iGEM started just at the beginning of 2013 winter vacation. When I stepped into the hall of the life and science building, many people had already been there and it was really exciting to think about that we would work together for a long time. Students here were all undergraduates or graduates holding different dreams of their own, and as for me, I dreamed of making many friends and doing something worth enriching the memory of my college life. However, we gathered here for the same reason and would fight for the same goal in the next few months.
The first day was about a brief introduction to iGEM and synthetic biology. The former team leader, Kai Kang, informed us of the work of software teams. He told us how many software teams were there and introduced every part of the competition to us and we were all looking forward to learning some programming skills and knowing other team members. What was more, I was surprised to find some of my classmates also sign up for the software team. In the afternoon, the first training ended with hope and happiness. All members were aware that there were so much to learn and to prepare and that we were really gonna do something. .

Since vocation had already started, the campus became quiet with a sense of winter. Only a few students left including us, candidates for the 2013 iGEM software team. Today began the second day of iGEM training program and the topic became more serious, the algorithms and methods in iGEM software.
A geology major as I was, these new things really aroused the interests of programming in me. Today, Kaifeng Chen gave the talk. The talk not only included the commonly used algorithms in computer science, like genetic algorithm and particle swarm optimization, but also gave an overall introduction to the languages that might be used in developing an iGEM software project. From the talk, I came to understand what excellent software should own: suitable algorithms with powerful functions. Besides, I was amazed at the power of interdisciplinary knowledge: applying the knowledge in the fields of engineering to solve the problems in synthetic biology, which is also the theme of the iGEM competition.
Today students listened carefully and all were really absorbed. For me, after this class, I was more interested in synthetic biology and more willing to join the team. Even problems and challenges may lie somewhere in the future, I have the faith and the confidence that my teammates and I have the competence to overcome them. .

Since vocation had already started, the campus became quiet with a sense of winter. Only a few students left including us, candidates for the 2013 iGEM software team. Today began the second day of iGEM training program and the topic became more serious, the algorithms and methods in iGEM software.
A geology major as I was, these new things really aroused the interests of programming in me. Today, Kaifeng Chen gave the talk. The talk not only included the commonly used algorithms in computer science, like genetic algorithm and particle swarm optimization, but also gave an overall introduction to the languages that might be used in developing an iGEM software project. From the talk, I came to understand what excellent software should own: suitable algorithms with powerful functions. Besides, I was amazed at the power of interdisciplinary knowledge: applying the knowledge in the fields of engineering to solve the problems in synthetic biology, which is also the theme of the iGEM competition.
Today students listened carefully and all were really absorbed. For me, after this class, I was more interested in synthetic biology and more willing to join the team. Even problems and challenges may lie somewhere in the future, I have the faith and the confidence that my teammates and I have the competence to overcome them. .

It was getting hotter and we are getting busier since we were all assigned for our own missions in the last meeting. It was time to get to work and try not to waste time. There were not so many people in Room 363 yet because some of them were still preparing their tests. I was supposed to write code for the fourth part, optimized output. Yet since the other two people in my group were still busy, I decided to learn some Photoshop and C++. C++ had many in common with C, but it was an object-oriented language which seemed more complex but more useful. Xingyu Liao and Tianhao Zhang were discussing their parts when I got there. They had already achieved a lot but were facing some problems this time. Though it was a little difficult for me to catch up with them, they really did much research in equations for system stability. Our team leader, Chenkun Wang, who was gonna write code in SBOL, had surprisingly finished most of it.
In the afternoon, I was still trying to photoshop some pictures meanwhile search ways to realize certain effects on the Internet. After skimming through wikis last year, some ideas for our logo this year seemed to emerge in my mind. Chenkun Wang and I were discussing about the schedule for the next month, hoping we could finish the main codes soon. It was a fruitful day and all of us were happy to see that we were progressing fast.

Today Chen Shao was coming to work with me. The optimized output part was about giving user the requested expression concentration of the gene the user assigns. The two of us were thinking about showing all possible expression concentration value of certain gene by drawing a graph and let the user choose any concentration he or she want. We also came up with the idea that our users would have concentration requests for more than one gene, thus we could give users the freedom to choose several genes and input concentrations they need. However, what confused us was that what the expression concentration really represents, mRNA concentration or protein concentration, we searched on the Internet, then found out that it means the concentration of mRNA. We had to some extent solved our problems and would wait for Pei Zhang to come back and join in our discussion.
Our captain had spent all day discussing with every member of this team trying to catch up with each part as well as writing his own code. Talking to him was really a fun and he was more like a close friend to all of us. As for Xingyu Liao and Tianhao Zhang, they were asked many questions by me because I was gonna use their function and I needed to know what kind of parameter should I give to that function. Unfortunately, I still could not understand how their function works and I thought I would try harder tomorrow. .

After discussing with Xingyu Liao and Chenkun Wang, we realized that we had totally different understanding on Xingyu Liao’s function, which lead to an ultimate change for the fourth part. Because target gene expression concentration was not supposed to change with the initial value, we were going to give the function a new network instead of gene concentration. That was the birth of the reversing engineering part and to realize it we decided to apply optimization algorithm. In the meantime, Jingyang Li was coming back with his new computer. He had read many paper and started writing his part, sequence alignment, which was indeed useful if they would finish it well. Jinyang, the soul of our team, knew how to inspire and encourage us in time. And he was so creative and learned that he told us many incredibly wonderful ideas for the team logo, wiki and interface. Haosen Tan, working on the same part with Jinyang, had already finished a large part of his own code.
In the evening, Chen Shao and I worked trying to find a proper algorithm for the new part and the whole team worked late today until 11:00 pm.

With our software progressing in regular pace, we had become close friends to each other. The warmth and peace really moved me and when I looked back, everything in this team was full of fun and happiness. We were strangers in the beginning though studied in the same school, and then when suddenly everything seemed changed because of this competition, we were chasing the same dream together and became a team, a real team. I wasn’t an outgoing girl and for most of the time, I used to stand beside crowd watching people smiling, laughing and chatting. For the first time I finally felt like part of a group and I would thank Jinyang Li because it was him who persuaded me to sign up for iGEM.
Chenkun had finished his own part and put all the data in a file for our convenience. Xingyu was a little bothered with how to set the coefficients of the equations properly. His part was the key of our software and different coefficients would definitely cause different results. I was busy with learning particle swarm algorithm in the meantime and Shaohua and Monan were focusing on the design of the wiki. After working for two hours, I stood up, walking around the lab and glad to see my teammates still working hard on their computers.

July had come to its end and we all wished we could finished writing our code soon.

I spent two days writing PSO part and finally I finished most of it. It was time for me to debug. Taking a deep breath, I pressed the button and, unsurprisingly, there were many bugs. After debugging, I decided to pair programme with Jinyang since my programme still could not run and his part also had some problems.
I was explaining my programme to him the whole afternoon and in the evening, we were solving his problems in sequence alignment together. Pair programming was undeniably efficient and we had conquered most problem in a day. Tomorrow, I would try linear function in PSO to see whether the result would be right.
Monan was really enjoying in designing the wiki these days and he was busy figuring out how to reach the effect on the website Jinyang introduced in the afternoon. He didn’t show up very often in spring semester, thus we were not familiar with him at first. After a month, we found out him to be a humorous and optimistic guy, who was always energetic and had the ability to make us laugh no matter when. Other member of the team were also occupied with their own work the whole day. As for me, I hope I would succeed in debug my code tomorrow.

It was a beautiful day at the beginning of this beautiful August. Everything was working out smoothly. Last night we had a small group meeting mainly for choosing a popular and proper style for our wiki. Shaohua and Monan showed us many kinds of button, title bar and wiki. After discussion, we decided to try two different styles, chinese style and minimalism style.
We were busy thinking the name for our software today so that we could design our team logo wishing the name could be used in the logo. GeIn had already been a choice in our name list and Jinyang came up with idea, Prometheus, which indicated forethought and conformed with the prediction part. Xingyu’s calculation part was encapsulated as a class and I prepared to use his function in PSO in order to see the final result in my part. What was more, we realized there were some unsolved problems in the application. Since the GRN was a sparse matrix, the fourth part could seem useless sometimes. We had to find a way to solve this problem.
This day passed and we would welcome another beautiful day tomorrow. We all agreed we should hurry up a little because we had loads of things to do despite writing code for the software.

Our team leader, Chenkun Wang had desighed a logo for the team. USTC was magically hided in the head of a unicorn and a “software” was beside the unicorn head. This style was a little like logo for sports brand, yet ingenious.
Jinyang was focusing on his part these days trying to figure out a way to make the sequence alignment more persuasive instead of building on too many assumptions. He was thinking of using AAS in comparison and this idea was indeed more convincing than comparing DNA sequence directly. He was really a guy loving digging into everything and also a completist.
I was kind of carefree today because I had finished my part, thus I could spend more time discussing with others about their work. It was really inspiring to join in discussions of a relatively new work.
Shuai Ma, responsible for the interface for the software, was talking with Chenkun and Hao Xu, the team adviser, about QT via QQ group. Xingyu was still fighting with the equations, wishing that he would find a best way to set the coefficients. Monan and Shaohua was burying in themselves in wiki design and of course, constantly told some funnyt jokes unconsciously.

Tianhao Zhang was back from home today and offered to write Clotho because he had learned Java in his own. We were happy to see that all the work was equally divided to everyone. Today I was discussing the sequence alignment with Jinyang because I had many questions about how they succeeded in transforming similarity to regulatory relationship. Gladly, he said I did help a lot and wrote the questions down. I would come back home tomorrow and I left the Lab early today.