July

Abstract

This is the first week that we started our team work. We hold a meeting to allocate everyone’s work. We are divided into 3 groups. The first group is focused on reading paper to learn what is terminator. The second group is responsible for software. The third group should build a web page for our software. None of us is specialist for computer language or biology, so our work is hard.

Week 1

7.15.2012-7.21.2012

7.15.2012

Paper Group：

1. We read some paper, focused on studying two of them.

2. We tried to find paper on terminator efficiency, but we didn’t make much progress.

Software Group:

We wrote a small program with C++. It can return LH and nt when input stem loop and T tail sequence. If delta G is known, it will give d score automatically.

Web Group:

1. We prepared the first draft wiki and decided to improve it later when we have more experience on web design.

2. We borrowed a couple of books about C# and web design from the library.

7.16.2012

Paper Group:

1. We created a table of terminator efficiency including fields of name, description, sequence, stem, loop, tail and efficiency.

2. We searched web of knowledge and google scholar for transcription terminator paper.

3. We emailed authors of those paper to clear out confution and ask questions about T.E.

Software Group:

We learned some basic knowledge of C#, wrote a program to calculate d score and nt. But users have to type in the free energy. Web group:

1. We learned how to build a simple web page.

2. We spent the whole night in solving a simple but strange problem. Fortunately we conquered it.

7.17.2012

Paper Group:

1. We found some information on terminator and some specific terminators, learned the progress of writing our RNA fold program.

2. We searched more terminator efficiency data, read some materials about how to write a paper, what to be prepared and concerned.

Software Group:

We continued our C# programming study, improved our program to calculate d score and nt.

Web Group:

1. We learned how to use dreamweaver to design a simple web page.

2. We learned how to build a database.

7.18.2012

Paper Group:

1. We visited some terminator structure and mechanism websites.

2. We read a paper about terminator; contacted several researchers to get information. We tried to imitate existing algorithm to determine terminator’s secondary structure. The first version of the program has been developed and we are going to test it.

3. We added more records to the TE database.

Software Group:

We improved the input validation program and made the class-”d_score_calculator” more usable. We read the manual of mfold and calculated the free energy of 1-loop by ourselves. But the free energy of 2-loop is still a problem.

Web Group:

1. We designed our team logo; learned how to build a server for our website.

2. We obtained and installed all the softwares we are going to use.

3. We were still trying to design a user-friendly web page.

7.19.2012

Paper Group:

1. We read some paper on terminator efficiency and found lots of models about the mechanism of terminator.

2. We learned some knowledge about double terminator which we didn’t know before. He also built a database about terminator efficiency which is a big contribution to our group.

Software Group:

1. We converted Liu Xing’s C++ program into C#, added the input validation function. Then we created an interface for the hairpin score calculation.

2. We calculated the free energy of 2-loop containing a bulge loop and a hairpin loop.

Web Group:

1. We learned how to use WPF to build a windows program and updated our server.

2. We built up the basic structure of our web page.

7.20.2012

Paper Group:

1. We read some paper on two RNA polymerase termination models, which has a higher view of terminator mechanism; and paper on termination mechanism models.

2. We updated and optimized TE database.

3. We improved the stem loop determination algorithm and modularized program.

Software Group:

We programmed the algorithm to make sure the structure of the terminator is clear.

Web Group:

1. We continued building a windows program.

2. We continued improving our web page.

7.21.2012

Paper Group:

1. We did a second view of all paper and “why we do a research of terminator efficiency”.

2. We updated our database again.

Software Group:

1. We continued optimizing our algorithm.

2. We read some paper and material. We can create the algorithm based on one pair of “closing base pair”.

Web Group:

1. We finished the UI of our windows application program.

2. We continued improving our web page.