iGEM 2015 — Team CCA_SanDiego

# Team:CCA SanDiego/Notebook

CCA San Diego iGEM 2015

* [CCA San Diego iGEM](https://2015.igem.org/Team%3ACCA_SanDiego)
* Project
  + [Introduction](https://2015.igem.org/Team%3ACCA_SanDiego/Project#introduction)
  + [Methods](https://2015.igem.org/Team%3ACCA_SanDiego/Project#methods)
  + [Results](https://2015.igem.org/Team%3ACCA_SanDiego/Project#results)
* [Team](https://2015.igem.org/Team%3ACCA_SanDiego/Team)
* [Notebook](https://2015.igem.org/Team%3ACCA_SanDiego/Notebook)
* [Attributions](https://2015.igem.org/Team%3ACCA_SanDiego/Attributions)
* [Human Practices](https://2015.igem.org/Team%3ACCA_SanDiego/HumanPractice)

# Notebook

Julia Wisnia and Miya Coimbra officially formed the CCA iGEM team and began plans to recruit members through word-of-mouth, publication in school announcements, and contacts with high school science teachers.

18 September 2014

Our initial members, including Julia Wisnia, Miya Coimbra, Ariel Braunstein, Olivia Shiah, Amanda Matheson, and Vivian Patton, held the first official meeting. We conducted research on potential projects. Suggestions included a smog filter composed of organic compounds to carry out anoxic decomposition, a method to mimic the glutamate protein pump in the brain to ensure the glutamate-GABA balance, a way to mimic the manner by which animals can predict coming natural disasters such as earthquakes, and gene repair through harnessing of the RAD51 gene.

2 October 2014

Julia Wisnia, Miya Coimbra, Ariel Braunstein, Olivia Shiah, Amanda Matheson, Vivian Patton, Ravi Agarwal, and Maggie Chen met to continue brainstorming projects. We decided that mimicking animal detection of earthquakes was not a feasible option for synthetic biology using E. coli since it would likely require a complex nervous system. New ideas were conceived of (including possibilities for electrosynthesis, quorum sensing, and prevention of Fetal Alcohol Syndrome), but still the most plausible candidate for a synthetic biology application was determined to be gene repair using RAD51.

9 October 2014

Another meeting was held among Julia Wisnia, Miya Coimbra, Ariel Braunstein, Olivia Shiah, Amanda Matheson, Vivian Patton, Ravi Agarwal, Maggie Chen, and Harrison Harris. Further research on potential projects was conducted. We also discussed iGEM fees and possible ways to fundraise; ideas included a bake sale, donations from family, and fundraising programs through local restaurants (such as Souplantation and Rubio’s). Miya Coimbra and Julia Wisnia discussed their attempts to find graduate student mentors from UCSD through email contact; unfortunately, responses are fairly intermittent.

23 October 2014

Today was a finals day for CCA students, so school ended early (12:25 p.m.). An after-school meeting was scheduled to Skype with three new potential mentors (Jenhan Tao, Sophia Hirakis, and Benjamin Kellman). The meeting was attended by Julia, Miya, Ariel, and Olivia; it was fairly brief and primarily went over the potential projects that we had brainstormed earlier.

28 October 2014

Miya, Ariel, Olivia, Amanda, Ravi, and Maggie attended a meeting to discuss fundraising. Souplantation gives a larger percentage of proceeds for fundraising events and is likely to be more popular among families, so we decided to schedule an appointment with them to host an event.

30 October 2014

A fundraising event was held in the evening for families and friends to eat at Souplantation and for some of the proceeds to go toward funding our iGEM activities. Julia, Miya, Olivia, Amanda, Vivian, and Ravi attended.

6 November 2014

Julia, Miya, Ariel, Olivia, Vivian, Ravi, Maggie, and Harrison attended a meeting after school to discuss topics and mentors. Unfortunately, based on prior discussions

13 November 2014

Julia, Miya, Ariel, Olivia, Vivian, Ravi, Maggie, and Harrison attended a meeting after school to review the basic methodology of various wet lab techniques like PCR, gel electrophoresis, transfection and cell culture in order to prepare for the wet lab work that would come later in the project.

20 November 2014

Julia, Miya, Ariel, Amanda, Olivia, Ravi, Harrison, Maggie, and Vivian met with Sophia Hirakis at the Salk Institute to review a wide range of biology concepts that would be helpful in the development and completion of our project.

2 December 2014

Julia, Miya, Ariel, Amanda, Olivia, Ravi, Harrison, Maggie, and Vivian attended a meeting after school with Benjamin Kellman to review more concepts. This time we focused mostly on DNA and its structure and function, as well as ways that it can be altered.

10 December 2014

Julia and Miya had a meeting with the mentors concerning the logistics of the project, such as where the team would meet, what time the meetings would be, and days of the week. They also talked about a general computational approach that we could apply to our project.

12 December 2014

Winter Break 20 December 2014 - 4 January 2015

15 January 2015

Over break we individually reviewed articles and online tutorials to better familiarize ourselves with synthetic biology concepts.

20 January 2015

Julia, Miya, Ariel, Amanda, Olivia, Ravi, Harrison, Maggie, and Vivian attended a meeting after school with Benjamin Kellman to review more concepts. This time we focused mostly on DNA and its structure, function and ways that it can be altered.

22 January 2015

Miya and Julia began our outreach program by volunteering at Solana Ranch, a local elementary school. They tutored students of all ages in any subject, but the focus was on STEM.

23 January 2015

Three iGEM team members went to Solana Ranch to tutor students with a focus on STEM subjects.

27 January 2015

Julia, Miya, Ariel, Amanda, Olivia, Ravi, Harrison, Maggie, and Vivian met with Sophia Hirakis at the Salk Institute to review a wide range of biology concepts that would be helpful in the development and completion of our project.

29 January 2015

Miya, Maggie and Olivia went to Solana Ranch to tutor students with a focus on STEM subjects.

30 January 2015

Maggie and Julia iGEM team members went to Solana Ranch to tutor students with a focus on STEM subjects.

3 February 2015

Miya, Ariel, Maggie, Vivian, and Harrison met after school to discuss the upcoming elections for club treasurer and vice president, as well as fundraising ideas to cover the registration cost.

5 February 2015

Our team received a generous donation of $2500 from a local company, Cymer. This donation helped provide the funding necessary to register for the Jamboree and let us continue the project. Our whole team was very grateful and we sent a thank you note signed by the whole team to each of the company executives.

10 February 2015

Miya and Amanda went to Solana Ranch to tutor students.

12 February 2015

iGEM team members submitted their votes online and elected Olivia as vice president and Maggie as treasurer for the team. Also, three iGEM team members went to Solana Ranch to tutor students.

17 February 2015

Ariel and Amanda went to Solana Ranch to tutor students.

24 February 2015

The iGEM team went to UCSD where they continued working on VMD tutorials in order to prepare for their simulations.

3 March 2015

Three iGEM team members went to Solana Ranch to tutor students.

5 March 2015

Three iGEM team members went to Solana Ranch to tutor students.

10 March 2015

Three iGEM team members went to Solana Ranch to tutor students, while the other iGEM members begin working on a Visual Molecular Dynamics (VMD) tutorial. The program is used to visualize, and analyze 3-D molecules, which we used later in our project.

12 March 2015

Ariel and Miya went to Solana Ranch to tutor students, while the rest of the team goes to UCSD to continue VMD tutorials.

17 March 2015

Three iGEM team members went to Solana Ranch to tutor students.

19 March 2015

Amanda, Miya, Julia, Ariel, Maggie, Olivia, and Vivian met at UCSD in order to continue brainstorming ideas for our project.

24 March 2015

Vivian and two other iGEM team members went to Solana Ranch to tutor students.

31 March 2015

Amanda, Miya, Julia, Ariel, Maggie, Olivia, and Vivian met at UCSD to continue to brainstorming project ideas, and working on the VMD tutorial.

9 April 2015

Olivia and two other iGEM team members went to Solana Ranch to tutor students.

14 April 2015

Julia and Maggie went to Solana Ranch, a local elementary school, to tutor students with a focus on STEM subjects.

16 April 2015

Amanda, Miya, Julia, Ariel, Maggie, Olivia, and Vivian met at UCSD to continue to brainstorming project ideas, and working on the VMD tutorial.

21 April 2015

Harrison, Julia and Amanda went to Solana Ranch to tutor students.

23 April 2015

Amanda, Miya, Julia, Ariel, Maggie, Olivia, and Vivian met at UCSD to continue to brainstorming project ideas, and working on the VMD tutorial.

28 April 2015

Vivian and Miya went to Solana Ranch to tutor students.

30 April 2015

Amanda, Miya, Julia, Ariel, Maggie, Olivia, and Vivian met at UCSD to continue to brainstorming project ideas, and working on the VMD tutorial.

5 May 2015

Julia and two other iGEM team members went to Solana Ranch to tutor students.

7 May 2015

Amanda, Miya, Julia, Ariel, Maggie, Olivia, and Vivian met at UCSD to continue to brainstorming project ideas, and working on the VMD tutorial.

12 May 2015

Three iGEM team members went to Solana Ranch to tutor students.

14 May 2015

Amanda, Miya, Julia, Ariel, Maggie, Olivia, and Vivian met at UCSD and completed the VMD tutorial. We then moved on to the Assisted Model Building with Energy Refinement (AMBER) tutorial. AMBER is used to simulate the way molecules act in different environments. We would use this program later in our project.

19 May 2015

Three iGEM team members went to Solana Ranch to tutor students.

21 May 2015

Amanda, Miya, Julia, Ariel, Maggie, Olivia, and Vivian met at UCSD and continued working on the AMBER tutorial. We also began finalizing our project idea, and began doing more research on biosensors.

26 May 2015

Three iGEM team members went to Solana Ranch to tutor students.

28 May 2015

Amanda, Miya, Julia, Ariel, Maggie, Olivia, and Vivian met at UCSD and continued working on the AMBER tutorial. We also continued to do research on biosensors.

2 June 2015

Three iGEM team members went to Solana Ranch to tutor students.

4 June 2015

Amanda, Miya, Julia, Ariel, Maggie, Olivia, and Vivian met at UCSD and continued working on the AMBER tutorial. We also continued to do research on biosensors.

9 June 2015

Three iGEM team members went to Solana Ranch to tutor students.

11 June 2015

Amanda, Miya, Julia, Ariel, Maggie, Olivia, and Vivian met at UCSD and finished the AMBER tutorial. We also continued to do research on biosensors.

16 June 2015

Three iGEM team members went to Solana Ranch to tutor students. This was our last day of tutoring because the school year was ending, so we had to say goodbye to some students who we had been working with since January.

18 June 2015

Julia, Miya, Ariel, Amanda, Olivia, Vivian, Ravi, Maggie, and Harrison went to Salk Institute to meet with Sophia Hirakis to discuss our project brainstorming ideas and begin to narrow them down.

23 June 2015

Julia, Miya, Ariel, Amanda, Vivian, and Maggie attend the first iGEM meeting of the summer at Urey Hall, UCSD.

25 June 2015

The team continues with the tutorials to familiarize themselves with the programs they will be using. They have completed the AMBER tutorial and now move onto the NAMD tutorial, the program that will allow them to run the biosensor in the environments they will create in AMBER.

30 June 2015

Students continue with the NAMD tutorial. Their mentors guide them with the future applications of this tutorial.

2 July 2015

Julia, Miya, Ariel, Amanda, Oliva, and Maggie continue with the first NAMD tutorial out of 3.

7 July 2015

Students continue with tutorials and taking notes on what they are learning so they are able to recall the information when they begin designing parameters and the biosensor.

9 July 2015

Students finish the second NAMD tutorial, and now to move onto the third.

14 July 2015

Students continue with the third and final NAMD tutorial.

16 July 2015

Students complete the third NAMD tutorial, and now dive into designing their project.

21 July 2015

Students begin designating parameters and conditions under which they will test their biosensors. They use the information they used from the AMBER tutorials to guide them as they design an environment similar to the body in ph, temperature, etc.

23 July 2015

Julia, Miya, Amanda, Olivia, and Ariel continue researching biosensors and working to design a more effective biosensor. Aided by their mentors, they continue designing parameters and experiments to be run.

28 July 2015

The team continues working with AMBER to design their project.

30 July 2015

The team nears the end of designing environments to run the biosensor with, but still have a few representations to complete. Work continues with AMBER.

4 August 2015

Julia, Miya, Oliva, Amanda, and Ariel work to edit the text files that will be used in the NAMD simulations.

6 August 2015

Julia, Miya, and Olivia move on to editing the final project representations, and are almost ready to create .pdb files with the text they have already screened for additional hydrogen molecules, anomalies, etc.

11 August 2015

Julia, Miya, and Olivia have a short meeting with mentors to discuss what the next month will look like for the team. They decide that they will run simulations and begin work on the team’s wiki page.

13 August 2015

The team uses the text files they have been creating to run the simulations, and run them through Cambridge University’s website, WebCSD to create the .pdb files that will later be used to produce the .prmtop files needed to run the simulations.

18 August 2015

Work on the wiki begins as the project is still underway. The mentors tell students to begin by writing short blurbs about themselves to give people an idea of who the team is in addition to the work we are doing.

20 August 2015

Wiki work continues. One of the team’s main goals is to create their project abstract, and finish their project description. They are able to complete the abstract, but only get about halfway through the project description.

25 August 2015

Olivia and Amanda continue work on the project description while Ariel and Julia begin work on the Human Practices and Safety pages. Julia researches cases of wet lab work becoming dangerous for not only the lab members, but also the communities surrounding the labs.

27 August 2015

Under the guidance of our mentors, Julia and Amanda worked on continuing writing pages for the wiki. Julia worked on the Human Practices and Safety pages, while Amanda worked on compiling and designing the Notebook. We also began to review and compile the team page based on the individual biographies sent in by the various members.

3 September 2015