Team:BostonU/HumanPractices

From 2014.igem.org

Revision as of 03:39, 16 October 2014

• TEAM
• PROJECT
  • Overview
  • Priority Encoder
  • MoClo Assembly Method
  • Low Copy Backbones
  • Tandem Promoters
  • Fusion Proteins
  • Repressor Proteins
  • Multiplexing
  • BioDesign Automation Tools
  • Future Work
• ACHIEVEMENTS
  • Data Collected
  • Parts Submitted
  • Chimera Workflow
  • Chimera Example
  • Medal Fulfillment
• NOTEBOOK
  • Training
  • Protocols
  • Backbones
  • Tandem Promoters and Repressors
  • Fusion Proteins
• CONSIDERATIONS
  • Collaborations
  • Measurement Track
  • Safety
  • Interlab Study
  • NEGEM
  • Policy and Practices
• ACKNOWLEDGEMENTS

Policy and Practices

Working in the CIDAR lab space, our iGEM team quickly became interested in integrating technology with biology. Once we were introduced to the topic of bio-design automation (BDA), we became curious about the current state of the art for BDA. We wanted to know not only if there were workflows for integrating computational tools into wet lab work, but also how much these tools are actually used in the lab. As we began thinking about a project, our leading question became: Can we develop a more integrated BDA workflow that is better than the current state of the art? Fortunately, we were able to volunteer at a the sixth International Workshop on Bio-Design Automation (IWBDA) at the beginning of summer. This was the perfect opportunity to learn about the current state of Bio-Design Automation and identify obstacles to BDA integration. Through conversation with one of the conference's keynote speakers, Professor Orit Shaer, we also became interested in answering the question: Can we integrate Google Glass into that workflow?(Refer to Google Glass section below).

IWBDA

As volunteers, we signed in the workshop speakers and attendants, helped with the posters, and set up the event venue. We were also able to attend the talks and poster presentations. This workshop was an important influencing factor on our project design. It gave us an opportunity to learn about the current research and concerns in the field, which shaped the direction and goals of our project.

One of the keynote speakers, Orit Shaer from Wellesley College, spoke about Human-Computer Interaction. She focused on tools that use reality-based interfaces and the considerations necessary for developing these tools. After listening to her presentation, we had the opportunity to talk with her. As a wetlab team interested in bio-design automation and experimental-computational integration, we thought it would be valuable to continue collaboration with Dr. Shaer’s lab at Wellesley. Her lab develops software tools for education and use in the wet lab.

One of the talks at the conference was given by Dr. Jacob Beal from BBN Technologies. He talked about the evolution of the TASBE Tools from when it was introduced to now, when the TASBE Tools is commonly used to predictively design constructs in mammalian cells. The past BU iGEM teams had used the Tools and our adviser, Dr. Haddock was very familiar with it, but that talk made us, the teammates, believe in potential of the TASBE Tools in the testing of constructs in E. Coli and the significance of predictive and accurate design. The talk was, thus, very influential in strengthening our motivation for the Chimera Workflow.

In addition to the talks and poster sessions, the IWBDA workshop included discussion sessions amongst all of the attendees. Topics focused on how to overcome the miscommunications between biologists and computer scientists as well as how to promote bio-design automation in our education systems. These discussions allowed us to talk more informally with the presenters and exchange our opinions and suggestions. We were also able to hear about current problems that exist between experimental and computational efforts, which gave us ideas about what needs to be improved.

NEGEM

From this conference, we learned the value of bringing together researchers from different labs to discuss, learn, and educate each other. Because of this, we decided to host the Third Annual NEGEM . Several other Northeast iGEM teams (MIT, Harvard, Tufts, WPI, Rutgers) and Wellesley came to Boston University twice over the summer to present their projects, discuss, and receive feedback. Each team had fifteen minutes to present their overall project idea, progress, timeline, and future goals to the other teams. After each presentation, there would be a Q&A session where other students could offer troubleshooting advice, ask for clarification, or offer critiques. During our lunch breaks, we held question led discussions about technological difficulties each team faced and how bio-design automation (BDA) could solve these obstacles. Our lunch was sponsored by BDAC. In October, we will have a final NEGEM meeting. Each team will give a formal presentation, representative of how they will present at the iGEM Giant Jamboree. This will be an opportunity to give final advice about the project and how to present it. We will also have time to show off our Wiki pages and make any last minute changes before the wiki freeze.

Google Glass

Alan using The Glass in the Wellesley HCI Computer lab

Throughout the summer we met up with students from Wellesley to teach them about biological concepts and lab protocols and to learn about their projects. In past collaborations with Wellesley, our iGEM teams have mostly used their surface projects. This year, the Wellesley lab had a new technology project, the Google Glass. Our team felt that the Google Glass could have much more practical applications to the wetlab. We tested out the Google Glass for several weeks and gave them feedback on the features they have been developing. For example, they were able to upload our protocols on the Google Glass, which allowed us to see the protocol step by step without carrying around our notebooks. We were also able to provide a “client prospective” for their projects. Since they are developing software for use in the lab, we helped them decide which features would be most useful and improvements that could make their products more appealing. While we decided not to integrate the Google Glass into our current workflow, we think it could be a very useful tool in the wetlab with a few additions.

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