Principles, Practices and Hardware

13th of September - George Church (Harvard), Megan Palmer (Stanford), David Kong (MIT), Jean-michel Molenaar (Tufts)

Recordings

Presentations and slides

  • 9:00-9:15: Welcome to HTGAA 2017 by Jean-Michel and David! David will also discuss community bio globally, course improvements and a course overview.
  • 9:15-10:00: Introduction of HTGAA and scope by George
  • 10:00-10:10: break
  • 10:10-11:10: Megan on ethics & safety
  • 11:10-11:30: David on Bio Hardware
  • 11:50: Information on next classes, lab logistics, and class mechanics by Jean-Michel

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Class assignments

Ethics, safety and security are essential considerations throughout (and beyond!) this class. We have therefore designed an assignment this week to give you a strong foundation, and then will ask you to reflect each week and in the design of your final project.

You can find suggestions for completing your assignments in this document and examples from previous classes below.

First Week

As you are setting up your lab lab/space to grow (almost) anything, including for projects you are considering undertaking through the course, please answer the following questions on your class page. We also strongly suggest that you use these questions to create or update a guide for your lab.

  1. Risk/Safety Level: What is the Safety Level of Your Lab (e.g. BSL1, BSL2, other)? Do you have different spaces with different safety levels? If so, describe which activities are done in different spaces. Include a picture of your lab. For help on safety and risk levels see the iGEM Risk Group Page
  2. Work Area: Which work areas do you use for handling biological materials? (e.g open benches, biosafety cabinet, fume hoods etc)? Include a picture of your work spaces.
  3. Training: Have you received, or will you receive, any ethics and/or safety training? Who provides this training? Briefly describe any topics covered.
  4. Rules and Regulations: Which laws and regulations (locally, nationally and internationally) apply to your lab? Include links to any oversight institutions/organizations and policies, and describe which specific rules are pertinent to your lab and project and why.
  5. Organization and Practices: How do you enforce these rules? Who is responsible for ensuring safety in you lab/space? What happens when safety issues are raised?
  6. Uncertainties: Are there any areas where you are uncertain about how to apply these rules, and whether they are relevant to your lab and/or work?
  7. Getting Help: Who can you work with to resolve any problems or uncertainties (both to figure out how you can adhere to standards and update them if needed)? How difficult are they to contact?
  8. Beyond the Rules: Are there activities in your lab/project which you think may have ethical, safety or security concerns that are not fully covered by current rules and standards? If so, please briefly describe them.
  9. Other Information: Is there anything else we should know about your lab?
  10. BONUS: Designing for Safety and Ethics: Do you think the design of current regulations is sufficient to ensure safe and ethical practices? If not, how else could you approach the design? We’re interested in your ideas for strategies that could be used to promote safe and ethical practices as it becomes easier to grow almost anything (i.e. monitoring people or information, building safety into the design of equipment, etc). Can you think of any useful examples from other fields?
Every Week Thereafter

In a seperate section on your week 1 class page, answer the following question after each week's class:

  • Weekly Reflection:Do your activities this week raise new ethics and/or safety considerations you had not considered in week 1? Describe what activities have raised these considerations and any changes you have implemented in response.
For Your Final Project

Find a creative way to reflect on the following questions through the design and implementation of your final project:

  • Your Project: Is your project safe, responsible and good for the world?
  • Beyond This Class: How can you help prepare yourself, and the world, for many more people being able to grow (almost) anything?

Example Assignments

A few examples from the 2016 class (note: there is room for improvement!)

This assignment was less involved in 2015, but here are a few examples:

Useful Resources

Hardware

The HTGAA inventory of hardware, reagents, and Synthetic Biology One videos can be found here:

https://docs.google.com/spreadsheets/d/1YRWQRTBSgn1aUY-WVLG3K8riCbV-ZATtPElDXcY88gQ/

Hardware Homework

Design and build a piece of open hardware for engineering biology.

For the duration of the class, you will need various tools to execute the experimental homeworks. Build at least one piece of open hardware for your lab. This assignment is due by the end of the class, but please share your hardware at any homework review when it is complete!

Here is a (non-exclusive) list of hardware project area suggestions:

Experiment Execution. Throughput and reproducibility are key limits to what can be accomplished in synthetic biology. Any hardware that accelerates the design, test, build, and learn cycle and/or makes experimental results more reliable and reproducible will have a significant impact on synthetic biology.

Sensors. Data acquisition for biological measurement—from optical density to fluorescence measurements—require sensors. Projects based on novel sensing technologies, or innovative remixes of current sensors, are welcome topics.

Microscopy. The ability to visualize biological systems is one of the most critical enabling technologies for biology. In class, we've learned about a variety of imaging techniques that can enable, for example, expansion microscopy and FISSEQ.

Liquid Handling. We exist in the pipette era of biology. Fluidic machines—from microfluidics to liquid handling robots—can help us realize the longstanding vision of an automated biological future.

Complexity Management. Synthetic biologists constantly manage complexity, from sample tracking to running multiple parallel experiments. Great hardware can help organize and systematize without scaling up confusion.

Bioreactors. Engineered organisms typically require culturing in an in vitro environment. Great hardware can help organisms grow according to experimental parameters and execute their engineered functions.

Bio-printing. We have learned in class about ways to work with biological materials to create structures. From inkjets to larger deposition systems, hardware is critical for precisely spatially orienting bio-materials.

Bio-Made Hardware. Hardware can help synthetic biologists engineer biology, but biology can also be used to engineer hardware. Consider also projects that use genetically engineered machines to create structures, mechanisms, and other devices.

Reading

TABSE: A Tool-Chain to Accelerate Synthetic Biological Engineering http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.467.7189&rep=rep1&type=pdf

Lab Making | The Book: HackteriaLab 2014 - Yogyakarta, by Urs Gaudenz, Sachiko Hirosue http://hackteria.org/wp-content/uploads/2015/09/LabMaking_HLab14book-Sep10-Pages-59-61.pdf

Open Source Generic Lab Equipement and Scientific Devices http://de.slideshare.net/mrgaudi/open-source-generic-lab-equipement-gaudilabs?ref=http://hackteria.org/wiki/Generic_Lab_Equipment

Beyond Black Boxes: Bringing Transparency and Aesthetics Back to Scientific Investigation http://hackteria.org/wiki/Syntheses_of_%22Beyond_Black_Boxes%22

Overview on Generic Lab Equipment http://hackteria.org/wiki/Generic_Lab_Equipment

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