====== (Open) Hardware for Engineering Biology ======

** 31st of August - David Sun Kong, Ph.D. (MIT) **
[[http://bio.academany.org/slides/02-Kong-Open%20Hardware-FINAL.pdf|Slides]]
[[http://connectmedia.waag.org/AcadeMany/bio-2016/08/31/index.html|Recordings]]
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Engineering biology requires great hardware. Executing biological protocols necessitates a variety of tools, from liquid handling systems to centrifuges to culture machines and microscopes. This week we will have several guest lecturers speak about their hardware projects, including:

  * Bethan Wolfenden (Co-Founder, Bento Labs) http://bento.bio/ - [[http://bio.academany.org/slides/Bento_HTGAA_2016.pdf|Slides]]
  * Julie Legault (Founder & CEO, Amino Labs) http://www.amino.bio/ [[https://www.dropbox.com/sh/3xj7b6brocly2yv/AAAjNBdtNY95D1RKXiSs25jta?dl=0|Slides and more]] [[http://bio.academany.org/slides/aminohtgaa2016.pdf|Download link for slides only]]
  * Justin Pahara (Chief Scientist, Amino Labs | COO, Synbiota) http://www.synbiota.com


David Sun Kong, Ph.D.

====== Homework ======

Design and build a piece of open hardware for biology.

  * **Due 9/7/16:** The design for your hardware and an early prototype.
  * **Due 9/28/16:** The completed hardware, fully documented, including data proving it works to your technical specifications.

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There are many areas where hardware interfaces with synthetic biology and biological construction. Here is a (non-exclusive) list of 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