Introduction to Synthetic Biology

Introduction to Synthetic Biology 20th February 2014 @ Innovation Endeavors, Palo Alto, CA


1. An Introduction to Synthetic Biology.

We will discuss the core principles of biology, including safety, terminology, inputs, outputs and processes. We will develop a framework for organizing the lessons to come and adapt to working in a science that always finds room for exceptions. We will conclude by covering some simple, yet foundational experiments utilizing these principles that prepare us for the integrated approach to synthetic biology that follows.

2. The Cell is a Microscopic Chemical Factory.

Cell function and regulation can be thought of as the workers, machinery, and management of a factory, accepting deliveries and work orders, shipping out product, and performing repairs, upgrades and modifications. From this top-down analysis of cellular function, we will replace our machinery with enzymes, our deliveries with small molecules, and our management with DNA and its regulators. We will take a brief look at how various types of cellular communication keeps the whole system running.

3. Structure-Activity Relationships.

As we delve deeper into the cell, we see that the way each part functions is correlated to it’s size, shape and activity. Mobility, orientation, and cellular localization also play critical roles in function. As we find similarities in structure and function across multiple systems, we can improve our classification of these parts. These broad categories then allow us to further organize biomolecules by type and function into a rapidly expanding toolkit

4. Manipulating Organisms, Cells, Genes and Genomes.

Now that we have a core understanding of native cellular function and know some methods of analysis, we turn to the core suite of the SynBio toolkit: molecular cloning, directed evolution, screens, and selections. We begin to develop our own methods for probing pathways and functions and learn to steer the cellular machine to an engineered function.

5. Synthetic Biology for Brewing.

The traditional baliwick of bioengineering is the improved production of biomolecules through fermentation. Advances in synthetic biology change what we can make and how well we make it. We cover early examples, such as adding a single gene to an existing pathway, then more modern bioengineering, where entire synthetic pathways are developed along with a suite of support genes that improve cellular function and stability under these taxing conditions.

6. Thinking with Cells and Cellular Computing.

Cellular systems do not use a CPU. Gaining superior control of a cell requires building logical systems with computer science inspiration, and we discuss several methods of introducing logic circuits into living orgnisms. Likewise, the distributed cellular system has useful computing applications! We will also touch on support technologies for synthetic biology, such as GUI tools, database management, and in vitro DNA synthesis improvements.

7. Understanding Genetically Modified Organisms.

GMOs are an emerging concern in the global collective mind. In this section we analyze the concerns, promises, and technology of multi-cellular organism modification and their use outside the laboratory environment. An international approach is used to probe where our concerns really lie and how those concerns match up with the current state of GMO development and regulation.

8. New Companies and Technologies in the Bioeconomy.

Get an overview of synthetic biology start-up companies and industry players. We’ll also discuss how new technologies are changing the landscape of biotechnology and look at predictions of future technologies to come.



You will get an introduction to the world of biology, biotechnology and synthetic biology. We start with an input/output approach to biological systems, then explain where biological molecules come from and how they are formed, what they look like and how they perform such a wide variety of functions. We then see how these very same properties of native cell function allow us to probe, manipulate, and modify cell function. With this core knowledge in hand, we’ll discuss state of the art industry applications, such as the ability of biological systems to produce a huge variety of chemicals including alcohols, fuels and drugs and what modern methods are used for the manipulation of biological systems. We will cover how biological systems compute and perform logic, and how biology can be engineered for such activities. The risks and benefits of genetically modified organisms will be discussed and the start-up and industry landscape and new technologies will be reviewed.



This course is designed for people with little or no previous knowledge of biology but with some background in the shared engineering skillset of creative problem solving, iteration, classification, and archiving results. We will use analogies and stories from computer science and engineering to describe how cells, genes and organisms function and highlight the differences between these systems, both on a physical level and in terms of technological development. This approach helps us find useful places to apply our effort to improve synthetic biology and to craft high quality projects. If you already have an understanding of biology and are looking for an intermediate or advanced courses in synthetic biology or biotechnology then please contact us.



Introduction to Synthetic Biology is a new course conceptualized and written by Dr. Josh Gilmore and Dr. John Cumbers. The course provides a one-day interactive class for teaching synthetic biology to non-experts. The course is written for tech-professionals in other fields such as computer science, to learn about the growing power of biology to perform useful tasks and make high value products from drugs to spiders silk. We focus on analyzing the similarities and differences in our fields of study to make these lessons accessible, inspirational, and memorable.



We’ll be using a number of modern teaching aids to make it easy for you to get the most out of the course. For example, we’ve structured the modules in manageable segments with core stories, examples, and cross-references to back up the content being explained. We cut through the jargon and help you tackle the latest research by using primarily literature and industry copy in the class. The core course competencies are reinforced in a variety of ways, including interactive Q&A



08:30 - 09:00
Registration & coffee
09:00 - 09:10
Welcome and Introductions
09:10 - 09:50
Module 1: An Introduction to Synthetic Biology
09:50 - 10:30
Module 2: The Cell is a Microscopic Chemical Factory
10:30 - 10:50
10:50 - 11:30
Module 3: Jenny Rooke - Structure-Activity Relationships
11:30 - 12:10
Module 4: Manipulating Organisms, Cells, Genes and Genomes
12:10 - 13:00
13:00 - 13:40
Michael Fero - Hands on Biological Design
13:40 - 14:20
Module 5: Jeff Dietrich - Synthetic Biology for Brewing
14:20 - 15:00
Module 6: Thinking with Cells and Cellular Computing
15:00 - 15:20
15:20 - 16:00
Guest speaker: Karsten Temme
16:00 - 16:40
Module 7: Understanding Genetically Modified Organisms
16:40 - 17:20
Module 8: New Companies and Technologies in the Bioeconomy
17:20 - 17:30
Wrap up


Our class sizes are small (around 25 people) so that you can maximize your time with the instructors and guest speakers.

Early Bird registration is $450 and will be available until 17th February 2014. After this date, regular registration is $550. We also offer student registrations for $275 for the Early Bird and $375 regular registration. We provide lunch, tea, coffee and snacks throughout the day.

If you need to cancel, please let us know at least 24 hours in advance. You can then transfer your registration to another class or transfer it to someone else.


Innovation Endeavors
575 High Street Suite 400
Palo Alto, CA 94301