Dev/Engineering/Webinars
Engineering Webinars
On this page you will find information on: 2021 Engineering Webinar Series, and Previous Webinars.
This season the Engineering Committee will be hosting online events to connect with teams. Join us for new webinars throughout the season and check out the Previous Webinars at the bottom of this page for useful content as you begin working on your projects.
2021 Engineering Webinar Series
The Engineering Committee will be continuing their Webinar Series this year! Please see the schedule below.
If you are unable to join them as they happen live, we will post the recorded videos of these webinars here and on the iGEM Video Universe so you can watch them at your convenience.
In this webinar, we will go over what makes a good iGEM project and how to start the process of brainstorming your project. We will cover some of the iGEM timeline and highlight important features that every successful iGEM project and research project should consider.
In this Modeling Webinar (Part I) we will go from ODEs (ordinary differential equations) and the law of mass action to Hill functions, their derivation, and how to use them to model the regulation of gene expression and inducible promoters. Additionally, we will explore Hill functions and explain the effects of parameters on activators, repressors, hybrid promoters, and the corresponding protein expression levels of GFP or any other reporter gene.
You have defined your project and now you need to start planning and designing your genetic engineering approach. Seems like a daunting task! In this webinar we will cover “what you need to consider before starting to clone '': we will give an overview on available databases to identify relevant genes and coding sequences as well as we will give advice on a good cloning strategy and available assembly methods.
This webinar begins with a general introduction to fluorescence and OD, including a comparison of plate readers and other types of instruments, factors affecting fluorescence, and how to pick colors based on excitation and emission spectra. The second block of the webinar focuses on calibration of measurements for fluorescence and OD, and on debugging such measurements. Finally, we will end this session with a discussion of how to interpret and debug calibrated plate reader data.
In this modeling webinar (Part II) we will focus on how to use the previously learned concepts to model genetic circuits with ODEs and Hill functions. A circuit that is capable of "sense-compute-act" is used as an example. Then, we will learn how to relate this model with experimental data from this genetic circuit. Finally, we will focus on a more complex circuit, the Incoherent feed-forward motif to compare the results obtained from the model and its experimental measurements, enriching this way the model and completing one turn of the DBTL cycle.
In this webinar, we will first relate synthetic biology and core concepts to the DNA assembly techniques that are commonly implemented within iGEM and the synthetic biology community. We will then give an overview of key basic molecular biology techniques. Finally, we will look at DNA parts to help you design sequences for your iGEM projects.
This webinar will discuss the array of design considerations for your genetic circuit when beginning a synthetic biology project. We will cover the basics of designing your biological circuits using examples of various approaches for different outputs. Furthermore, we will examine optimization methods for your system, different failure modes of genetic circuit design and much more!
In this webinar, we will introduce commonly used DNA assembly techniques, such as Gibson and Golden Gate Assembly. We will discuss how to employ each assembly strategy in the lab environment and how each process works at the molecular level.
This webinar will present the overall process of genome engineering. We will discuss different approaches and techniques used to engineer organisms from getting the DNA in to genome editing including CRSIPR/Cas approaches.
This webinar begins with an introduction to flow cytometry, including how these instruments operate and the types of data that they produce. The second block of the webinar focuses on calibration of measurements for fluorescence and cell size, and on debugging such measurements. Finally, we will end this session with a discussion of how to interpret and debug calibrated flow cytometry data.
The explosion in DNA sequencing has provided a lot of biological parts to use in your projects. But how do you select the right ones? Computational approaches can help. This webinar will introduce teams to analysis of genes by sequence analysis, and some approaches to analyzing protein sequences, particularly similar sequences, to identify primary, secondary and tertiary structural clues to help you select the best one for your projects.
Webinars - Curated 2020 Content
The 2020 Measurement Committee hosted a series of weekly webinars to help iGEM teams with your projects! Planned topics include taking your ideas into the lab, designing DNA sequences, DNA part assembly from classical to modern methods, engineering your organism, modeling your project, measuring cellular phenotypes like fluorescence, and how to purify and characterize protein products.
Week 0 - Introduction to the Summer Webinars from the Measurement Committee
June 9: During this first session, we will briefly give an overview on the summer webinar series, describing what we hope to accomplish and what we hope that you will get out of attending. This webinar, and all of the following webinars, will be made available online after the webinar is finished. Additional related content can be found online.
- Part 1: Project Overview
- Part 2: Using Databases
- Part 3: Cloning Strategy
Week 1 - iGEM Summer Webinars: Getting Started
June 16: The first session of the iGEM Measurement committee’s summer webinars opens with an overview of how and where to start your project, as well as what you can plan and design. The second block will be a beginner’s guide on how to utilize databases effectively in conjunction with bioinformatics tools. We will end this session with an overview of the decision making process when choosing a cloning strategy.
Supplementary material:
- Databases & Bioinformatics Tools for Beginners Practicum DOWNLOAD (.DOCX file, 16KB)
- Webinar 1 Supplemental Materials and links DOWNLOAD (.DOCX file, 9KB)
- Part 1: Modeling - ODEs
- Part 2: Introduction to Hill Functions
- Part 3: Examples of Hill Functions
Week 2A - Modeling: ODEs and Hill Functions
June 23:In this Modeling Webinar (Part I) we will go from ODEs (ordinary differential equations) and the law of mass action to Hill functions, their derivation, and how to use them to model the regulation of gene expression and inducible promoters. Additionally, we will explore Hill functions and explain the effects of parameters on activators, repressors, hybrid promoters, and the corresponding protein expression levels of GFP or any other reporter gene.
Supplementary material:
- iGEM-Measurement-Tools Github Link : https://github.com/iGEM-Measurement-Tools/Modeling-Tutorials
- Part 1: DNA Parts
- Part 2: Part Collections
- Part 3: Basic Techniques
Week 2B - DNA parts and Basic Molecular Biology
June 23:In this molecular biology webinar, we will cover important concepts including, standard parts and why they are important in synthetic biology, what the iGEM registry is, and what a "part collection" is. Additionally, we will introduce you to core molecular biology techniques, giving you links to videos and protocols. Additionally, we will highlight a few important "part collections", the measurement data affiliated with these collections, and why these measurements as well as the part registry are so important when deciding what DNA parts to use.
Week 3A - Modeling circuits with ODEs and experimental data
June 30:In this modeling webinar (Part II) we will focus on how to use the previously learned concepts to model genetic circuits with ODEs and Hill functions. A circuit that is capable of "sense-compute-act" is used as an example. Then, we will learn how to relate this model with experimental data from this genetic circuit. Finally, we will focus on a more complex circuit, the Incoherent feed-forward motif to compare the results obtained from the model and its experimental measurements, enriching this way the model and completing one turn of the DBTL cycle.
Supplementary material:
- iGEM-Measurement-Tools Github Link : https://github.com/iGEM-Measurement-Tools/Modeling-Tutorials
- Part 1: Designing Primers
- Part 2: Golden Gate Assembly
- Part 3: MoClo (Modular Assembly)
Week 3B - DNA Assembly Techniques
June 30:In this molecular biology webinar, we will cover the creation of DNA primers for use in PCR reactions. We will also introduce the key concepts behind Golden Gate Assembly, why it is useful when working with DNA "parts", and then go into using Modular Cloning. There will be demonstrations of designing primers and using DNA parts that are Golden Gate compatible using various Web Apps. iGEM students should also review the iGEM partners page to learn about how to get free DNA synthesis services!
- Part 1: Designing Primers
- Part 2: Golden Gate Assembly
Week 4 - Gibson Assembly and Yeast
July 7:In this molecular biology webinar, we will cover what Gibson Assembly is and how to create a plasmid using this powerful technique. Additionally, we will go over some of the basics of working with yeast and how yeast can be used to also assemble large amounts of DNA using their endogenous pathways.
- Part 1: Theory of fluorescence
- Part 2: Calibrating for fluorescence and OD
- Part 3: Interpreting calibrated plate reader data
Week 5A - Quantifying fluorescence and cell count with plate readers
July 14:This webinar begins with a general introduction to fluorescence and OD, including a comparison of plate readers and other types of instruments, factors affecting fluorescence, and how to pick colors based on excitation and emission spectra. The second block of the webinar focuses on calibration of measurements for fluorescence and OD, and on debugging such measurements. Finally, we will end this session with a discussion of how to interpret and debug calibrated plate reader data.
- Part 1: Intro to Cell-Free systems
- Part 2: Making Cell-Free systems
- Part 3: PURE system
Week 5B - Cell-Free Systems
July 14:This webinar will cover Cell-free (CF) systems. These systems contain all of the cellular components necessary for transcription and/or translation, depending on the specific CF system being used. We will outline why this is an exciting area of research as well as how to use and make these systems.
Week 6A - Quantifying fluorescence and cell phenotypes with flow cytometry
July 21: This webinar begins with an introduction to flow cytometry, including how these instruments operate and the types of data that they produce. The second block of the webinar focuses on calibration of measurements for fluorescence and cell size, and on debugging such measurements. Finally, we will end this session with a discussion of how to interpret and debug calibrated flow cytometry data.
- Part 1: Transformation of E. coli: Electroporation & Chemical
- Part 2: Conjugation
- Part 3: Sanger Sequencing
Week 6B - Transformation and Sequencing
July 21: In this molecular biology webinar, we will cover some of the most important techniques for genetically modifying bacteria. We will cover standard electroporation and chemical transformation techniques for E. coli. We will also cover conjugation, a technique commonly used to genetically engineer organisms that are less well studied or organisms that cannot be easily electroporated or chemically transformed. Finally, we will cover the process of Sanger sequencing, look over a sequencing result, and demonstrate how to align sequencing results to a reference file.
- Part 1: Introduction
- Part 2: Experimental techniques
- Part 3: gRNA Design
Week 7 - CRISPR
July 28
- Part 1: Protein Biochemistry Fundamentals
- Part 2: Protein Purification Strategies
- Part 3: Evaluating Protein Purity
Week 8 - Protein Purification and Characterization
August 4: This Webinar will provide an overview of protein characterization that covers analytical techniques used to purify recombinant proteins and evaluate protein purity. The topics primarily focus on methods employed to characterize the physicochemical properties of targeted proteins. We will begin by discussing important aspects of protein structure taken into consideration when purifying a protein of interest. We will then provide guidelines for selecting appropriate purification methods and evaluating purity using qualitative and quantitative techniques.
iGEM Foundation
The International Genetically Engineered Machine (iGEM) Foundation is an independent, non-profit organization dedicated to the advancement of synthetic biology, education and competition, and the development of an open community and collaboration. Visit us at igem.org
Contact
hq AT igem DOT org
45 Prospect Street
Cambridge, MA 02139
Due to COVID-19, iGEM staff are working remotely and cannot receive phone calls.
Please contact us by email.
