Engineering/Test

Test

On this page you will find information on: Introduction, How to use Protocols.io, and iGEM's Standard Protocols

Introduction

Design testing by good measurement is essential to ensure that work done by iGEM teams can be used by future teams and the community as a whole.

At iGEM, we believe that good measurements are the foundation on which scientific progress and societal impact are built. It is not enough to simply perform experiments or build DNA constructs, instead iGEM teams (and researchers in general) should carefully consider what aspects of a device/system need to be characterised, and the purpose of any experiments performed. It is also essential to realise that good measurement doesn't stop once an experiment has been performed; the way in which data is presented is also very important. Ensuring that appropriate data visualization, statistical analyses, and units are used, along with careful and complete documentation of how the experiment was performed, will help ensure that future iGEM teams and researchers can make the most of your work.

Measurement should be considered early on in the design of a team's project, and should guide decisions as the project is executed. Teams can also engage in a wide variety of other measurement activities, including collaborating to test reproducibility, design new and better assays, and create low-cost instruments to make measurement more accessible.

The measurement aspect of a project is also an opportunity for team members to explore the twin questions of knowledge at the heart of science and engineering. How do we know what we know? How can we predict what will happen when we create something new? We must grapple with these questions if we wish to make responsible choices both as individuals and as a society, and the work done by iGEM teams is one of the many components of that effort.

How to use Protocols.io

iGEM is allowing and encouraging teams to use Protocols.io to create and share their methods instead of putting them on their wikis. Protocols.io is an online, open-access tool for collaboratively creating, sharing and discussing protocols. It supports both wet and dry work.

Teams using protocols.io must still adhere to the wiki freeze deadline. Protocols.io allows authors to “publish” their protocols, making them publicly accessible and generating a digital object identifier (DOI), which also functions as an online link to the protocol. Once published, a protocol cannot be edited.

  • Teams using protocols.io must publish their protocols and place the DOI link generated on the methods section of their wiki, making sure judges can see what links will lead to which protocols.
  • Teams can also use these DOI links in their part submissions to describe what protocols the parts were used in.
  • We recommend teams use “iGEM” as a keyword in the protocols to facilitate other teams finding their work in the future.
  • To make the most of the collaborative features provided by protocols.io, we recommend students all sign up individually and create a group on protocols.io for their team.

Note:

Protocols cannot be edited after publication, but new versions can be generated. Judges will only consider the version you publish before the wiki freeze, but you are free to generate new versions after the freeze for future teams to use.

iGEM's Standard Measurement Protocols

Each of these can be accessed on Protocols.io by pressing the Protocol button or in PDF format using the PDF button. Some protocols also have an associated Excel data analysis template, which you can find by pressing the Excel button.

Every lab has different equipment with different settings, and measurements of fluorescence or absorbance are often reported using arbitrary units (AU). These AU values from different labs cannot be directly compared. These protocols are for use with the iGEM Measurement Kit, which each team can create themselves with the purchase of a few components. The iGEM Measurement Kit refers to resources that allow calibration of plate readers for fluorescent intensity and cell density measurements. Once these calibration protocols have been performed, you’ll be able to convert the arbitrary units you produce during your project into standard units. This will make your results much more powerful by making them directly comparable with those of other teams who have also calibrated their equipment.

Measurement Kit Components:

Item Supplier Order Details Website
Microsphere Particles NanoCym 950uM size particles https://nanocym.com/product/silocym/
Fluorescein sodium salt Sigma-Aldrich Product number: 46970 https://www.sigmaaldrich.com/catalog/product/sigma/46970
Texas Red (Sulforhodamine 101 acid chloride) Sigma-Aldrich Product number: S3388 https://www.sigmaaldrich.com/catalog/product/sigma/s3388

iGEM 2020 Plate Reader Abs600 (OD) Calibration

Use this protocol to be able to convert 600 nm absorbance measurements into an estimated equivalent number of cells. Example data

iGEM 2020 Plate Reader Green Fluorescence Calibration

Use this protocol to be able to convert green fluorescence measurements into an estimated equivalent fluorescent molecules per cell. Example data

iGEM 2020 Flow Cytometry Fluorescence Calibration

Use this protocol to convert measurements of flourescence in your flow cytometer to MEFL units. Example data

iGEM 2020 Plate Reader Red Fluorescence Calibration

Use this protocol to be able to convert red fluorescence measurements into an estimated equivalent fluorescent molecules per cell.

Other iGEM Measurement Protocols

Flow Cytometry Cell Size Calibration

Use this protocol to convert flow cytometry forward scatter to Eμm.

Abs600 Inter-equipment Conversion with LUDOX

Use this protocol to be able to convert absorbance (OD600) data from your plate reader into a comparable OD600 measurement which would be obtained in a spectrophotometer.

Conversion of OD600 to Colony Forming Units (CFUs)

Use this protocol to be able to convert your OD600 measurements into CFUs.

Cell Measurement Protocol

A standard testing protocol for various parts in the registry, using a plate reader.

Have a resource to contribute?

Please email the Engineering Committee at engineering [AT] igem [DOT] org and provide links to material with a short description. We’ll check it out and if we believe it will be helpful, we’ll add it to this page!