Measurement/Protocols

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Protocols

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

This year, 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.

Measurement Validation

The iGEM Measurement Committee is now offering measurement validation to all teams!

We are offering measurement validation for three iGEM protocols at this time (details for these are shown below at iGEM's Standard Protocols):

• iGEM 2019 Plate Reader Fluorescence Calibration
• iGEM 2019 Plate Reader Abs600 (OD) Calibration
• iGEM 2019 Flow Cytometry Fluorescence Calibration

If you make measurements using any of these three protocols, you can submit the resulting Excel calculation sheet to the Measurement Committee for validation. To submit your Excel sheets, please email the Excel sheets to us at measurement [AT] igem [DOT] org.

We will use the values in the sheet to generate a "diagnostic report" for you, either validating that your protocol appears to have worked as expected or else indicating potential problems that you may need to address.

We strongly encourage all teams to use these protocols in their project, if possible. Validating measurements can help find problems in protocols or instruments, make it easier to debug your system, make your data easier to use, and increase the future impact of your project!

How to use Protocols.io

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.

These protocols are for use with the iGEM Measurement Kit included in your 2019 Distribution Kit. The Measurement Kit includes one tube of the silica microsphere beads for use in the the Particle Standard Curve with Microspheres protocol and three tubes of fluorescein sodium salt for use in the Fluorescence Standard Curve with Fluorescein protocol.

iGEM 2019 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

PROTOCOL

PDF

EXCEL

iGEM 2019 Plate Reader Fluorescence Calibration

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

PROTOCOL

PDF

EXCEL

iGEM 2019 Flow Cytometry Fluorescence Calibration

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

PROTOCOL

PDF

EXCEL

Other iGEM Measurement Protocols

Flow Cytometry Cell Size Calibration

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

PROTOCOL

PDF

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.

PROTOCOL

PDF

EXCEL

Conversion of OD₆₀₀ to Colony Forming Units (CFUs)

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

PROTOCOL

PDF

EXCEL

Cell Measurement Protocol

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

PROTOCOL

PDF

Have a protocol to contribute?

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