Difference between revisions of "Tracks/Measurement/Interlab study"

 
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<h1>2016 iGEM InterLab Measurement Study</h1>
 
<h1>2016 iGEM InterLab Measurement Study</h1>
 
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Results of the 2016 interlab study:
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Congratulation to all of the 92 teams who participated in this year's interlab study, and who helped contribute to a momentous result: high-precision replication of fluorescence measurements in equivalent units around the world!
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During iGEM we showed preliminary analysis of the results in the InterLab study workshop, and are posting the slides online here as well for everybody to see: <a href="https://static.igem.org/mediawiki/2016/d/dd/IGEM2016-Interlab-Results-Presentation.pdf">iGEM 2016 Interlab Results Presentation</a>
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<p><b><font color="purple">InterLab Sign up Deadline: June 30, 2016. </b> Email <i>measurement AT igem DOT org</i> to sign up!</p></font></p>
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<ul><b><i>Please note: this email will reach the entire Measurement Committee. Please wait for either Jake, Markus, or Traci to reply before sending any other emails to iGEM HQ to avoid confusion!</b></i></ul><br>
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<p><b><font color="purple">Data Submission Deadline: September 2, 2016. </b></font><br>
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Over the past two years, iGEM has advanced the frontiers of science with the two biggest interlaboratory studies even done in synthetic biology.  These studies establishing a baseline for replicability of fluorescence measurements and identified likely key sources of error, and have now been published as an open-access journal article in PLOS ONE.  
 
Over the past two years, iGEM has advanced the frontiers of science with the two biggest interlaboratory studies even done in synthetic biology.  These studies establishing a baseline for replicability of fluorescence measurements and identified likely key sources of error, and have now been published as an open-access journal article in PLOS ONE.  
 
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To read the article, you can either click on the image to the right or go directly to the following URL: http://dx.doi.org/10.1371/journal.pone.0150182.
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To read the article, you can either click on the image to the right or go directly to the following URL: <a href="http://dx.doi.org/10.1371/journal.pone.0150182">http://dx.doi.org/10.1371/journal.pone.0150182</a>.
 
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<h2>This sounds great! How does my team sign up?</h2>
 
<h2>This sounds great! How does my team sign up?</h2>
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Sign up by sending an email to <b><i>measurement (at) igem (dot) org</b></i> with your team name and an email address we can use to contact you during the season.  
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Sign up by sending an email to <b><i>measurement (at) igem (dot) org</b></i> with your team name and an email address we can use to contact you during the season. The sign up deadline is <b><font color=purple>June 30th, 2016</b></font color>.
  
 
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<h2>2016 InterLab Kit</h2>
 
<h2>2016 InterLab Kit</h2>
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This year, we are providing teams with the <a href="http://parts.igem.org/Help:InterLab_Measurement_Kit">InterLab Measurement Kit</a> in the Distribution Kit that teams will receive from iGEM HQ. This is meant to make participating in the InterLab easier, as it removes cloning steps from the process. (For teams who still wish to clone the InterLab parts, please send an email to <b><i>measurement (at) igem (dot) org</b></i> for instructions.)
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This year, we are providing teams with all of the devices they will need for the InterLab Study. Along with the Distribution Plates, teams will receive an InterLab Kit from iGEM HQ in the Distribution Kit. For more details, please read the documentation for our <a href="http://parts.igem.org/Help:InterLab_Measurement_Kit">2016 InterLab Measurement Kit</a> (URL: http://parts.igem.org/Help:InterLab_Measurement_Kit). This kit is meant to make participating in the InterLab easier, as it removes cloning steps from the process. (For teams who still wish to clone the InterLab parts, please send an email to <b><i>measurement (at) igem (dot) org</b></i> for instructions.)
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The <a href="http://parts.igem.org/Help:InterLab_Measurement_Kit">InterLab Measurement Kit</a> includes:
 
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<h2>InterLab Protocols and Forms</h2>
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<p>Teams who participate in the 2016 InterLab Study are asked to follow the protocols below and to submit data using the forms and files provided. Teams can choose to follow one or both of these protocols! You can also decide to use a different instrument if you cannot access a plate reader or flow cytometer. Please email us at <i>measurement (at) igem (dot) org</i> to set up an alternative experiment.
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Please note: the protocols have been created using Google Forms. If you require an alternative / cannot view them, please email us at <i>measurement (at) igem (dot) org</i> for an alternative file format.
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Prior to starting the protocols below, please transform the 5 plasmids (Positive Control, Negative Control, Test Device 1, Test Device 2, and Test Device 3) from the <a href="http://parts.igem.org/Help:InterLab_Measurement_Kit">InterLab Measurement Kit</a> into the strain of <i>E. coli</i> you plan to use. We recommend using our <a href="http://parts.igem.org/Help:Protocols/Transformation">Transformation Protocol</a>, but any plasmid transformation protocol should work well if you have an alternative. <br><br>
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<b>Important Notes</b>
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<ol>Each plasmid tube contains 10uL of 100pg/uL concentrated plasmid DNA in Qiagen's <a href="https://www.qiagen.com/us/shop/lab-basics/buffers-and-reagents/buffer-eb/#orderinginformation">Buffer EB</a></ol>
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<ol>Remember to SPIN DOWN each tube prior to use to collect all liquid at the bottom of your tube.</ol>
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<ol>Each device is in the <a href="http://parts.igem.org/Part:pSB1C3">pSB1C3</a> plasmid backbone.</ol>
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<ol>If you have any problems with your Measurement Kit tubes (ex: you have an empty tube), please email Traci (traci AT igem DOT org) for help.</ol>
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<p><ul><b>Extra Credit:</b> For extra credit, figure out a way to improve on one of the protocols below.  Examples of improvements could include improving measurement precision, making a protocol easier or cheaper, or creating ways to validate that a protocol has gone right or to debug a protocol that goes wrong. All teams who make such an improvement will receive additional recognition, and all improvements will be considered for adding into iGEM's recommended protocols!</p>
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Once your cells are transformed and you have colonies, you can start the protocols below!
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<p>Data for the interlab study should be submitted by September 2nd, 2016.
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      Plate Reader
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        Flow Cytometer
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Latest revision as of 19:23, 15 November 2016


2016 iGEM InterLab Measurement Study

Results of the 2016 interlab study: Congratulation to all of the 92 teams who participated in this year's interlab study, and who helped contribute to a momentous result: high-precision replication of fluorescence measurements in equivalent units around the world! During iGEM we showed preliminary analysis of the results in the InterLab study workshop, and are posting the slides online here as well for everybody to see: iGEM 2016 Interlab Results Presentation

InterLab Sign up Deadline: June 30, 2016. Email measurement AT igem DOT org to sign up!

    Please note: this email will reach the entire Measurement Committee. Please wait for either Jake, Markus, or Traci to reply before sending any other emails to iGEM HQ to avoid confusion!

Data Submission Deadline: September 2, 2016.

All of the 2016 iGEM teams are invited and encouraged to participate in the Third International InterLaboratory Measurement Study in synthetic biology. We’re hoping this study will get you excited for iGEM and help prepare you for the summer! Please note: this is an optional and voluntary exercise for all teams.

A Brief History of the InterLab

Over the past two years, iGEM has advanced the frontiers of science with the two biggest interlaboratory studies even done in synthetic biology. These studies establishing a baseline for replicability of fluorescence measurements and identified likely key sources of error, and have now been published as an open-access journal article in PLOS ONE.

To read the article, you can either click on the image to the right or go directly to the following URL: http://dx.doi.org/10.1371/journal.pone.0150182.

Overview for the 2016 InterLab

We aim to improve the tools available to both the iGEM community and the synthetic biology community as a whole. One of the big challenges in synthetic biology is that measurements of fluorescence usually cannot be compared because they are reported in different units or because different groups process data in different ways.

Often we work around this by doing some sort of “relative expression” comparison; however, being unable to directly compare measurements makes it harder to debug engineered biological constructs, harder to effectively share constructs between labs, and harder even to just interpret your experimental controls.

Imagine if somebody asked how tall you were, and you couldn’t say “160 centimeters” but could only say, “10% shorter than my friend”! Without absolute units you cannot even say precisely how much shorter you are!

Goal for the 2016 InterLab

This year, we have two protocols for measuring GFP fluorescence that will result in common, comparable units for teams to test out. We have a major question we want to explore with your help: How close can the numbers be when fluorescence is measured all around the world?

So, can you measure GFP fluorescence somewhere in your lab? Does working on an international, collaborative experiment sound exciting? Then this is the perfect study for you!

This sounds great! How does my team sign up?

Sign up by sending an email to measurement (at) igem (dot) org with your team name and an email address we can use to contact you during the season. The sign up deadline is June 30th, 2016.

Please note: Even if your lab or the organisms you work with mean that you can’t measure GFP from the specific devices provided for this study, we want every team to be able to participate! Please email measurement (at) igem (dot) org and we will work out an alternative.
And remember, all teams who participate in the InterLab study will be acknowledged at the 2016 Giant Jamboree and earn a special InterLab Prize!

2016 InterLab Kit

This year, we are providing teams with all of the devices they will need for the InterLab Study. Along with the Distribution Plates, teams will receive an InterLab Kit from iGEM HQ in the Distribution Kit. For more details, please read the documentation for our 2016 InterLab Measurement Kit (URL: http://parts.igem.org/Help:InterLab_Measurement_Kit). This kit is meant to make participating in the InterLab easier, as it removes cloning steps from the process. (For teams who still wish to clone the InterLab parts, please send an email to measurement (at) igem (dot) org for instructions.)

InterLab Protocols and Forms

Teams who participate in the 2016 InterLab Study are asked to follow the protocols below and to submit data using the forms and files provided. Teams can choose to follow one or both of these protocols! You can also decide to use a different instrument if you cannot access a plate reader or flow cytometer. Please email us at measurement (at) igem (dot) org to set up an alternative experiment.

Please note: the protocols have been created using Google Forms. If you require an alternative / cannot view them, please email us at measurement (at) igem (dot) org for an alternative file format.

Prior to starting the protocols below, please transform the 5 plasmids (Positive Control, Negative Control, Test Device 1, Test Device 2, and Test Device 3) from the InterLab Measurement Kit into the strain of E. coli you plan to use. We recommend using our Transformation Protocol, but any plasmid transformation protocol should work well if you have an alternative.

Important Notes

    Each plasmid tube contains 10uL of 100pg/uL concentrated plasmid DNA in Qiagen's Buffer EB
    Remember to SPIN DOWN each tube prior to use to collect all liquid at the bottom of your tube.
    Each device is in the pSB1C3 plasmid backbone.
    If you have any problems with your Measurement Kit tubes (ex: you have an empty tube), please email Traci (traci AT igem DOT org) for help.


    Extra Credit: For extra credit, figure out a way to improve on one of the protocols below. Examples of improvements could include improving measurement precision, making a protocol easier or cheaper, or creating ways to validate that a protocol has gone right or to debug a protocol that goes wrong. All teams who make such an improvement will receive additional recognition, and all improvements will be considered for adding into iGEM's recommended protocols!


Once your cells are transformed and you have colonies, you can start the protocols below!

Data for the interlab study should be submitted by September 2nd, 2016.

Plate Reader
Flow Cytometer