Team:Grenoble/Human Practice/BSS

From 2012.igem.org

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<section>
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<a href="https://2012.igem.org/Team:Grenoble/Human_Practice/BSS#1">Design</a> •
 +
<a href="https://2012.igem.org/Team:Grenoble/Human_Practice/BSS#2">Other teams opinion</a> •
 +
<a href="https://2012.igem.org/Team:Grenoble/Human_Practice/BSS#3">Collaboration</a> •
 +
<a href="https://2012.igem.org/Team:Grenoble/Human_Practice/BSS#4">Why is this important ?</a> •
 +
<a href="https://2012.igem.org/Team:Grenoble/Human_Practice/BSS#5">Improvement</a>
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</section>
 +
<section>
<section>
<h1>BioBrick Safety Sheet (BSS)</h1>
<h1>BioBrick Safety Sheet (BSS)</h1>
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<br/>
<br/>
<section>
<section>
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<h2>Design of the Biobrick Safety Sheet</h2>
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<h2 id="1">Design of the Biobrick Safety Sheet</h2>
<br/>
<br/>
Synthetic biology is a new and emerging discipline with a lot of potential but also with an important part of risk. But unlike other disciplines such as chemistry there is no standard and reliable way of assessing risk!  
Synthetic biology is a new and emerging discipline with a lot of potential but also with an important part of risk. But unlike other disciplines such as chemistry there is no standard and reliable way of assessing risk!  
</br>
</br>
</br>
</br>
-
Where does every component of our Biobrick come from? What was its initial function in nature? Should we fear a particular interaction with another component? Has a particular mutation been observed? These are the question that each biologist has asked himself at least once but couldn’t find an answer because it’s too complicated and exhausting!
+
Where does every component of our Biobrick come from? What was its initial function in nature? Should we fear a particular interaction with another component? Has a particular mutation been observed? These are the question that each biologist has asked himself at least once but could not find an answer because it is too complicated and exhausting!
</br>
</br>
</br>
</br>
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</br>
</br>
<ul><li>A section where we specify the biobrick, the origin and the initial function of each component in nature (promoter, rbs, coding sequence…), the intrinsic safety of each component and the other components it could interact with.<br/><br/></li>
<ul><li>A section where we specify the biobrick, the origin and the initial function of each component in nature (promoter, rbs, coding sequence…), the intrinsic safety of each component and the other components it could interact with.<br/><br/></li>
-
<li>A section that lists: the random interactions we observed during the construction, the results of at least one experiment that considers the environment in which the biobrick will evolve and other experiments we think it’s important to consider in order to assess the biobrick risk level.</li></ul>
+
<li>A section that lists: the random interactions we observed during the construction, the results of at least one experiment that considers the environment in which the biobrick will evolve and other experiments we think it is important to consider in order to assess the biobrick risk level.</li></ul>
</br>
</br>
</br>
</br>
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</section>
</section>
<section>
<section>
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<h2>Other teams opinion about BSS</h2>
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<h2 id="2">Other teams opinion about BSS</h2>
<br/>
<br/>
-
As we wanted the BSS structure to be clear and concise. We early contacted as many iGEM teams as possible in order to have feedbacks about the idea and possible improvements. For this purpose we used matchmaker <a href="https://2012.igem.org/Team:NTNU_Trondheim/Matchmaker  
+
As we wanted the BSS structure to be clear and concise, we early contacted as many iGEM teams as possible. For this purpose we used the NTNU Trondheim  <a href="https://2012.igem.org/Team:NTNU_Trondheim/Matchmaker  
-
">click here</a> by posting a request. We’ve also sent an e-mail to all the European teams.
+
">matchmaker</a> by posting a request. We have also sent an e-mail to all the European teams.
</br>
</br>
</br>
</br>
-
You can find below the list of the teams that gave feedbacks.
+
You can find below the list of the teams that gave answers.
</br>
</br>
</br>
</br>
<center><img src="https://static.igem.org/mediawiki/2012/7/70/Photo_nadia_grenoble_4.png" alt="" />
<center><img src="https://static.igem.org/mediawiki/2012/7/70/Photo_nadia_grenoble_4.png" alt="" />
</br>
</br>
-
<span class='legend'> We've already had feedbacks about the BSS from Virginia, Edinburgh, Groningen and Paris iGEM Teams </span></center>
+
<span class='legend'> We have already had answers about the BSS from Virginia, Edinburgh, Groningen and Paris iGEM Teams </span></center>
</br>
</br>
 +
</br>We gratefully thank these teams.
</br>
</br>
-
What appears is that many other teams think that the Registry of Standard Biological Parts, gives already  many information that the BSS also gives. Thus it is considered by many teams as another way to store the biological information. What was blamed , is that  there is no link between what already exists and this new sheet. Moreover some of those teams said that this BioBrick Safety Sheet could be seen as a competitor to the preexisting Registry…
 
</br>
</br>
 +
According to Edinburgh, what appears for them and probably also for other teams is that the Registry of Standard Biological Parts gives already much information that the BSS also stored. Thus it could be considered as another way to store biological information. What was blamed is that there is no link between what already exists and this new sheet. Moreover it was said that this BioBrick Safety Sheet could be seen as a competitor to the preexisting Registry, even it is not the purpose.
 +
</section>
 +
<section>
 +
<h2 id="3">A project linked with other iGEM Teams: collaboration</h2>
</br>
</br>
-
Because of these feedbacks we managed to revise our project. Indeed our goal is not to set up a concurrent system, but more to improve what already exists.
+
As far as the two last teams are concerned, we made a videoconferencing with iGEM Paris Bettencourt team.
 +
Thanks to the partnership with them, we had more information about the point of view of another iGEM Team. Moreover we discovered that our idea is complementary to their work.  While they are trying to design tools to improve the safety and work on a way to quantify the biological risk, we are dealing with the information required to assess the risk. Our project is the base of the risk analysis.  
</br>
</br>
</br>
</br>
-
Helped by other teams, we saw that it would be an utopia to have teams using directly the BSS.  That is why we worked on a way to link our idea to the Registry of Standard Biological Parts.
+
The structuring of the information would be great for their project because by designing tools, it is also important to know if they would be relevant. Thus our project is in accordance with what is currently done.
-
A way to do it would be to add another tab on BioBrick webpage that could be named Safety.  
+
-
In this part all the information about the way the BioBrick has been used environments in which it would evolve would be listed. In addition, drawbacks and bad effects that appeared would be explained.
+
</br>
</br>
</br>
</br>
-
But in the same time, it seems practical to keep the sheet available for teams, if they need to communicate on what they are doing or using. We should not forget that the website is free for everyone. Therefore other people and especially non biologists can have access to the information. This tool would be then a way of improving the comprehension of synthetic biology for the uninitiated.  
+
Their feedbacks finally lead to a whole <b>collaboration with Paris Bettencourt</b>. Indeed, once the first skype session organized, we kept contact and could give them feedbacks about their own project. We also had the opportunity to move to Paris on Sunday the 16th and participate to the debate they organized about a possible regulation of GMOs use. You can find <a href="https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Debate">here</a> more details about the event.  
</br>
</br>
</br>
</br>
 +
But they advised us the same thing as the Edinburgh team, that is to say that we should put a link with what already exists.
 +
</br>
 +
</br>
 +
Because of these feedbacks we managed to revise our project. Indeed our goal is not to set up a concurrent system, but more to improve what already exists.
 +
</br>
 +
</br>
 +
We saw that it would be an utopia to have teams using directly the BSS. That is why we worked on a way to link our idea to the Registry of Standard Biological Parts. A way to do it would be to add another tab on BioBrick webpage that could be named Safety. In this part all the information about the way the BioBrick has been used environments in which it would evolve would be listed. In addition, drawbacks and bad effects that appeared would be explained.
 +
</br>
 +
</br>
 +
As it seemed practical, we decided to keep the sheet available for teams, if they need to communicate on what they are doing or using. Therefore other people and especially non biologists can have access to the information.
 +
</br>
 +
</br>
 +
The last feedback was send by the team of Virginia. To sum up they gave to us  following advices.
 +
</br>
 +
</br>
 +
<ul>
 +
    <li>Consider keyword tagging, so that experts in specific contexts can go to the registry and rapidly find a narrower list of parts of particular interest to review. </li>
 +
    <li>Include links to a list of biosafety resources</li>
 +
    <li>DIYBio list of biosafety resources (see for example <a href="http://www.sandia.gov/ram/BIORAM.htm" target="_blank"> Sandia National Laboratories</a> - risk assessment framework </li>
 +
    <li>Include compatibility with relevant safety regulations -- global biosafety consensus? NIH? </li>
 +
    <li>Expand and standardize the symbol library on the sheet, at least to match the partsregistry </li>
 +
    <li>Potentially look at protein interaction networks to predict non-intuitive implications</li>
 +
</ul>
 +
</br>
 +
</br>
 +
These advices came relatively late, so we intend to use them for later. 
</section>
</section>
<section>
<section>
-
<h2>Why is this important ?</h2>
+
<h2 id="4">Why is this important ?</h2>
</br>
</br>
This approach is important because a lot of projects intend to use microorganisms outside laboratories.  it is essential to make research on protection means. But it is even more necessary to know which hazards we should expect. Therefore having information on what would happen makes protections more efficient.  
This approach is important because a lot of projects intend to use microorganisms outside laboratories.  it is essential to make research on protection means. But it is even more necessary to know which hazards we should expect. Therefore having information on what would happen makes protections more efficient.  
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</section>
</section>
<section>
<section>
-
<h2>A project linked with other iGEM Teams: collaboration</h2>
+
<h2 id="5">Improvement of the project and of the BSS</h2>
</br>
</br>
-
Thanks to the partnership with iGEM Paris Bettencourt team, we had more information about the point of view of another iGEM Team. Moreover we discovered that our idea is complementary to their work.  While they are trying to design tools to improve the safety and work on a way to quantify the biological risk, we are dealing with the information required to assess the risk. Our project is the base of the risk analysis.  
+
What was underlined during the presentation of this BSS is that the main sheet is turned to the experiment aspect, whereas it is also important to focus on the theoretical aspect. Therefore we added a part in which it is asked to think about what possible interactions between BioBricks could occur.
</br>
</br>
</br>
</br>
-
The structuring of the information would be great for their project because by designing tools, it is also important to know if they would be relevant. Thus our project is in accordance with what is currently done.
+
If this is correctly done, the perspective would probably lead the project to the creation of a software that would collect every possible interaction.  
</br>
</br>
</br>
</br>
-
Their feedbacks finally lead to a whole <b>collaboration with Paris Bettencourt</b>. Indeed, once the first skype session organized, we kept contact and could give them feedbacks about their own project. We also had the opportunity to move to Paris on Sunday the 16th and participate to the debate they organized about a possible regulation of GMOs use. <a href="https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Debate">Click here</a> if you want more details about the event.
+
for example, it is interesting to explain risks due to proteins, as:
-
</section>
+
<ul>
-
<section>
+
    <li>its own toxicity (e.g. toxins)</li>
-
<h2>Improvement of the project and of the BSS</h2>
+
    <li> toxicity associated to a substrate (oxygenase) or product(peroxydase)</li>
 +
    <li>its selectivity (adelylade cyclase)</li>
 +
</ul>
</br>
</br>
-
What was underlined during the presentation of this BSS is that the main sheet is turned to the experiment aspect, whereas it is also important to focus on the theoretical aspect. Therefore we added a part in which it is asked to think about what possible interactions between BioBricks could occur.
 
</br>
</br>
 +
It is also interesting to explain risks associated to transcription factors , as:
 +
<ul>
 +
    <li>DNA biding specificity (activation or inhibition)(e.g. ompR)</li>
 +
</ul>
</br>
</br>
-
If this is correctly done, the perspective would probably lead the project to the creation of a software that would collect every possible interaction.
+
</br>
 +
risk associated to promoters as:
 +
<ul>
 +
    <li>transcriptional factors specificity</li>
 +
</ul>
</section>
</section>
<section>
<section>
-
<h3>For the moment our BSS looks like <a href="https://static.igem.org/mediawiki/2012/c/c5/BSS4.pdf" target="_blank">this</a>.</h3>
+
<h3>For the moment our BSS look like <a href="https://static.igem.org/mediawiki/2012/6/6d/BSS_presentation.pdf" target="_blank">this</a>. And you can find how to complete it <a href="https://static.igem.org/mediawiki/2012/c/c5/BSS4.pdf" target="_blank">here</a>. You can find our filled BSS <a href="https://2012.igem.org/Team:Grenoble/Safety/Download#3">here</a></h3>
</section>
</section>
</div>
</div>

Latest revision as of 01:35, 27 September 2012

iGEM Grenoble 2012

iGEM Grenoble iGEM
iGEM 2012
main page
Project
Design • Other teams opinion • Collaboration • Why is this important ? • Improvement

BioBrick Safety Sheet (BSS)


Design of the Biobrick Safety Sheet


Synthetic biology is a new and emerging discipline with a lot of potential but also with an important part of risk. But unlike other disciplines such as chemistry there is no standard and reliable way of assessing risk!

Where does every component of our Biobrick come from? What was its initial function in nature? Should we fear a particular interaction with another component? Has a particular mutation been observed? These are the question that each biologist has asked himself at least once but could not find an answer because it is too complicated and exhausting!

To release your pain the Grenoble Team proposed to include safety informations in the registry part. Thus every team and every biologist would be able to have access to these information and even add his own observations and experimental results to enlarge the database.

To sum up, the Biobrick Safety Sheet includes mainly two sections:
  • A section where we specify the biobrick, the origin and the initial function of each component in nature (promoter, rbs, coding sequence…), the intrinsic safety of each component and the other components it could interact with.

  • A section that lists: the random interactions we observed during the construction, the results of at least one experiment that considers the environment in which the biobrick will evolve and other experiments we think it is important to consider in order to assess the biobrick risk level.


So, if every iGEM team cooperates and accepts to fill BSS, over years, the iGEM community will have access to a large biobricks database with the possible interactions for each biobrick in different environments. This will help have a deeper idea of the biobrick potential risk and thus enhance safety in synthetic biology.

Furthermore this BSS was also designed to help teams communicate with other laboratories during their projects. Indeed what has to be done when there is a lack of information is to contact experts in biology and synthetic biology. They may have a deeper point of view than iGEM team members. This can be an advantage for the project as well as the improvement of the safety. But if we want to have fruitful links with other partners, we have to put in place an efficient and understandable communication system for both parts. And the BSS was mainly designed for this.

Other teams opinion about BSS


As we wanted the BSS structure to be clear and concise, we early contacted as many iGEM teams as possible. For this purpose we used the NTNU Trondheim matchmaker by posting a request. We have also sent an e-mail to all the European teams.

You can find below the list of the teams that gave answers.


We have already had answers about the BSS from Virginia, Edinburgh, Groningen and Paris iGEM Teams


We gratefully thank these teams.

According to Edinburgh, what appears for them and probably also for other teams is that the Registry of Standard Biological Parts gives already much information that the BSS also stored. Thus it could be considered as another way to store biological information. What was blamed is that there is no link between what already exists and this new sheet. Moreover it was said that this BioBrick Safety Sheet could be seen as a competitor to the preexisting Registry, even it is not the purpose.

A project linked with other iGEM Teams: collaboration


As far as the two last teams are concerned, we made a videoconferencing with iGEM Paris Bettencourt team. Thanks to the partnership with them, we had more information about the point of view of another iGEM Team. Moreover we discovered that our idea is complementary to their work. While they are trying to design tools to improve the safety and work on a way to quantify the biological risk, we are dealing with the information required to assess the risk. Our project is the base of the risk analysis.

The structuring of the information would be great for their project because by designing tools, it is also important to know if they would be relevant. Thus our project is in accordance with what is currently done.

Their feedbacks finally lead to a whole collaboration with Paris Bettencourt. Indeed, once the first skype session organized, we kept contact and could give them feedbacks about their own project. We also had the opportunity to move to Paris on Sunday the 16th and participate to the debate they organized about a possible regulation of GMOs use. You can find here more details about the event.

But they advised us the same thing as the Edinburgh team, that is to say that we should put a link with what already exists.

Because of these feedbacks we managed to revise our project. Indeed our goal is not to set up a concurrent system, but more to improve what already exists.

We saw that it would be an utopia to have teams using directly the BSS. That is why we worked on a way to link our idea to the Registry of Standard Biological Parts. A way to do it would be to add another tab on BioBrick webpage that could be named Safety. In this part all the information about the way the BioBrick has been used environments in which it would evolve would be listed. In addition, drawbacks and bad effects that appeared would be explained.

As it seemed practical, we decided to keep the sheet available for teams, if they need to communicate on what they are doing or using. Therefore other people and especially non biologists can have access to the information.

The last feedback was send by the team of Virginia. To sum up they gave to us following advices.

  • Consider keyword tagging, so that experts in specific contexts can go to the registry and rapidly find a narrower list of parts of particular interest to review.
  • Include links to a list of biosafety resources
  • DIYBio list of biosafety resources (see for example Sandia National Laboratories - risk assessment framework
  • Include compatibility with relevant safety regulations -- global biosafety consensus? NIH?
  • Expand and standardize the symbol library on the sheet, at least to match the partsregistry
  • Potentially look at protein interaction networks to predict non-intuitive implications


These advices came relatively late, so we intend to use them for later.

Why is this important ?


This approach is important because a lot of projects intend to use microorganisms outside laboratories. it is essential to make research on protection means. But it is even more necessary to know which hazards we should expect. Therefore having information on what would happen makes protections more efficient.

Add to this, if we take a look at the number of iGEM teams that have competed since 2006, we notice that it is increasing steadilyand if the raise keeps the same we should have almost 350 teams in 2018.



Considering that each team uses around 10 BioBricks for their project, the number of BioBricks used each year would easily reach 3500.



Thus, it would become more and more difficult to find the required information about the risk assessment.

Last but not least biological systems are more and more complicated and need even more BioBricks. The number of BioBricks used would probably exceed the expected value.

For all these reasons, it is time to rationalize way to assess the risk. And in this purpose the first thing to do is to store the useful information in the clearest way. Our idea is then to link the BSS with the Registry of Standard Biological Parts.

Improvement of the project and of the BSS


What was underlined during the presentation of this BSS is that the main sheet is turned to the experiment aspect, whereas it is also important to focus on the theoretical aspect. Therefore we added a part in which it is asked to think about what possible interactions between BioBricks could occur.

If this is correctly done, the perspective would probably lead the project to the creation of a software that would collect every possible interaction.

for example, it is interesting to explain risks due to proteins, as:
  • its own toxicity (e.g. toxins)
  • toxicity associated to a substrate (oxygenase) or product(peroxydase)
  • its selectivity (adelylade cyclase)


It is also interesting to explain risks associated to transcription factors , as:
  • DNA biding specificity (activation or inhibition)(e.g. ompR)


risk associated to promoters as:
  • transcriptional factors specificity

For the moment our BSS look like this. And you can find how to complete it here. You can find our filled BSS here

Retrieved from "http://2012.igem.org/Team:Grenoble/Human_Practice/BSS"