Team:Grenoble/HumanPractice/developing

To resolve this communication difficulty and to facilitate the understanding and collaboration between us (modelers and biologists), we have explored means to develop a tool that allows us to carry out our project.

For this purpose we prepared two educational flyers:

• Flyer "Modeling for Biologists" which was realized by the biologists of our team, in order to explain to other biologist the essentials of model building.
• Flyer "Biology for Modelers"" performed by the members of our team involved in computer modeling.

Since our team spent a long period of time to overcome communication difficulties by developing the flyers, we would like to share our solution with present and future iGEM teams. Flyers could then be used by all the interdisciplinary teams during the initial phases, when the subject is going to be debated. It could also be integrated in the iGEM KIT, which may certainly facilitate its accessibility to the concerned teams.

Also, flyers could be used by Universities or even High Schools to explain the basics of synthetic biology and the complementarity between experimental and theoretical approaches in engineering.

1. Modeling for biologists

To elaborate this flyer, we tried to answer at following question : « What does a biologist need to know about modeling basics in order to efficiently collaborate with modelers?”.

Our approach was based on step by step building up of a differential equation construction. This equation expresses the variation of protein concentration as function of time. Below are the details of critical points exposed on this flyer:

1. Building the equation: as a first step, we identify the principal phenomena (synthesis, degradation, repression) and their respective parameters (protein concentration, synthesis rate, constant of degradation) involved in the construction of such equation. For that, we took GFP protein expression as an example.
2. Interpreting the curves: here we showed how to interpret the different cases obtained while resolving the differential equation.
3. Highlighting biologist intervention: finally, we underline the role of the biologist by precisely identifying the critical steps during its interaction with a modeler.

2. Biology for modelers

To elaborate this flyer, we tried to answer at following question: « What does modeler need to know about synthetic biology in order to efficiently work with biologists?”.

Our approach was based on the step by step description of genetic circuit construction. Below are the details of critical points exposed on this flyer:

1. Composition of the circuit: we first identify the main elements (Gene, Promoter, Terminator…) composing a genetic circuit and detail their interactions.
2. Circuit’s reguIation: here we present an example of a regulation network in which LacI and IPTG play the roles of a Respressor and Activator, respectively.
3. Highlighting modeler intervention: finally, we underline the role of the modeler by identifying the critical steps during its interaction with a biologist.

An understanding and consideration of the public perception of our Human Practice work is essential to ensure that we have achieved our fixed objective.

To estimate the educational impact of our flyers, we organized a meeting with 14 students (Graduate and PhD) from various backgrounds (Life Sciences, Engineering and Computer Science). All of them were completely external to our project and studying in fields non related to synthetic biology.

We prepared a quiz to be given to all participants to evaluate their interdisciplinary knowledge. Three major axes were then focused on:

1. Experimental and theorical aspects of a synthetic biology project (we took our system as a study case).
2. Interdisciplinarity in synthetic biology.
3. Composition of the flyers (contents and design).

The experiment was conducted in this way:

- Students were divided into two groups: group (A) received the flyers and group (B), as negative control, did not received them.
- In each group, the participants were paired in order to study the interaction aspect.
- Groups were physically departed to prevent contact during the test.
- The quiz was given to all participants. And at the same time, the flyers were given to the group A.
- All the participants were monitored during the test.
- The answers of the quiz were collected after 45 minutes.

At the end of the test, we also gave the flyers to the participants of group B and ask them whether they would have been useful. Finally, we invited all the participants to debate about interdisciplinarity in such discipline.

By collecting their different opinions and analyzing the videos, we made the following conclusions:

1.Participants of group B (without flyers) showed more difficulties than those of group A to interact and to understand the questions.
2.During the test the flyers were read several times by group A participants, revealing their utility as educational support.
3.The importance of modeling in synthetic biology needed to be more explicitly represented on our flyers. We complete them in this way. The new version is given here.
4. All the participants were convinced that biologists and modelers have to work closely together in order to carry out a project in synthetic biology, concluding that the vision and applications of this emerging field will certainly influence many other scientific and engineering disciplines.

The positive feedback received from the participants encouraged us to renew this experience with 10 students coming from Paris Descartes University by collaborating with iGEM Paris Bettencourt 2011 team. These students have freshly integrated the Master called Interdisciplinary Approach of Living (AIV: Approche Interdisciplinaire du Vivant) from the Center of Interdisciplinary Research (CIR).

The Quiz conditions were similar to those realized in Grenoble, except that for practical reasons, we have prepared numerical quiz. Students could then answered the questions on line.

Concerning the answers about the mechanism of the genetic system, we found that students from group A (Test with flyers) give more precise answers, which is in concordance with the previous results obtained in Grenoble. However, the interaction between students will be studied soon after analyzing the videos documents.

From this experience, we learned how to overcome interaction difficulties between scientists of different fields and foster efficient communication between team members coming. The interdisciplinary approach of synthetic biology made us to enlarge our views on topics that are indeed closely related to our work in iGEM, but that we sometimes forget when we are just ‘doing science and engineering.

Concretely, improve communication between theoricians and experimentalists of the team made us realize the necessity to:

1. Characterize the initial state of the system.
2. Identify the crucial elements of the Toggle Switch and the Quorum Sensing that should be measured.
3. Determine the necessary and sufficient set of parameters that specify context and biological state of our system.