Team:Madrid-OLM/Collaborations

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Collaborations

Parallel to the development of our project, we have made a series of collaborations with other teams in order to obtain mutual benefit.

Attendance to Meet Ups

The meets ups bring several advantages to the teams. It is one of the simplest ways to reach a greater number of people to whom you can explain your project. And therefore they allow you to know first-hand the projects of the rest of the teams so that you can consult and clarify doubts. These meetings also allow for more kindred and powerful collaborations thanks to knowing the rest of the teams in person. And last but not least, they allow you to practice exposing your project with a view to improving the Giant Jamboree.

Our team attended two meet ups that took place in the month of August.

• Marseille

  Mediterranean Meet Up (Marseille)

  

  This meet up took place between Thursday 9 and Friday 10 August in the city of Marseille and was organized by the team of this city, the Aix-Marseille. In it, all the teams from the Mediterranean area were summoned, so they ended up attending both France and Spain. Francisco, Gonzalo and Ivan attended this meet up on behalf of the team.

  The event began with a reception in which all teams had their first informal contact. Subsequently, a 5 minutes presentation of each of the projects was organized, summarizing the concept on which the project was based, the work carried out and the plans to complete it. After the exhibition, each team answered the questions from the jury and the rest of the teams.

  

  Later they invited us to a joint meal. In the afternoon it was organized a sightseeing tour of the city, but due to inclement weather, it had to be suspended, although we could enjoy a pleasant evening of board games and conversations with the rest of the teams. At night a meeting was also organized in a pub to end a day where we had met many new people.

  The second (and last day) had two interesting activities. The first was the meetings with different experts from the university, which privately asked each team about controversial issues. To see if these issues had been taken into account and the possible solutions and consequences were debated.

  

  To close the event, a poster presentation session was held, which was very enriching to know how to present our project in Boston.

  One of the things that were achieved in this meet up was the agreement with the UPF-CRG-Barcelona group to organize an activity in their meet up. An activity that is going to be explained in the following session (and that gave rise to a greater collaboration).

  
  
• Barcelona

  Spanish Meet Up (Barcelona)

  

  This meet up took place between Saturday 18 and Monday 20 August in the city of Barcelona and was organized by one of the two teams of this same city, the UPF-CRG-Barcelona. In it, all the teams from Spain were called, which all but the Valencia team attended. To this meet up they were representing the whole team: Laura, Iván and Francisco. The meet up took place in the Biomedical Research Park of Barcelona (PRBB), the centre where the host team operates and where they started with a welcome activity. This activity consisted of a game where each one of the assistants of each team presented themselves so that the subsequent environment was much more relaxed.

  The next activity was the one organized by our team. In this activity, we proposed to carry out a collaborative guide in which each group would give the main ideas on how they have solved the main problems that have arisen in iGEM. The structure we proposed was followed. We collected these ideas and wrote a complete guide. We explain this collaboration in a later section of the collaborations. After this, some playful activities were carried out on the beach, including volleyball games.

  

  During the morning of the second day, a more detailed presentation of each team's project was made. There were 30 minutes to expose each project in detail. This activity was very useful because the rest of the teams, besides getting to know the details of each project well, could intervene to give advice on how to make the presentations. Each team took a series of points in which they could be reinforced in the face of the presentation of the Giant Jamboree.

  In the afternoon the time was taken to take a tour of the tourist centre of the city and ended up having dinner with a picnic in the Parc Guell. A viewpoint that has views of the entire city at night.

  
  

  During the morning of the last day, to close the meet up, we were able to attend to some enriching expert talks. They offered us their views on synthetic biology and they explained the works in which they are immersed today.

  
  

Back to Meet up Index

Organization of a Meet Up: Another European Meet Up

Reason

After attending two meet ups we realized that these meetings are very enriching experiences in preparation for the Giant Jamboree. One of the main reasons for these meet ups is to get to know and know the project of other teams. Another reason is that it also serves to practice the presentations of the project and its results. And finally, serve to open the network of contacts beyond the contest itself.

We realized that the events to which more teams come are usually the first ones to be organized, and in these, although if they serve to obtain collaborations, do not fulfil so much the function of practising to present the results of your project due to at the beginning of the summer there are no results.

This year the European meet up was on July 20. Date in which novice teams, without sufficient contacts, do not yet know how to deal with these events and do not have the necessary funds to attend. And teams with more experience do not yet have conclusive results. With this context, we proposed this ambitious project: Make another European meet up. We invited all the teams of the continent in mid-September. A date that was supposed to be the best for the organization of new teams and with the possibility of simulating the final event.

Event

The event was organized between September 14 and 16. Although this event was given as much publicity as possible and contact was made with all possible teams in Europe, attendance was low due to several factors:

• - Spain is geographically at one end of Europe and travel is expensive.

• - The teams were short of funds and were saving for the trip to Boston.

• - The event was announced at the beginning of September, many teams did not have room to manoeuvre in their organization to attend

Despite these inconveniences, we had assistance from several participants of some teams (all of them came from within the Spanish territory thanks to the facilities for transport). Although there was an extensive program of activities, these had to be adjusted and reorganized so that the maximum number of attendees could enjoy them.

Activities

The event began on Friday the 14th in the afternoon with the main course. In it, after the reception of the attendees, we gave way to a series of very interesting expert presentations. We were able to count on the attendance of the following personalities:

Victor de Lorenzo

He is one of the Spanish most relevant researchers in the Synthetic Biology field. He works in the National Biotechnology Center (CNB) a part of the Superior Council of Scientific Investigations (CSIC). His laboratory is specialized in solving environmental issues using genetically engineered Pseudomonas putida. He gave us an interesting talk about "Synthetic Biology in the rescue of the planet Earth".

Saul Ares

He is a researcher of the CNB too. His work is central in the mathematical modelling of Synthetic Biology systems. He has also collaborated with previous iGEM teams. His presentation talked about "How do cyanobacteria count to ten".

Krzysztof Wabnik

He is a Young Investigator Researcher of the Center for Biotechnology and Plant Genomics (CBGP) at the Polytechnic University of Madrid (UPM). The group he is leading uses multilevel computer model simulations, synthetic biology experiments and microfluidics. The name of his presentation was: "Combining computational and synthetic biology approaches to understand the dynamics of plant hormone signalling circuits".

After the presentation of the three speakers, we had a space of time in which attendees could discuss and exchange points of view with them on how the field of synthetic biology would evolve.

After the talks a social event was held in which the attending teams could relax having dinner in the centre of Madrid with one of the most typical activities here: go out for tapas.

The second day was inaugurated with a visit to the university to show the facilities where our team works. Also it was explained which procedures are used in each of the sections that were visited.

Subsequently, the presentations of the projects were made. A simulation of the presentation was carried out as it should be done in Boston, to learn how to take the time and try to correct the excesses or lack of time in each section that was exposed.

In the afternoon there was a tour around Madrid, where the most iconic places in the city were shown. And although there were activities scheduled for the next day, this was the activity that closed the meet up, since the attending teams had organized to return to their cities after this tour.

Conclusion

It was an event that few people could attend, due to the conditions explained above, but from which the attendees took many advantages. Holding such an event in September could be much more crowded if it was announced from the beginning of the summer and allowed the rest of the teams to organize around it. As it provides a series of very useful tools for the presentation of Boston.

iGEM guide for new teams in Spain

This initiative emerged in the meet up of Marseille with a view to carrying it out in the meet up of Barcelona. In it, we agreed with the team of UPF-CRG-Barcelona organize an activity in their meet up.

Spain is a country with a low participation of teams in iGEM compared to other European countries. We have been the first team that has emerged in the city of Madrid. At the time of forming the team and carrying out all the activities of the contest, we usually find ourselves with a lack of knowledge. To promote the emergence of new teams in our country and facilitate the resolution of the problems they have at the beginning we decided to create a guide. In this guide, the main aspects of iGEM will be collected and explained and a series of tips will be given to face them. These tips would be a sharing of the way this year had each team to deal with them.

With this idea in mind, we presented the collaboration during the meet up to the rest of the teams and they were all happy to help. The participating teams in this collaboration besides ours are:

• - UPF-CRG-Barcelona.

• - BIO-IQS-Barcelona.

• - Navarra BG (High School).

Initially, we have an index of main points of iGEM and we made a brainstorming where each team could contribute their ways of solving these aspects or could suggest new sections. For this part of the activity, a glass of the centre where the meet up was made was used and each participant was free to put the ideas in the section he wanted, writing on the glass.

After the great participation of all members, a large amount of content was collected and recorded. This content served as the basis for information for the drafting of the final guide. With which we hope it will help the teams of years to come and that, thanks to the availability of this guide, will emerge in more cities.

The final guide can be downloaded at the following link

Guide PDF

Collaboration with Tec-Monterrey Team

We met the Tec-Monterrey team thanks to the fact that they got in touch with us through social networks. As we share a language with this team it has been easier for us to relate and thanks to it, 2 collaborations have come out:

Computational modeling of structures of interest

This has been the most important collaboration with this team. Our team has a member with knowledge of prediction and editing computation of biological molecule structures. They asked us if we could obtain the structure of 3 proteins of interest for their project and perform some animation in which the protein was observed from different points of view. To obtain all the structures of the proteins, the procedure explained in the Computational improvement section was followed:

Protein Structure Predicion

The 3 proteins were the following ones:

• CAS1 and CAS2

  These two proteins often form a complex and have been studied on numerous occasions. The animations are the following:

  

  
• RT EC86

  This protein is a retrotranscriptase. And yet it has not been so studied and its structure had to be predicted.

  

Mentoring in the wiki building

For the reason that in our team there is no one specialized in web design and wiki building, nobody had the necessary knowledge to start with the formation of the wiki. That's why we took advantage of the fact that we already had contact with this team to ask them to mentor us in some decisions when building the wiki. He was asked for help us in understanding how to upload the different files, about the operation of the templates and the scripts.

Mentoring of Valencia Team

For the reason that in our team there is no one specialized in web design and wiki building, nobody had the necessary knowledge to start with the formation of the wiki. Knowing it's not a trivial task, we decided to contact an experience team in iGEM such as Valencia UPV and take advantage of their experience to help us building and working with the wiki.

They offered to mentor us when building our own wiki, as it was a great opportunity to make a collaboration between teams, we happily agreed.

We schedule a meeting via Skype with two of their teammates in charged of software ( Héctor and Blanca) who guided us through the main concerns we had at the moment:

• - A general explanation of how the media wiki platform works.

• - How to upload the different files.

• - The operation of the templates and the scripts.

They also shared with us some useful trick, they have learn along the way, as well as adviced and troublesome points to avoid. This help us to save a lot of time and allow us to start working the soon as possible.

Finally they make some recommendations about web templates that are compatible with the wiki platform and which ones has worked the best for them and where we can get them.