iGEM EPFL 2018


With CAPOEIRA the team accomplished to bring one step closer the promise of personalised oncology. However, this work wouldn’t have been possible without the unconditional help and support of many of those wothers. In this page we would like to thank all of these people and acknowledge their contribution in our project.

Idea Conception

The idea of working on cancer came during the brainstorming sessions, during the project ideation session of the team. We investigated the problems that we could target and we talk to a few professors to understand the clinical needs. We thank Prof. Elisa Oricchio for her input in this part of the project.

Laboratory Work

  • All the experiments and assays performed during the project were done by the team members. Due to the immense scope of the project, the lab work was divided into specific subteams each assigned with one part of the project.

  • Moustafa, Violette, Thomas, Laurine and Theophile, worked in the design, production, purification and expression of the encapsulin-based vaccine. Furthermore, they worked on the design of the biobrick parts submitted to IGEM.

  • Daniel and Moustafa, worked on the in-vitro dendritic cell assays for uptake and presentation of antigens.

  • Reza, Cindy, Ahmed and Samuel, developed the ctDNA amplification and detection assays for both testing vaccine efficiency and cancer relapse using CRISPR/Cas12a.
  • Marco and Mehdi, were involved in the design of the miRNA amplification and detection assays with CRISPR/cas12a.

  • Software, Wiki and Design

  • Daniel was responsible for developing the Ginga software to translate whole exome sequencing data into a personalised neoantigen library.

  • Theophile was the main person in charge of designing and arranging the wiki. However, all the team contributed to the content creation and final state of the wiki.

  • Laurine was in charge of designing the team graphic identity, logos and figures for the wiki, poster and presentation, with the help of the rest of the team.

  • Human Practices

    Throughout the project all the members of the team had the chance to participate in the human practice modalities. Most interviews were arranged and organized by the team members and attended by a few of the team members according to availability and relevance to each of the parts of the project.

  • The main contributors to the Human Practice page in the wiki were Laurine, Sam and Daniel. The main contributor to the Entrepreneurship page was Reza.
  • The Symposium of Citizen Sciences Association in Paris and the Ethical Conference in Grenoble was attended by Laurine.

  • Planet Sante Conference and ISREC panel discussion was attended by Laurine and Samuel.

  • The conference Horizons of Cancer Biology and Therapy organised by ISREC was attended by Daniel, Reza and Moustafa.

  • Figure 1.A Art Exhibition organised by Veneta Valeria Gerganova, was attended by major part of the team and the initial collaboration about our planned Synthetic Biology event were done by Laurine and Violette.

  • The 2018 Frontiers Conference at EPFL was attended by all the team members, throughout the different days.

  • The Synthetic Biology symposition at UNIL organised by Alice Berhin was attended by Daniel, Reza and Moustafa.

  • Koniz Summer School Synthetic Biology presentation was organised by Cindy. The workshop using the cell-free kit from 2017 EPFL iGEM team, was instruct by Moustafa, Theophile, Thomas, Violette and Grégoire Michielin.

  • Moustafa, Daniel and Samuel attended the European Meetup in Munich.

  • Thomas represented the team in the Eurasian Meetup hosted in Shenzhen, China.

  • Supervisors

    Sebastian Maerkl is the principle instructor of the 2018 EPFL iGEM Team. His main role was to manage the entire project and also give advice in the direction taken by the team. His help was vital to get funding for the project from our two main sponsors: Nikon and SISF. In addition, he is been able to secure EPFL funding over the years for the IGEM team and we hope this will continue in future years. His guidance in wiki design, presentation and overall technical design decisions of the project have been invaluable for the team. Furthermore, Sebastian Maerkl also provided helpful resources and access to his laboratory, Laboratory of Biological Network characterization (LBNC).
    Grégoire Michielin, Michael Crone and Ivan Istomin were our advisors and instructors and probably the people from outside the team that know the project and its intricacy the best. Their feedback in our design experiments and direction of the project subparts has been incredibly helpful. We specially thank Grégoire Michielin for helping us in the design of the cell free expression system and protein purification, Michael Crone for helping us with cloning, plasmid design and the CRISPR/cas12a assay and Ivan Istomin for helping us with the biobrick design and organising our human practices.

    General Support

  • DLL Laboratory, The 2018 EPFL was hosted at the Discovery, Learning, Laboratory (DLL) at EPFL. The laboratory provided all necessary basic materials and buffers, and most of the measurement equipment used during the project including, the fluorescence plate reader, cell incubator, thermocycler and more.

  • Josiane Smith-Clerc, she is the administrator of the DLL laboratory and provided support for purchasing and ordering new stock of basic laboratory equipment, including pipette tips, buffers, gloves and others.

  • Pierre-Etienne Bourban, co-director of DLL-STI Engineering and chief responsible for the DLL laboratory. Also provided general support of the project and the DLL laboratory.

  • Li Tang, Head of the Laboratory for Biomaterials in Immunoengineering. Allowing us to access his laboratory and resources for the in-vitro dendritic cell assays of our therapeutic.

  • Martine Truan, Secretary of the LBNC laboratory. She helped us with the logistics of the project, mainly keeping track of the team budget, organising the trip to Boston and arranging the deliveries that the team had.

  • The Proteomics Core Facility (PCF) at EPFL. The laboratory helped us carry out the mass-spectrometry identification of our expressed Encapsulin protein. Special thanks to Dr. Marc Moniatte for his expertise in selecting the best method to perform the measurement, setting up the parameters and for helping us in the interpretation of the results.

  • Lab Support

  • Lixia Wei: PhD student at the Laboratory for Biomaterials in Immunoengineering. Helped us designing the protocols and quantities for the in-vitro dendritic cell antigen presentation assays, including an induction to FACS and flow cytometry.

  • Project Support and Advice

  • Prof. Elisa Oricchio. She gave us guidance and support at the beginning of the project to identify a problem in the field of cancer.

  • Prof. Olivier Michielin: He gave us vital insight in understanding the medical need and current practice and therapy for melanoma. He also helped us in directing the project.

  • Difficult Technique Support

  • Jacques Henri Morisod , he is the responsible of the Synthezaser NanoZS from Malvern at the Molecular and Hybrid Materials Characterization Center (MHMC). Jacques, gave the team an introduction on the usage and software of the machine. However, all DLS measurements were performed without his support.
  • Marlies Mürnseer, Technical Application Specialist at Nanolive. Marlies helped us set-up and perform the live holotomographic image of the in-vitro assays of dendritic cell antigen uptake using their Nanolive technology.
  • Kulsum Farshori, Applications Specialist for Education at Nanolive. Kulsum helped us set-up and perform the live holotomographic image of the in-vitro assays of dendritic cell antigen uptake using their Nanolive technology.
  • Lixia Wei, PhD student at the Laboratory for Biomaterials in Immunoengineering. She collaborated with extracting the bone marrow dendritic cells from mice and providing them to us for the in-vitro validation.

  • Wiki Support

  • Pietro Airaghi, student from 2016 EPFL iGEM team. Gave advice on wiki the wiki design and template.

  • Gucevska Natalija, student from 2017 EPFL iGEM team. She gave us insightful information about how to create the wiki and the restrictions and problems that we might have when implementing it.

  • Fundraising Help and Advice

  • Luc Henry, secretary at Hackuarium (Biohacking Space located in Lausanne): He gave the team a few institutions’ contact details and advised on how to fundraise for the synthetic biology symposium.

  • Human Practices Support

  • Prof. Olivier Michielin. Helped us in our integrated human practices and applied design by giving us clinical insight of the melanoma treatment problem.

  • Mme Michèle Constantin. Helped us in our integrated human practices by discussing with us about the need of patient, and the way to imply them in our project.

  • Prof. David Gfeller. Helped us in our integrated human practices and applied design by giving us relevant information on the current state of neoantigen discovery.

  • Prof. Elisa Oricchio. Helped us in our integrated human practices and applied design by helping us identifying problems in the cancer field.

  • Prof. Daniel Speizer. Helped us in our integrated human practices and applied design by giving us insight on the project.

  • Roger Clerc. Helped us in our integrated human practices and applied design by giving us his insight on the project from the industrial perspective.

  • Luc Henry. Helped us in our integrated human practices and applied design by giving us input from the biohacking community around us.

  • Presentation Coaching

  • Prof. Kenneth Oye. Kenneth gave the team very useful feedback about the IGEM competition, our deliverables and tips on how to take our project to the next level.

  • We would also like to thank all the other people, that have contributed in any shape of form to the project. Including all the people that came to see our poster and talk to us during conferences and the presentations we did. Your feedback was always appreciated, and helped us to build CAPOEIRA. Also a million thanks to Barry Ciocco for filming the team, taking the photos and creating the awesome team video.