Team:UPF Barcelona/Attributions
Team
Attributions
The UPF Barcelona ARIA iGEM team was responsible for almost every single aspect of the project: from making the initial research proposal, purchasing supplies and assets, coming up with collateral concepts, establishing protocols and executing computational and laboratory work.
Besides from it all, ARIA received help from advisors, instructors, consulting agencies and entrepreneurship mentors. This was greatly appreciated and therefore, we acknowledge it below.
What the team accomplished
ARIA Team
ARIA consists of 11 members who, putting common efforts together, were able to independently bring an end-to-end proposal with their resources. In this context, a natural bound between the wet lab and dry lab was successfully accomplished.
🤠 Auba Fuster Palà:- Team leader: project manager and organizer, team coordination and contact with instructors, mail managing, intra and inter team meetings leading, judging and safety form complementation, bureaucracy and administrative tasks coordination, deadlines and deliverables track and calendar managing.
- Wet lab team co-leader: task organizer, responsible for design, development, and testing of the CRISPR-based biosensors, results analysis, final conclusions, writing documentation and reagent ordering.
- Wiki web main responsible: template design, preparation of whole wiki general architecture and used components, 14 wiki pages design and programming. Wiki documentation writing and almost all wiki documentation revision and correction. Also, ideation, design and programming of ARIA’s Web Portal, and co-maintenance of it.
- Parts registry commander: thinking and designing the part collection and individual parts organization, documentation preparation and uploading to registry.
- Dry lab: model design development and simulations about CRISPR-Cas kinetics.
- Entrepreneurship and experts: searching for sponsors and mentors and documentation preparation for this aim, being a leading voice of scheduled meetings with sponsors, mentors and clinical experts, achieving our two principal sponsors (Arquicalcul and TASALIA), UPFlama participant, UPF Ventures Pitch for start-up investment speaker and grants applier.
- Communication and divulgation: UPF conference organizer, UPF conference and national congress speaker, MWC 4YFN assistant, social media material preparation and twitter account communication manager.
- Video Making: Presentation video interviewee, script writing, and filming coordination. Also, coordination and participation in promotional video.
- Design: help with ARIA logo design (principal designer is Ariadna Palmer, one of our collaborators), merchandising design and ordering, some wiki images design.
- 🍀 Joel Romero Hernández:
- Team leader: focused on promoting holistic approaches, horizontal management mechanisms and a set of integrated common goals. Intra and inter team meetings leading.
- Project Definition: conceived the general architecture of the system.
- Software Development: coordinated the computational research. Designed, implemented, and documented AlphaMine, ARIABuilder, OmegaCore, IRIS, and the Omega Architecture. Contributed to AlphaNeuro’s design. Creator and maintainer of GitHub repository.
- Web Development: concerning the wiki, built the pages for AlphaMine, ARIABuilder, OmegaCore, IRIS, Omega Architecture, Software Overview, Integrated Proof-of-concept and Omega's Results. In addition, integrated AlphaNeuro’s page, and contributed to the editing and revision of other general pages. Ideation, design and programming of ARIA’s Web Portal, and co-maintenance of it.
- Graphic Design: produced visual material and figures used in the wiki, the web portal, the documents, and the social media.
- Video Making: coordinated, written, edited, and animated the promotion video, apart from taking part in its production. Regarding the presentation video, contributed to the script writing and was interviewed on behalf of the computational team. Also made the Introduction and Software-related animations.
- Communication: speaker in the National Student Congress for Antibiotic Resistance and the UPF International Conference on the Tools to Avoid the Future Antibiotic Resistance Pandemic”. Made writing templates for the media divulgation.
- Sponsors, funding, and experts feedback group: concentrated on interacting with potential investors, clinicians, institutions, and researchers. Prepared the documentation to do so and oral presentations to do so. Acted as speaker at a UPF Ventures Pitch for start-up investment.
- 🤯 Teresa Castaño Cerdá:
- Wet Lab team co-leader: responsible for the design, development and testing of the CRISPR-based biosensors. Biomedical and state of the art research. Team organization and lab tasks assignment. In charge of last experiments individual performance (autolysis), results analysis and conclusions.
- Communication: contributed to disseminating our project and science as a whole by being part of the organizing committee and speaker in the National Student Congress for antibiotic resistance and as a participant in the PRBB Open Day communication activity.
- Social Media: Active involvement through social media forming small collaborations, in particular through Instagram.
- Video Making: Presentation video interviewee and script writing for the wet-lab development of the project.
- Wiki content: participation in the wiki design, documentation writing and graphic content creation.
- 🙃 Isaac Capallera Guirado:
- Software development: Responsible for the data extraction for the Alpha modules and the design, implementation and documentation of AlphaNeuro.
- Web development: Contributed to the integration of AlphaNeuro, its results page and the revision and editing of the pages for implementation and design.
- Communication: Speaker in the National Student Congress for Antibiotic Resistance and the UPF International Conference on the Tools to Avoid the Future Antibiotic Resistance Pandemic. Participated in divulging science in schools.
- Video making: Contributed to the script of the presentation video for the computational team. Participated in the promotion and presentation videos.
- Experts feedback group: Interacted with different multi-disciplinary experts to expose the project and receive feedback for future implementations.
- 🦦 Laura Sánchez Ruiz:
- Wiki web main responsible: template design, preparation of whole wiki general architecture and used components, wiki pages design and programming. Wiki documentation writing, revision and correction.
- Parts registry commander: thinking and designing the part collection and individual parts organization, documentation preparation and uploading to registry.
- Laboratory worker: participation in the design, development and testing of the CRISPR-based biosensors.
- Dry lab: model design development and simulations about CRISPR-Cas kinetics.
- Sponsors and funding and divulgation: searching for mentors and potential investors and assisting to scheduled meetings with them. Support in the social media and performing collaborations with other iGEM teams.
- 👽 Álvaro Martínez Marco:
- Entrepreneurship and experts: mentors, clinical experts, KOLs, investors and sponsors seeker, reports elaboration for this aim, contact with external institutions and, companies and grants, head of Start-UPFlama grant, Business Plan creation and market analysis, MWC 4YFN assistant, organizer of Intellectual Property (IP) advisory. Calendar management for some events.
- Communication and divulgation: UPF Conference organizer, LinkedIn responsible and networker, experts feedback organizer.
- Video making: Presentation video filming and final video script participation.
- Wiki content: wiki pages writing, illustrated audiovisual content and figures for the wiki, web page, descriptive documents and social media.
- Software Development: researched public and accessible datasets, extracted useful information by means of web-scratch from national databases, implemented a model for identifying consensus sequences in organismo under study, and documented AlphaNeuro.
- CompLab team player: responsible for the state-of-the-art assessment, ideation and implementation of ideas proposals, contribution to the group’s software advance.
- 🐒 Laisa Bonin Rallo:
- Wet Lab team co-leader: responsible for the design, development and testing of the CRISPR-based biosensors. Biomedical and state of the art research. Team organization and lab tasks assignment. In charge of results analysis and conclusions, as well as protocol and lab notebook compilation.
- Communication: speaker in the UPF ARIA congress, contributed to social media activity.
- Human practices: preparation and performance of scientific divulgation activities in the educational context.
- Video Making: Presentation video interviewee and script writing for the wet-lab development of the project.
- Wiki content: participation in the wiki design, documentation writing and graphic content creation.
- 😴 Francesc Carandell Verdaguer:
- Software development: Responsible for the design, development and implementation of software, specifically in the data acquisition and construction of the Deep Learning models of AlphaNeuro.
- Human practices: Organizator and conductor of the sessions to approach and divulge science to children and teenagers.
- Communication: Participant and interviewee during the PRBB Open Day activity.
- Video making: Presentation video interviewee and script writing for the computational team.
- Wiki content: Contributed to the design, engineering, documentation and results pages of AlphaNeuro, and concepted and designed figures for the aforementioned pages. Also participated in the documentation of several Human practices and Communication pages.
- 🚀 Lídia Martínez Dalmau:
- Wiki web main responsible: programing and construction of ARIA’s webpage and documentation writing.
- Laboratory worker: participation in the building and testing of the CRISPR-Cas12a biosensors.
- Experts feedback: In charge of actively contacting and searching for research and clinical experts to obtain feedback and optimize our system.
- Communication: Involved in dissemination events. Public Engagement and Communication Manager at the social network LinkedIn.
- 🤡 Marc Borràs Sánchez:
- Software development: Responsible for the data acquisition, design, implementation and documentation of AlphaNeuro.
- Video making: Scripted the presentation video as well as participating actively in it representing the computational team.
- Human practices: Responsible for the organization and design of the activities to divulge science in schools and high schools, as well as a conductor of such events.
- Experts feedback group: Participated in meetings with multi-disciplinary clinicians and researchers to expose our project and receive feedback to further improve it.
- 💃🏽 Loreto Coma Brovia:
- Laboratory worker: participation in the building and testing of the CRISPR-Cas12a biosensors, as well as protocol compilation.
- Wiki content: contributed to the creation of wiki designs and social media material.
- Human Practices: organization and performance of scientific divulgation activities in the academic area.
External support
- General support
We are indebted to the instructors Marc Güell Cargol (PI at Translational Synthetic Biology Lab), Javier Macia Santamaría (PI at Synthetic Biology for Biomedical Applications Lab) and Javier Santos Moreno (Postdoc researcher at Translational Synthetic Biology Lab) for landing the project’s proposal.
- Lab support
We are indebted to the Translational Synthetic Biology Lab members Javier Santos Moreno (Postdoc researcher at Translational Synthetic Biology Lab), Nastassia Knödlseder (PhD student at Translational Synthetic Biology Lab), Guillermo Nevot Sánchez (PhD student at Translational Synthetic Biology Lab), Sira Mogas Díez (PhD student at Synthetic Biology for Biomedical Applications Lab) for guiding and mentoring scientifically the roadmap that was desired to be followed in the wet laboratory set up, as well as to Guillem Murciano.
- Project specific support
We are indebted to Cristina Fernández for making possible project management, funding and logistics; to Esther Riambau for her business view orientation; to Albert Domingo for his unconditional and warm support, as well as his UPFlama entrepreneurship program acceptance; to Mari Carmen Cebrián for her photographies and scientific communication in the UPF website; to Regina López for her help with bureaucracy and administration: to Avencia Sánchez-Mejías for her regulatory and organizational support and to Auria Albacete for the mentorship and onepager making advice.
- Project development advice
We are indebted to David Romero (Amazon Web Services) for his kind words and institutional support; to the Drs. Carmen Muñoz, Juan Pablo Horcajada and Alex Smithson for their clinical professional guidance in our main project concept; to Mónica Rodríguez for our PRBB OpenDay presence acceptance; and to La Factoria team for their backup and filming in the final project’s video (Nil and Marcos).
- Fundraising help and advice
We are indebted to Jorge Isern (Isern Patentes y Marcas) for his guidance into the Intellectual Property affairs; to UPF Secretary workers for their networking with the different university departments we wanted to approach and to Marc Santandreu for his put in contact with an investor.
- Difficult technique support
We are indebted to Jordi García-Ojalvo (Dynamical Systems UPF Biology Lab) for his mathematical background help and to Jordi Pla from Ricard Solé’s UPF Complex Systems Lab for his untiring support when needed.
- Wiki support
We are indebted to former iGEM 2020 UPF Team members, Miriam Caravaca, Nerea Álvarez and Quim Martí as well as to Blanca Madorrán Coca for their guidance in the WIKI construction. Jordi Pla, from iGEM 2018, also helped our team with wiki advice.
- Peer-reviewing support
We are indebted to Jairo Mocha, Andreas Meyerhans, Robert Castelo and Pilar Rivera for their constructive review of the preliminary version of our project’s report. And finally, we are very grateful to the rest of staff in the University Pompeu Fabra, without whose sincere support, our project goals would have not been achieved.
- Human practices support
We are indebted to Ferran Llunell for his social media promotions in the UPF channels, to Esteban Martínez (RECONBY UniZar iGEM Team) for being the ambassador of the Zaragoza side from our inter-iGEMs collaboration, to Julio De Oliveira, Nour Hammouch, Isabel Ramón and Manuel Recuerda, AECS (Association of students of health sciences in Catalonia) and FEEF (Spanish Federation of Pharmacy Students) representatives, for their collaboration and willingness to help in the organization of the National Congress on Resistance to Antibiotics; to Pablo Gimeno for his amazing dedication in the production of the final video as well as social media content and backup with the help of his colleagues Francesc Balada and María Linares; to Joaquim Gea for his disposal when organizing students talks; to Institut Bernat Metge and Institut Barri Bessós for allowing us to perform scientific divulgation in their facilities and encouraging students to take part on them.
- Institutional support
Besides it all, we are extremely grateful for every single helper in the chain during the last months, as well as to our institutional support, the University Pompeu Fabra for its opportunity and ongoing support. Specially, to the Experimental Health Sciences Department and Consell Social for the financial funding. Moreover, we also want to thank Barcelona Biomedical Research Park for the amazing work space. In addition, thanks to UPFund for holding our crowdfunding campaign and for all the people who made their little contribution with a donation.
Synthetic biology background at UPF
The brainstorming sessions began in April 2021, being June 2021 the month in which the specific project’s pipeline was defined. The entrance to the PRBB facilities and laboratory itself was produced in July 2021, and the deep development began to be noticeable during August 2021.
iGEM course
Biomedical engineering (GEBM) as well as Human Biology degrees, the ones where the whole ARIA team study at, has this elective subject that begins more than half a year before iGEM Competition starts. Acceptance of students is limited and based on a previous selection process. The GEBM gives UPF students the opportunity to participate in the Competition and push the boundaries of synthetic biology by tackling everyday issues facing the world.
The course is intended to provide the future iGEM contestants with the basic architecture of the competition, as well as with some deeper synthetic biology fundamentals in order to inspire the enrolled students about some fields that can be potential candidates for the main R&D.
The course syllabus can be accessed below:
Synthetic biology course
This subject is an elective course in the 3rd year of the aforementioned academic studies. It has the single prerequisite of having basic knowledge of molecular biology and genetics. The skills it gives are the following:
- Design and analysis of experiments in Synthetic biology
- Understanding and usage of genome editing technologies
- Translational and applied genome engineering
- Entrepreneurship and Industrial Synthetic biology
- Ethical implications of research beyond the laboratory
Finally, the course outcomes are learning the basic technologies to build genetically modified organisms (GMOs), how to design and analyze synthetic biological circuits and studying in detail applications of synthetic biology and some of their professional outcomes: academic research, entrepreneurship, industry, clinical needs and practise.
The course materials can be accessed freely under previous request, since they are distributed by the responsibles of this aforementioned material. The syllabus can be accessed below:
