Synthetic Biology (the engineering of biology) is the application of the engineering principles to biology in order to build synthetic biological systems. This is a new and fascinating interdisciplinary field (born in 2000 in MIT Artificial Intelligence Lab), where engineers, physicists, and computer scientists have a new opportunity to apply their engineering concepts and tools: Biology is the new hardware and software that can be programmed.
In our group we address the following research questions:
- Biological information processing: How cells communicate, process biological signals and take decisions?
- Synthetic Biology and DNA Computing: How can we design new smart DNA/RNA computing devices able to operate in vivo?
- Artificial Intelligence in vivo: How to apply artificial intelligence principles to program smart living cellular computers? How to engineer a programmable biocircuit able to learn to classify living cells? How to engineer a programmable living drug?
- Artificial Intelligence in Biology: How to apply evolutionary computing and deep learning tools for the design of better biocircuits and selection of biomarkers?
- Multicellular analog computing: Most biocircuits developed so far are based on Boolean algebra and use a digital/binary abstraction to operate with biological signals. How could we design new robust analog and multicellular biocircuits?
- Individual/agent based models (IBM) for multicellular systems biology: How to simulate interactions between bacteria in a microbial ecosystem? How to use an IBM to help microbiologists to reverse engineer the microbiota and forward engineer probiotics? Can we reprogram the microbiota? How to predict antibiotic resistance and horizontal gene transfer spread in a microbial population using an IBM?
- Bio-design automation and Programmable Biology: We produce software to simulate multicellular genetic circuits (gro simulator) and to automatize biology experiments (BioBlocks language). Computer scientists have portable laptops. Can we engineer portable labs for running biological experiments? We are programming open-source portable biolabs using BioBlocks and Arduino cards.
Our FP7 EU FET-Proactive research projects:
PhD positions available in LIA group. If you are a great programmer (an engineer or physicist) that likes biology and wants to program cells and DNA, code biology or engineer life contact us (candidates should send by email: CV, academic transcripts and a motivation letter). We love people passionate about research that wants to deep into the unknown.
iGEM: We want to assemble a team (biotechnologists + computer scientists) in UPM for next iGEM competitions. Do you want to join us?
Introduction to Synthetic Biology
You may find some documents in this section to introduce the reader to Synthetic Biology:
- Alfonso’s talk in Valencia, Spain, in ISBBC Summer School, June 2017: “Synthetic Biology for computer scientists in 2 hours“.
- Alfonso’s talk in Temuco, Chile – November 2013: “Biología Programable: 18 FAQs sobre Biología Sintética de un informático“. Slides of the talk in pdf (In Spanish).
- Link in Youtube to Alfonso’s talk in Chile: BIOLOGÍA PROGRAMABLE: 18 FAQs (vídeo).
- Alfonso’s talk in Santiago, Chile (Universidad Diego Portales) Nov. 2013- “Programmable Biology: 18 FAQs on Synthetic Biology of a computer scientist“. Slides of the talk in English.
- Alfonso’s talk on Artificial Intelligence in vivo in ESIC, Spain, 2018.
Description of PLASWIRES synthetic biology FP7 FET research project. Report included in UPM Journal, n.28, June 2014 (in Spanish). Report on PLASWIRES in English.
Some introductory material to Synthetic Biology
If you prefer to read:
- Tinkering with Life. By Jef Akst. The Scientist, October 1, 2011.
- Synthetic Life. By W. Wayt Gibbs. Scientific American, May 2004.
- Engineering Life. By the Bio FAB group. Scientific American, June 2006.
- Synthetic Biology: Bits and pieces come to life. James Collins . Nature 483, S8–S10 (01 March 2012) doi:10.1038/483S8a
- Q&A: Circuit capacity. James Collins Nature 483, S11 (01 March 2012) doi:10.1038/483S11a
If you prefer to watch:
- Conferencia en Chile 2013 de Alfonso R. Patón: “Biología Programable: 18 FAQs sobre Biología Sintética de un informático”.
- Synthetic Biology – intro video by Jim Collins. (12 minutes).
- Synthetic Biology Explained (6 minutes).
- Synthetic Biology – intro video (3 minutes).
- Memorias de ADN: Vídeo 1min. de RTVE.ES (Telediario La 1; comentarios Alfonso R. Patón)
- Towards programmable antibiotics and in silico microbiota.
Conference: I International Conference and Workshop: Microbiota: What’s cooking? Place: Padrón, Spain. Date: October 10, 2019.
- Alfonso Rodríguez-Patón talk in a UIMP summer course on August 2019.