Synthetic Biology and Biosystems Control Lab

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We focus our research on the application of systems engineering and control for synthetic biology and bio-systems, as well as the evaluation and control of bio-processes.

At the laboratory, we work on designing prototypes and the proofs of concept for our developments, ranging from genetic circuits for the regulation of metabolic routes to control algorithms and the evaluation of bioreactors.

Combining computing and experimental capacities, we use the DBTL (design, build, test and learn) circuit of bio-engineering, thanks to our vast experience in the modeling and simulation of biological processes, always taking into account the different participating scales: from biological (genetic) parts, to biological devices, strains and microorganisms and their metabolism, as well as the experimental conditions of bio-processes.

In addition, automated build and test strains come from robotic platforms and the experimental results give feedback to the design phase, using artificial intelligence, machine learning and optimization. Thus, we can learn from these experimental data and improve the model predictions and the factor-response relation in the design.

This totally automated workflow meets all the flexibility requirements for an agile design and thus it is expected to be widely adopted in future biology production systems.

Get to know us better

Contact

Alejandro Vignoni
vignoni@isa.upv.es

We focus our research on the application of systems engineering and control for synthetic biology and bio-systems, as well as the evaluation and control of bio-processes.

At the laboratory, we work on designing prototypes and the proofs of concept for our developments, ranging from genetic circuits for the regulation of metabolic routes to control algorithms and the evaluation of bioreactors.

Combining computing and experimental capacities, we use the DBTL (design, build, test and learn) circuit of bio-engineering, thanks to our vast experience in the modeling and simulation of biological processes, always taking into account the different participating scales: from biological (genetic) parts, to biological devices, strains and microorganisms and their metabolism, as well as the experimental conditions of bio-processes.

In addition, automated build and test strains come from robotic platforms and the experimental results give feedback to the design phase, using artificial intelligence, machine learning and optimization. Thus, we can learn from these experimental data and improve the model predictions and the factor-response relation in the design.

This totally automated workflow meets all the flexibility requirements for an agile design and thus it is expected to be widely adopted in future biology production systems.

Get to know us better

Contact

Alejandro Vignoni
vignoni@isa.upv.es
cof

Equipment

  • OPENTRONS OT-2 ROBOT: Liquid handling robot with two pipette heads with single channel and 8 channel for volumes from 1 to 1000uL. Temperature Module 4-96ºC and capacity for plates up to 96 samples. Magnetic Module.
  • Agilent-Biotek Cytation 3 Cell Imaging Multi-mode Reader.
  • Plate reader and inverted microscope. It supports a slide, 96-well plates and cell culture dishes, hemocytometer, chamber slides.
  • Thermal Cycler Tecne Prime3.
  • Orbital Shaking Incubator Stuart / SI500.
  • Refrigerator -80: Fryka Kältetechnik.
  • Freezers: Liebherr Premium (4 and -20ºC).
  • Memmert oven.
  • Selecta autoclave.
  • Electrophoresis station.
  • Laminar flow cabinet.

Capacities

Our facilities have everything necessary to accelerate the design of biological systems.

With regard to the design, we have specialized software and toolboxes at https://github.com/sb2cl, as well as the cluster of the ai2 Institute.

For the genetic circuit building, we have the OT-2 handler robot, capable of automating processes, such as DNA extraction, serial dilutions, experimental designs, DNA assembly with cloning techniques such as GoldenGate, PCR, and Colony detection PCR.

For the testing tasks, we have the capacity for small-scale microorganism growth and high-throughput measures with the plate reader, as well as obtaining measurements of fluorescence intensity, luminescence, time-resolved fluorescence, fluorescence polarization, filter-based fluorescence, fluorescence with a monochromator and open-field fluorescence imaging, high contrast bright-field, bright-field, phase-contrast (with a lens up to 40x available).

Fluorescence measurements with different colors (green, red, blue) are done in a calibrated manner against standard solutions in order to share the data obtained with several laboratories across the world.