research-fluigi-1 Design and Simulate Genetic Circuits on a Chip
Fluigi is a Computer Aided Design (CAD) framework for creating microfluidic devices for use in synthetic biology. These devices are designed to help overcome the size and complexity limitations of conventional, intracellular genetic circuit designs by physically separating circuit components and precisely controlling the flow of fluid between them.

Fluigi provides tools to optimize the layout of genetic circuits on a microfluidic chip, to generate the control sequence of the required valves, and to simulate the expected behavior of the chip and the genetic circuits it contains.

This software provides an important step towards the integration of synthetic biological devices with microfluidic platforms.

Check out the entire range of Fluigi Microfluidics Projects.

Key features

  • Define boolean logic expressions to represent circuit inputs and outputs.
  • Minimize expressions to eliminate redundant logic.
  • Convert minimal expressions into logic gates, which represent available genetic circuits.
  • Define constraints for circuit mapping.
  • Place and route genetic circuits on the microfluidic device to optimize chip layout.
  • Generate valve controls to operate flow between genetic circuits.
  • Simulate chip behavior using valve control sequence.

Funding

  • Boston University Dean’s Catalyst Award

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Fluigi is currently under development, and is not yet available for download.

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Selected Fluigi publications:

  • R. Silva, S. Bhatia, and D. Densmore, “A reconfigurable continuous-flow fluidic routing fabric using a modular, scalable primitive,” Lab chip, vol. 16, pp. 2730-2741, 2016. doi:10.1039/C6LC00477F
    [BibTeX] [Abstract] [Download PDF]
    Microfluidic devices{,} by definition{,} are required to move liquids from one physical location to another. Given a finite and frequently fixed set of physical channels to route fluids{,} a primitive design element that allows reconfigurable routing of that fluid from any of n input ports to any n output ports will dramatically change the paradigms by which these chips are designed and applied. Furthermore{,} if these elements are {"}regular{"} regarding their design{,} the programming and fabrication of these elements becomes scalable. This paper presents such a design element called a transposer. We illustrate the design{,} fabrication and operation of a single transposer. We then scale this design to create a programmable fabric towards a general-purpose{,} reconfigurable microfluidic platform analogous to the Field Programmable Gate Array (FPGA) found in digital electronics.

    @Article{C6LC00477F,
    author = {Silva, Ryan and Bhatia, Swapnil and Densmore, Douglas},
    title = {A reconfigurable continuous-flow fluidic routing fabric using a modular{,} scalable primitive},
    journal = {Lab Chip},
    year = {2016},
    volume = {16},
    pages = {2730-2741},
    abstract = {Microfluidic devices{,} by definition{,} are required to move liquids from one physical location to another. Given a finite and frequently fixed set of physical channels to route fluids{,} a primitive design element that allows reconfigurable routing of that fluid from any of n input ports to any n output ports will dramatically change the paradigms by which these chips are designed and applied. Furthermore{,} if these elements are {"}regular{"} regarding their design{,} the programming and fabrication of these elements becomes scalable. This paper presents such a design element called a transposer. We illustrate the design{,} fabrication and operation of a single transposer. We then scale this design to create a programmable fabric towards a general-purpose{,} reconfigurable microfluidic platform analogous to the Field Programmable Gate Array (FPGA) found in digital electronics.},
    doi = {10.1039/C6LC00477F},
    issue = {14},
    publisher = {The Royal Society of Chemistry},
    url = {http://dx.doi.org/10.1039/C6LC00477F}
    }

  • A. Lashkaripour, L. Ortiz, M. Pavan, R. Sanka, and D. Densmore, Cell-free transcription and translation reactions with droplet microfluidics, 2016.
    [BibTeX] [Download PDF]
    @Misc{EBRC16,
    author = {Lashkaripour, Ali and Ortiz, Luis and Pavan, Marilene and Sanka, Radhakrishna and Densmore, Douglas},
    title = {Cell-Free Transcription and Translation Reactions with Droplet Microfluidics},
    howpublished = {talk presented at the Engineering Biology Research Consortium (EBRC)},
    month = Nov,
    year = {2016},
    url = {http://cidarlab.org/wp-content/uploads/2016/11/Ali-EBRC.pdf}
    }

  • H. Huang and D. Densmore, Fluigi: microfluidic device synthesis for synthetic biology, 2014.
    [BibTeX] [Download PDF]
    @Misc{Fluigi_huang_SBB_2014,
    Title = {Fluigi: Microfluidic Device Synthesis for Synthetic Biology},
    Author = {Huang, Haiyao and Densmore, Douglas},
    HowPublished = {poster presented at Synthetic Biology: Boston},
    Year = {2014},
    Journal = {Synthetic Biology: Boston},
    URL = {http://cidarlab.org/wp-content/uploads/2014/12/sb2_poster.pdf}
    }

  • H. Huang and D. Densmore, “Fluigi: microfluidic device synthesis for synthetic biology,” J. emerg. technol. comput. syst. special issue on synthetic biology, vol. 11, iss. 3, p. 26:1–26:19, 2014. doi:10.1145/2660773
    [BibTeX] [Download PDF]
    @Article{Huang:2014:FMD:2711453.2660773,
    Title = {Fluigi: Microfluidic Device Synthesis for Synthetic Biology},
    Author = {Huang, Haiyao and Densmore, Douglas},
    Journal = {J. Emerg. Technol. Comput. Syst. Special Issue on Synthetic Biology},
    Year = {2014},
    Month = dec,
    Number = {3},
    Pages = {26:1--26:19},
    Volume = {11},
    Acmid = {2660773},
    Address = {New York, NY, USA},
    Articleno = {26},
    DOI = {10.1145/2660773},
    ISSN = {1550-4832},
    Issue_date = {December 2014},
    Keywords = {Synthetic biology, genetic circuits, microfluidics},
    Numpages = {19},
    Owner = {Aaron},
    Publisher = {ACM},
    Timestamp = {2015.01.28},
    URL = {http://doi.acm.org/10.1145/2660773}
    }

  • H. Huang, “Fluigi: an end-to-end software workflow for microfluidic design,” PhD Thesis, 2015.
    [BibTeX] [Download PDF]
    @PhdThesis{Huang2014,
    Title = {Fluigi: An end-to-end Software Workflow for Microfluidic Design},
    Author = {Huang, Haiyao},
    School = {Boston University},
    Year = {2015},
    URL = {http://cidarlab.org/wp-content/uploads/2016/02/ch_2015_thesis.pdf}
    }

  • H. Huang and D. Densmore, “Integration of microfluidics into the synthetic biology design flow,” Lab on a chip, vol. 14, iss. 18, pp. 3459-3474, 2014.
    [BibTeX] [Download PDF]
    @Article{huang2014integration,
    Title = {Integration of microfluidics into the synthetic biology design flow},
    Author = {Huang, Haiyao and Densmore, Douglas},
    Journal = {Lab on a Chip},
    Year = {2014},
    Number = {18},
    Pages = {3459--3474},
    Volume = {14},
    Publisher = {Royal Society of Chemistry},
    URL = {http://pubs.rsc.org/en/content/articlelanding/2014/lc/c4lc00509k#!divAbstract}
    }

  • H. Huang, S. Bhatia, A. Khalil, and D. Densmore, Fluigi: a computer aided design framework for combining microfluidics and synthetic biology, 2013.
    [BibTeX] [Download PDF]
    @Misc{HuangSB62013,
    Title = {Fluigi: a computer aided design framework for combining microfluidics and synthetic biology},
    Author = {Huang, Haiyao and Bhatia, Swapnil and Khalil, Ahmad and Densmore, Douglas},
    HowPublished = {poster presented at the 6th International Meeting on Synthetic Biology (SB6.0)},
    Month = {July},
    Year = {2013},
    Keywords = {posters, synthetic biology},
    Owner = {Aaron Heuckroth},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/HuangSB62013.pdf}
    }

  • R. Sanka, H. Huang, R. Silva, and D. Densmore, Mint – microfluidic netlist, 2016.
    [BibTeX] [Abstract] [Download PDF]
    http://cidarlab.org/wp-content/uploads/2016/09/mint-iwbda16.pdf

    @Misc{mintiwbda16,
    author = {Sanka, Radhakrishna and Huang, Haiyao and Silva, Ryan and Densmore, Douglas},
    title = {MINT - Microfluidic Netlist},
    howpublished = {talk presented at the International Workshop on Bio-Design Automation (IWBDA)},
    month = aug,
    year = {2016},
    abstract = {http://cidarlab.org/wp-content/uploads/2016/09/mint-iwbda16.pdf},
    url = {http://cidarlab.org/wp-content/uploads/2016/09/MINT-IWBDA-2016-Poster-Template-copy.pdf}
    }

  • E. Oberortner, H. Huang, S. Bhatia, and D. Densmore, Eugene 2.0: a domain-specific language to specify constraint synthetic biological devices, 2012.
    [BibTeX] [Download PDF]
    @Misc{OberortnerSynBERC2012,
    Title = {Eugene 2.0: A Domain-specific Language to Specify Constraint Synthetic Biological Devices},
    Author = {Oberortner, Ernst and Huang, Haiyao and Bhatia, Swapnil and Densmore, Douglas},
    HowPublished = {poster presented at the SynBERC Spring Retreat, University of California-Berkeley},
    Month = {March},
    Year = {2012},
    Keywords = {eugene, posters, synthetic biology},
    Location = {SynBERC},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/OberortnerSynBERC2012.pdf}
    }

  • L. Ortiz, T. Costa, and D. Densmore, Modular assembly of an electronically integrated genetic circuit library, 2016.
    [BibTeX] [Download PDF]
    @Misc{ortiz2016tc,
    author = {Luis Ortiz and Thomas Costa and Douglas Densmore},
    title = {Modular Assembly of an Electronically Integrated Genetic Circuit Library},
    howpublished = {Poster presented at the International Workshop on Bio-Design Automation (IWBDA)},
    month = {August},
    year = {2016},
    url = {http://cidarlab.org/wp-content/uploads/2016/09/Luis-Ortiz-IWBDA-2016-Poster_Small.pdf}
    }

  • R. Silva, Heuckroth Aaron, C. Huang, A. Rolfe, and D. Densmore, Makerfluidics: microfluidics for all, 2015.
    [BibTeX] [Download PDF]
    @Misc{SilvaSynberc2015,
    Title = {MakerFluidics: Microfluidics for all},
    Author = {Silva, Ryan and Heuckroth, Aaron, and Huang, Cassie and Rolfe, Aparna and Densmore, Douglas},
    HowPublished = {poster presented at Synberc: Fall 2015},
    Month = {September},
    Year = {2015},
    Keywords = {posters, synthetic biology},
    URL = {http://cidarlab.org/wp-content/uploads/2016/02/Synberc_MakerFluidics_Poster_Silva.pdf}
    }

  • R. Silva, P. Dow, R. Dubay, C. Lissandrello, J. Holder, D. Densmore, and J. Fiering, “Rapid prototyping and parametric optimization of plastic acoustofluidic devices for blood–bacteria separation,” Biomedical microdevices, vol. 19, iss. 3, p. 70, 2017. doi:10.1007/s10544-017-0210-3
    [BibTeX] [Abstract] [Download PDF]
    Acoustic manipulation has emerged as a versatile method for microfluidic separation and concentration of particles and cells. Most recent demonstrations of the technology use piezoelectric actuators to excite resonant modes in silicon or glass microchannels. Here, we focus on acoustic manipulation in disposable, plastic microchannels in order to enable a low-cost processing tool for point-of-care diagnostics. Unfortunately, the performance of resonant acoustofluidic devices in plastic is hampered by a lack of a predictive model. In this paper, we build and test a plastic blood–bacteria separation device informed by a design of experiments approach, parametric rapid prototyping, and screening by image-processing. We demonstrate that the new device geometry can separate bacteria from blood while operating at 275{%} greater flow rate as well as reduce the power requirement by 82{%}, while maintaining equivalent separation performance and resolution when compared to the previously published plastic acoustofluidic separation device.

    @Article{Silva2017,
    author = {Silva, R. and Dow, P. and Dubay, R. and Lissandrello, C. and Holder, J. and Densmore, D. and Fiering, J.},
    title = {Rapid prototyping and parametric optimization of plastic acoustofluidic devices for blood--bacteria separation},
    journal = {Biomedical Microdevices},
    year = {2017},
    volume = {19},
    number = {3},
    pages = {70},
    month = {Aug},
    issn = {1572-8781},
    abstract = {Acoustic manipulation has emerged as a versatile method for microfluidic separation and concentration of particles and cells. Most recent demonstrations of the technology use piezoelectric actuators to excite resonant modes in silicon or glass microchannels. Here, we focus on acoustic manipulation in disposable, plastic microchannels in order to enable a low-cost processing tool for point-of-care diagnostics. Unfortunately, the performance of resonant acoustofluidic devices in plastic is hampered by a lack of a predictive model. In this paper, we build and test a plastic blood--bacteria separation device informed by a design of experiments approach, parametric rapid prototyping, and screening by image-processing. We demonstrate that the new device geometry can separate bacteria from blood while operating at 275{%} greater flow rate as well as reduce the power requirement by 82{%}, while maintaining equivalent separation performance and resolution when compared to the previously published plastic acoustofluidic separation device.},
    bdsk-url-1 = {https://doi.org/10.1007/s10544-017-0210-3},
    bdsk-url-2 = {http://dx.doi.org/10.1007/s10544-017-0210-3},
    day = {04},
    doi = {10.1007/s10544-017-0210-3},
    url = {https://doi.org/10.1007/s10544-017-0210-3},
    }

CIDAR Project Lead

Cassie Huang huangh@bu.edu

Cassie Huang
huangh@bu.edu

CIDAR Collaborators:

Swapnil Bhatia, PhD

Aaron Heuckroth

Ryan Silva