Cloud Columba: Accessible Design Automation Platform for Production and Inspiration: Invited Paper

Design automation for continuous-flow microfluidic large-scale integration (mLSI) biochips has made remarkable progress over the past few years. Nowadays a biochip containing up to hundreds of components can be automatically synthesized within a few minutes. However, the current advanced design automation tools are mostly developed for research use, which focus essentially on the algorithmic performance but overlook the accessibility. Therefore, we have started the Cloud Columba project since 2017 to provide users from different backgrounds with easy access to the state-of-the-art design automation approaches. Without being limited by the computing power of their end devices, users just need to formulate their design requests in a high abstraction level, based on which the cloud server will automatically synthesize a customized manufacturing-ready biochip design, which can be viewed and stored using simply a web browser. With the computer-synthesized designs, Cloud Columba supports application developers to explore a wider range of possibilities, and algorithm developers to validate and improve their ideas based on a practical foundation.

[1]  Philip Brisk,et al.  Diagonal Component Expansion for Flow-Layer Placement of Flow-Based Microfluidic Biochips , 2017, ACM Trans. Embed. Comput. Syst..

[2]  S. Quake,et al.  The RootChip: An Integrated Microfluidic Chip for Plant Science[W][OA] , 2011, Plant Cell.

[3]  S. Quake,et al.  Microfluidic Large-Scale Integration , 2002, Science.

[4]  Ulf Schlichtmann,et al.  Reliability-aware synthesis for flow-based microfluidic biochips by dynamic-device mapping , 2015, 2015 52nd ACM/EDAC/IEEE Design Automation Conference (DAC).

[5]  Douglas Densmore,et al.  3DμF - Interactive Design Environment for Continuous Flow Microfluidic Devices , 2019, Scientific Reports.

[6]  Philip Brisk,et al.  Scheduling and Fluid Routing for Flow-Based Microfluidic Laboratories-on-a-Chip , 2018, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems.

[7]  Ulf Schlichtmann,et al.  Columba 2.0: A Co-Layout Synthesis Tool for Continuous-Flow Microfluidic Biochips , 2018, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems.

[8]  S. Quake,et al.  Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat , 2005, Science.

[9]  Ulf Schlichtmann,et al.  Columba S: A Scalable Co-Layout Design Automation Tool for Microfluidic Large-Scale Integration , 2018, 2018 55th ACM/ESDA/IEEE Design Automation Conference (DAC).

[10]  Ulf Schlichtmann,et al.  Storage and Caching: Synthesis of Flow-Based Microfluidic Biochips , 2015, IEEE Design & Test.

[11]  Ulf Schlichtmann,et al.  Component-oriented high-level synthesis for continuous-flow microfluidics considering hybrid-scheduling , 2017, 2017 54th ACM/EDAC/IEEE Design Automation Conference (DAC).

[12]  Ramesh Karri,et al.  Desieve the Attacker: Thwarting IP Theft in Sieve-Valve-based Biochips , 2019, 2019 Design, Automation & Test in Europe Conference & Exhibition (DATE).

[13]  S. Quake,et al.  High-performance binary protein interaction screening in a microfluidic format. , 2012, Analytical chemistry.

[14]  Mohamed Ibrahim,et al.  An Efficient Fault-Tolerant Valve-Based Microfluidic Routing Fabric for Droplet Barcoding in Single-Cell Analysis , 2020, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems.

[15]  Vincent Studer,et al.  A nanoliter-scale nucleic acid processor with parallel architecture , 2004, Nature Biotechnology.

[16]  Sudip Roy,et al.  Dilution and Mixing Algorithms for Flow-Based Microfluidic Biochips , 2017, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems.

[17]  S. Quake,et al.  Monolithic microfabricated valves and pumps by multilayer soft lithography. , 2000, Science.

[18]  Howard Y. Chang,et al.  High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation. , 2012, Lab on a chip.

[19]  Stephen Quake,et al.  A nanoliter rotary device for polymerase chain reaction , 2002, Electrophoresis.

[20]  Stephen R Quake,et al.  Microfluidic single-cell mRNA isolation and analysis. , 2006, Analytical chemistry.

[21]  Joseph B Hiatt,et al.  Automated microfluidic chromatin immunoprecipitation from 2,000 cells. , 2009, Lab on a chip.

[22]  Ulf Schlichtmann,et al.  Sieve-valve-aware synthesis of flow-based microfluidic biochips considering specific biological execution limitations , 2016, 2016 Design, Automation & Test in Europe Conference & Exhibition (DATE).

[23]  Ulf Schlichtmann,et al.  Columba: Co-layout synthesis for continuous-flow microfluidic biochips , 2016, 2016 53nd ACM/EDAC/IEEE Design Automation Conference (DAC).

[24]  Robert Wille,et al.  Physical Co-Design of Flow and Control Layers for Flow-Based Microfluidic Biochips , 2018, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems.

[25]  Ulf Schlichtmann,et al.  Transport or store? Synthesizing flow-based microfluidic biochips using distributed channel storage , 2017, 2017 54th ACM/EDAC/IEEE Design Automation Conference (DAC).

[26]  Axel Scherer,et al.  A microfluidic processor for gene expression profiling of single human embryonic stem cells. , 2008, Lab on a chip.

[27]  Ulf Schlichtmann,et al.  Reliability-Aware Synthesis With Dynamic Device Mapping and Fluid Routing for Flow-Based Microfluidic Biochips , 2016, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems.