• Mirela Alistar

    2014 - 2018 Postdoc in the HCI lab at Hasso Plattner Institute

    Advisor: Prof. Patrick Baudisch

    2010 - 2014 PhD in Computer Engineering from Technical University of Denmark

    Thesis: Compilation and synthesis of fault-tolerant digital microfluidic biochips

    Advisors: Prof. Paul Pop and Prof. Jan Madsen

    Personal biochips

    I envision a future where “biochips” will serve as generic medical platforms that can be adapted to the needs of people, therefore enabling personalized medicine. Biochips manipulate droplets of fluids (e.g., split, merge, mix) in order to automate "bio-protocols", i.e., processes traditionally performed in wet labs, such as in-vitro diagnosis on a droplet of blood. Because biochips automate lab procedures, they have the potential to run biomedical protocols as if they were software.

    I have pursued my vision by addressing biochips from a computer science perspective, i.e., as cyber-physical systems. Specifically, I created my own hardware, worked on the system-level software (real-time synthesis and fault-tolerant CAD tools), and I am currently developing a user-facing system for interactive editing of a bio-protocol.

  • Books co-authored

    1. Fault-tolerant digital microfluidic biochips

    Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen. Springer'16.

    This book describes for researchers in the fields of compiler technology, design and test, and electronic design automation the new area of digital microfluidic biochips (DMBs), and thus offers a new application area for their methods. The authors present a routing-based model of operation execution, along with several associated compilation approaches, which progressively relax the assumption that operations execute inside fixed rectangular modules. Since operations can experience transient faults during the execution of a bioassay, the authors show how to use both offline (design time) and online (runtime) recovery strategies. The book also presents methods for the synthesis of fault-tolerant application-specific DMB architectures.

  • Journal papers

    4. OpenDrop: an integrated do-it-yourself platform for personal use of biochips

    Mirela Alistar, Urs Gaudenz. Bioengineering'17.

    OpenDrop consists of a do-it-yourself biochip, an automated software tool with visual interface and a detailed technique for at-home operations of microfluidics. We address the main challenges that users may encounter: accessibility, bio-protocol design and interaction with microfluidics. Our work provides a step towards a future in which everyone will be able to use microfluidic devices for their personal applications.

    3. Synthesis of application-specific fault-tolerant digital microfluidic biochip architectures

    Mirela Alistar, Paul Pop, Jan Madsen. TCAD'16.

    The current industrial trend is to produce biochips in the form of disposable cartridges, designed to execute specific bio-protocols. We propose the first methodology that automates the design of application-specific biochips, aiming at obtaining low-cost biochips, while maximizing fault-tolerance to fabrication defects.

    2. Synthesis of biochemical applications on digital microfluidic biochips with operation execution time variability

    Mirela Alistar, Paul Pop. Integration VLSI'15.

    Due to variability and randomness in biochemical reactions, droplet operations may finish earlier than expected. To exploit the resulted slack in the schedule, we implement a quasi-static compilation that takes advantage of both static and dynamic error recovery techniques. We determine offline a database of alternative implementations. During the execution of the bio-protocol, several implementations are selected based on the current execution scenario.

    1. Redundancy optimization for error recovery in digital microfluidic biochips

    Mirela Alistar, Paul Pop, Jan Madsen. DAEM'15.

    During the execution of a bio-protocol, transient faults can occur and alter the droplet volumes. We propose two error recovery approaches: (1) create the copy droplet sequentially, after the error is detected (i.e., time redundancy), or (2) create the copy droplet in parallel, before the error is detected (i.e., space redundancy). Because neither time nor space redundancy is better, we implement a decision algorithm that optimizes their tradeoff for the actual context.

  • Conference papers

    7. Towards droplet size-aware biochemical application compilation for AM-EWOD biochips

    Mirela Alistar, Paul Pop. DTIP'15.

    So far, to simply the compilation problem, researchers have assumed an abstract droplet size of one electrode. We develop the first routing algorithm for biochips that considers the real size of droplets. Our work targets a novel biochip architecture based on Active Matrix Electrowetting on Dielectric, which enables large arrays (i.e., of thousands electrodes).

     

    6. Online synthesis for operation execution time variability on digital microfluidic biochips

    Mirela Alistar, Paul Pop. ISIC'14.

    So far, droplet operations on biochips were scheduled considered an expected finish time. However, mixing and incubation of droplets depend on their chemical composition and may finish earlier than expected. We exploit the resulted slack in the schedule through an adaptive compilation strategy triggered at runtime, when operations experience variability in their execution time.

    5. . Operation placement for application-specific digital microfluidic biochips

    Mirela Alistar, Paul Pop. DTIP'13.

    In this paper, we demonstrate that operations finish faster when the droplets are moved in closed circular paths. We implement a novel placement strategy for application-specific biochips (i.e., non-rectangular), based on circular-route modules.

    4. Application-specific fault-tolerant architecture synthesis for digital microfluidic biochips

    Mirela Alistar, Paul Pop, Jan Madsen. ASPDAC'13.

    So far, biochips were considered to be of rectangular shape. However, in practice, non-regular architectures are common for application-specific biochips. We develop an algorithm that synthesizes application-specific biochips. Furthermore, our approach increases the fabrication yield by introducing redundant electrodes to tolerate fabrication defects.

    3. Online synthesis for error recovery in digital microfluidic biochips with operation variability.

    Mirela Alistar, Paul Pop. DTIP'12.

    During the execution of a bio-protocol, the droplet volumes can vary erroneously due to parametric faults, thus impacting negatively the correctness of the application. We develop an adaptive algorithm that determines the appropriate recovery actions at the moment when faults are detected.

    2. Synthesis of biochemical applications on digital microfluidic biochips with operation variability

    Mirela Alistar, Paul Pop. DTIP'10.

    We propose an abstract model for a bio-protocol, consisting of a sequencing graph, which can capture all the fault scenarios in the application. We demonstrate that, by taking into account fault-occurrence information, we can derive better schedule implementations, which leads to shorter application completion times, even in the case of faults.

    1. Metamaterial Mechanisms

    Alexandra Ion, Johannes Frohnhofen, Mirela Alistar, Ludwig Wall, Jack Lindsay, Pedro Lopes, Hsiang-Ting Chen, Patrick Baudisch. UIST'16. Honorable Mention Award.

    So far, metamaterials are understood as materials - we want to think of them as mechanisms. We demonstrate metamaterial objects that perform a mechanical function. Such objects consists of a single block of material made of microscopic cells that coordinate macroscopic movement.

  • Academic workshops

    I have been evangelizing interactive systems based on biochips, by organizing hands-on workshops at conferences and academic retreats.

    Hands-on microfluidics

    Molecular communications, Ireland (2017)

    Experimental microalgae

    Art and Design Halle, Germany (2017)

    Real-time healthcare

    Embedded Systems Week, USA (2016)

    Digital biology summit

    Freies Museum, Berlin (2016)

    Design of microfluidic biochips

    Dagstuhl Seminar, Germany (2015)

    Rock'n Roll Bio

    Aalto University, Finland (2015)

  • Outreach activities (selection)

    I teach frequently outside of academia, in makerspaces and art galleries, with the purpose of engaging the public in a critical analysis of technology. In my role as founder or chairwoman of community wetlabs, I organize workshops to inspire enthusiasts of diverse backgrounds (e.g., engineering, art, design).

    Let it glow!

    [bioluminescence] [Photobacterium Phosphoreum]

    Trapped in transition

    [Synechococcus spp 6883] [microalgae]

    Merry CRISPR!

    [genetic engineering] [diy crispr]

    Vital invasion

    [bacteriophages] [microfluidics]

    TopLab

    [community lab] [DIYBio] [open science]

    Biologigaragen

    [community lab] [DIYBio] [open science]