• Mirela alistar

    (starting 2019) Assistant Professor at Atlas Institute and the Department of Computer Science, CU Boulder

    leading the Living Matter Lab

    teaching Introduction to Biodesign and Physical Interaction with Living Matter

    serving as PC for CHI'19 LBW, and GLVSI'17 Biochips track

    reviewing for TCAD, JETC, DATE, MJE, UIST, CHI

    advising digi.bio and bold.health startups

    co-founder and event organizer of >top - art & science project space in Berlin

    2015 - 2018 - Postdoc in the Human Computer Interaction lab of Patrick Baudisch at Hasso Plattner Institute

    2010 - 2014 - PhD student in the Embedded Systems Engineering lab (Paul Pop and Jan Madsen) at Technical University of Denmark

  • News

    New positions open! We are looking for PhD students, postdoctoral fellows and other enthusiastic folks to join our lab and do fun research with us. More information in the APPLY section.

     

    Biochips Summer School. Apply directly here or email me for further questions.

     

    May'19: I give a talk at Johannes Kepler University, hosted by Robert Wille

    May'19: I speak at the BioCHIP conference, contact me if you need free tickets [program]

    April'19: I teach a one-week biotech class at Art & Design College Weissensee Berlin [pictures]

    March'19: My collaborative art piece Semina Aeternitatis (with Margherita Pevere) is exhibited at Kunsthalle Rostock [pictures]

    March'19: I teach a 3-days workshop on digital microfluidics in Bucharest, Romania

    March'19: I organize and teach Culture and Colonies, at Ruine hq in Hannover

    Feb'19: I perform "Secreted Functions" with AslieMk, at >top in Berlin

    Nov'18: Panel speaker on the topic of reproducibility in biology at Berlin Science Week

    Oct'18: Attending the UIST'18 reception at Hasso Plattner Institute [video]

    Sept'18: I speak and give a workshop in Ukraine, at the sRNABio meeting. Learn more: [talk] [workshop]

    Aug'18: I had an art residency at the former tuberculosis hospital in Grabowsee and exhibited my work at Globe Gallery

    Jul'18: My bio-dream interactive installation is shown at >top in Berlin

  • Apply

    Biochips Summer School. Apply directly here or email me for further questions.

    Phd positions. We are looking for curious and ambitious candidates with backgrounds in one or more of the following areas:

    • Computer Science and Engineering: [CAD tools] [MEMS] [ hardware design] [embedded systems]
    • Biology: [microbiology] [synthetic biology] [bacteriophages] [E. coli] [cyanobacteria]
    • Nanotechnology: [microfluidics] [lithography] [micro-dispensers] [dual-phase plugs] [SAW biochips]
    • Art & Design: [bioart] [living matter] [interactive installations] [performances]

    If interested, please email your CV and a short introduction to learn more about you.

  • Research

    Vision

    Today, diagnosis requires patients to see a doctor to provide samples, which are then sent to a wetlab, then reported back to the doctor and the patient. This process can take valuable time during which patients live in uncertainty and disease is allowed to spread. What if instead doctors could perform the tests while the patient waits? Or, what if we could empower patients to perform selected tests at home, to help them decide whether to see a doctor in the first place?

    In my work, I investigate how to ubiquitize healthcare by moving the process of diagnosis closer to the patient. I pursue this vision by creating cyber-physical systems based on biochips.

    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.

    Personal biochips

    Fault-tolerant digital microfluidic biochips

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

    [book] We identify the research challenges in the new area of digital microfluidic biochips, targeting researchers in the fields of compiler technology, design and test, and electronic design automation, and thus offering a new application area for their methods. We propose 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, we show how to use both offline (design time) and online (runtime) recovery strategies.

    ==pdf==

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

    Mirela Alistar, Urs Gaudenz. Bioengineering'17.

    [journal paper] 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.

    ==pdf==

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

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

    [journal paper] 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.

    ==pdf==

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

    Mirela Alistar, Paul Pop. Integration VLSI'15.

    [journal paper] 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.

    ==pdf==

    Redundancy optimization for error recovery in digital microfluidic biochips

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

    [journal paper] 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).

    ==pdf==

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

    Mirela Alistar, Paul Pop. DTIP'15.

    [conference paper] 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.

    ==pdf==

    Redundancy optimization for error recovery in digital microfluidic biochips

    Mirela Alistar, Paul Pop. ISIC'14.

    [conference paper] 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.

    ==pdf==

    Operation placement for application-specific digital microfluidic biochips

    Mirela Alistar, Paul Pop. DTIP'13.

    [conference 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.

    ==pdf==

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

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

    [conference paper] 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.

    ==pdf==

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

    Mirela Alistar, Paul Pop. DTIP'12.

    [conference paper] 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.

    ==pdf==

    Synthesis of biochemical applications on digital microfluidic biochips with operation variability

    Mirela Alistar, Paul Pop. DTIP'10.

    [conference paper] 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.

    ==pdf==

    Other publications

    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.

    ==pdf== ==video==

  • Teaching

    Biochips Summer School

    Biochips Summer School

    July 22-26th, 2019 ATLAS Institute and Living Matter Lab, CU Boulder

    We encourage applications from PhD students with backgrounds in computer science and engineering, microfluidics, microbiology, mechanical engineering, material science and similar areas.

     

    Register here

    introduction to BioDesign

    Introduction to BioDesign

    July 8-19th 2019, Summer course at Technical University, Berlin

    The lectures will introduce the biological aspects of the target organisms (e.g., nutrients, metabolism, growth and reproduction), as well as various design techniques that enable interaction with the organisms through all five senses: visual, auditory, gustatory, olfactory, tactile.

     

    Register here

    Previous hands-on workshops

    Biochip workshop

    Bucharest, Romania (2019)

    pictures| instructables | testimonials

    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 (selection)

    Cultures and Colonies

    Ruine hq, Hannover, Germany (2019)

    artistic concept | pictures

    Secreted functions

    >top Berlin, Germany (2019)

    performance | pictures

    Let it glow!

    [bioluminescence] [Photobacterium Phosphoreum]

    Trapped in transition

    [Synechococcus spp 6883] [microalgae]

    TopLab

    [community lab] [DIYBio] [open science]

  • (bio)ART

    installations & performances

    Semina Aeternitatis takes a hybrid approach on immortality, by entwining human memories with bacterial inheritance. Can a non-human organism carry and pass on the nostalgic memory of a human being? What does it mean to inscribe a memory story, by means of biotechnological processes, in the DNA...
    Read more...
    Can we capture the magic of Grabowsee in a tiny bottle? The Perfume Distillation Machine is condensing vapor from a wide range of forest samples. The perfume distilled will be an all-too-honest, including as it does: hornets, pine cones, various random flowers, mud, dried leaves and resin....
    Read more...
    Phages are micro-organisms that invaded the planet one million years ago, having one main goal: to make life simply better. In spite of being the largest population on Earth, phages are so silent that their presence is defined by the absence of bacteria. In this hands-on workshop, expect a face...
    Read more...
    This hands-on workshop deals with a very unique organism: partially plant, as it feeds from the sun, but more similar to bacteria in its structure and behaviour. You will learn how to make food and nurture 3 different types of microalgae. We will spend the last part of the workshop designing...
    Read more...
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