• Postdoctoral Fellow

    Human Computer Interaction lab, professor Patrick Baudisch

    Hasso Plattner Institute, Germany

     

    mirela.alistar@hpi.de

  • Research Vision

    I dream of a future of democratic healthcare, where people will produce their own medication anytime anywhere. To get there, I have started with building a personal lab: a small portable device that can be easily configured to run biological experiments. Think of a tablet or notebook, just, instead of operating with information bits, it operates with cells and reagents embedded in droplets.

    Such a droplet machine is called officially a digital microfluidic biochip.

    The droplet machine

  • Projects

    Fast prototyping techniques for biochips

    Mirela Alistar, Christian Riis, Philip Meißner

    A digital biochip controls the droplets using electronics, i.e., by applying electrical voltage on the target electrode. To do so, a biochip needs: (1) an electronic circuit that switches on and off the voltage and (2) a wetware board that holds the droplets. I built FreeFlux as a modular biochip, where the electronic control is separated from the wetware (the droplets). The electrodes are detachable to enable customization. FreeFlux is very useful for fast prototyping, e.g., when designing new shapes for electrodes, reservoirs or mixers.

    DIY biochips

    Urs Gaudenz, Mirela Alistar

    OpenDrop is the first prototype of a personal lab. OpenDrop is designed to be a stand-alone platform, portable (the smallest platform in the world) and cheap. You can build it yourself using our open source resources. OpenDrop is a result of a strong international collaboration [pdf][github].

    Real-time compiler for biochips

    Mirela Alistar, Paul Pop, Jan Madsen

    To be executed on a biochip, a bio-protocol has to be compiled. Traditionally, the compilation step is done before the execution. To enable real-time decisions (such as error recovery actions), I developed an algorithm that compiles the bio-protocol in real-time, i.e., while it is executing on the biochip. [DTIP12,DAEM15]

    Fault-tolerant execution on biochips

    Mirela Alistar, Paul Pop

    The execution of a bio-protocol can experience faults that impact negatively the results. I developed error recovery strategies for both offline (at design time) and online (at runtime) scenarios. [DTIP10,IVLSI14]

    Automated design for biochips

    Mirela Alistar, Felix Mussman, Patrick Baudisch

    Low-cost biochips hold the promise people access to customized tests and procedures, thereby democratizing parts of health care. Unfortunately, designing such biochips for a specific bio-protocol requires substantial expertise, especially since it requires optimizing for multiple objectives, such as cost and execution time. To allow non-experts to design custom biochips, I have implemented several strategies that automate the design process, making the creation of biochips accessible for a wider audience. Moreover, my strategies use redundancy and estimations to guarantee a minimal level of fault-tolerance to fabrication defects. [ASPDAC13, TCAD16]

    Metamaterial Mechanisms

    A. Ion, J. Frohnhofen, L. Wall, R. Kovacs, Mirela Alistar, J. Lindsay, P. Lopes, H-T Chen, P. Baudisch
     

    So far, metamaterials were understood as materials—we want to think of them as machines. We demonstrate metamaterial objects that perform a mechanical function. Such metamaterial mechanisms consist of a single block of material the cells of which play together in a well-defined way in order to achieve macroscopic movement. [UIST'16]

  • Workshops

    Real-time healthcare

    Embedded Systems Week, USA

    With Jan Madsen, TY Ho and R. Wille

    [...]

    Design of microfluidic Biochips

    Dagstuhl Seminar, DE

    With Jan Madsen, TY Ho, R. Wille, Krish Chakrabarty

    [...]

    Rock'n Roll Bio

    Biofilia Laboratories, Helsinki

    With Urs Gaudens, Peter van Boheemen, Jaden Hastings et. al

    [...]

    Usability of system-level biochips

    NII Shonan Meeting, Japan

    [coming up]

    Sub:marine

    Re:publica conference, Berlin

    With Alessandro Volpato

    [coming up]

    Biocommons

    Rural hub, Italy

    With Eugenio Battaglia and 40 others :) [...].

    Do it together: Digital Biology

    Freies Museum, Berlin

    With Eugenio Battaglia, Urs Gaudens, etc [...].

  • DIY Bio

    Connecting the human kind with all the other kinds.

  • Curriculum Vitae

    Education

    2014 - Phd at DTU, advisors: Paul Pop and Jan Madsen

    2009 - M.Sc. in Computer Engineering

    Research internships

    2012 - Advanced Liquid Logics, France  (now part of Illumina)

     

    Professional appointments

    2015 - Postdoctoral fellow in HCI, advisor: Patrick Baudisch

    Teaching

    2016, 2017 - Project seminar

    2010, 2012 - Fault-tolerant systems

    2010 - Distributed systems

    2012, 2014 - Software reliability

    2010, 2011 - Fault-tolerant biochips

    Conference Papers

    2016 - A. Ion, J. Frohnhofen, M. Alistar, et al. Metamaterial Mechanisms. UIST. Honorable Mention Award.

    2015 - M. Alistar, P. Pop, J. Madsen. Towards droplet-size aware biochemical application compilation for AM-EWOD biochips. DTIP.

    2014 - M. Alistar, P. Pop. Online synthesis for operation execution time variability on digital microfluidic biochips. ISIC

    2013 - M. Alistar, P. Pop, J. Madsen. Operation placement for application-specific digital microfluidic biochips. DTIP

    2013 - M. Alistar, P. Pop, J. Madsen. Application-specific fault-tolerant architecture synthesis for digital microfluidic biochips. ASPDAC

    2012 - M. Alistar, P. Pop, J. Madsen. Online synthesis for error recovery in digital microfluidic biochips with operation variability. DTIP

    2010 - M. Alistar, P. Pop, J. Madsen. Synthesis of biochemical applications on digital microfluidic biochips with operation variability. DTIP

    Journal papers

    2017 - M. Alistar, U. Gaudens. OpenDrop: An Integrated Do-It-Yourself Platform for Personal Use of Biochips, Bioengineering

    2016 - M. Alistar, P. Pop, Jan Madsen. Synthesis of application-specific fault-tolerant digital microfluidic biochip architectures. TCAD

    2015 - M. Alistar, P. Pop. Synthesis of biochemical applications on digital microfluidic biochips with operation execution time variability. IVLSI

    2015 - M. Alistar, P. Pop, Jan Madsen. Redundancy optimization for error recovery in digital microfluidic biochips. DAEM

    Books

    2016 - Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen. Fault-tolerant digital microfluidic biochips. Springer.

    2014 - Mirela Alistar. Compilation and synthesis for fault-tolerant digital microfluidic biochips. PhD Thesis.

    Posters

    2014 - Paul Pop, Jan Madsen, Kasper Understrup, Mirela Alistar, Wajid Minhass. Programming language and toold for multipurpose lab-on-a-chip platforms. Lab-on-a Chip European Congress.

    2014 - Mirela Alistar. Compilation and Synthesis for fault-tolerant digital microfluidic bciohips. Date. Best Poster Award.

    2014 - Mirela Alistar, Paul Pop, Jan Madsen. Biochemical Application Compilation and Architecture Synthesis for Fault-Tolerant Digital Microfluidic Biochips. Lab-on-a Chip World Congress.

     

    Conferences (program commitee)

    2017 - TPC at ACM NanoCom

    2017 - Reviewer for UIST

    2017 - Reviewer for iVLSI

    2016 - TPC at GLS VLSI on Biochips track

    Journals (as reviewer)

    2017 - T. on Biomedical Circuits and Systems (TBioCAS)

    2017 - J. of Applied Materials and Interfaces

    2016 - J. of Emerging Technologies in Computing Systems (JETC)

    2015, 2016 - T. on Very Large Scale Integration (TVLSI)

     

    Talks

    06/17 University of Cape Town/SA

    06/17 Simon Fraser University/CA

    05/17 EPFL Laussane/CH

    05/17 Twente University/NL

    05/17 Bristol University/UK

    02/17 Shonan/JP

    02/17 Naturkundemusem/DE - Synthetic biology in home labs

    12/16 Singularity University Salon/DK - Printing your medicine

    09/16 SiLa/CH - Standardization in Lab Automation (keynote)

    05/16 OpenTech Summit/DE - A personal lab for everyone

    07/16 IWF Leibniz Institute/DE - Faul-tolerant Biochips

    02/16 Sussex University/UK - Fault-tolerant Biochips

    05/15 OpenTech Summit/DE - Digital Biology

    05/15 INASCON/CH - Biohacking (invited speaker)

    05/15 Bremen University/DE - Fault-tolerant Biochips

    03/15 SynBio for Future II/DE - OpenDrop (invited speaker)

    Workshops, tutorials (as organizer)

    2017 - Health Hack - HPI

    2017 - DIYBio workshops - MakerFaire Berlin

    2017 - Hands-on lab and tutorial Molecular Communications

    2017 - Microfluidics 101 - HPI

    2017 - Vital invasaion - ACUD

    2016 - Hands-on lab and tutorial ESWEEK

    2015 - Workshop on biochips Dagstuhl seminar

    2015 - Biochips research: information meeting

    2015 - Synthetic biology week course, Helsinki

     

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