• What is the BIOFAB?

     

    The UW Biofabrication Center (BIOFAB) is a unique service laboratory operating through the Electrical & Computer Engineering Department at the University of Washington. Clients use the Aquarium software to store sample information and remotely submit molecular biology and microbiology jobs. Technicians in the BIOFAB execute the protocols and upload the results to Aquarium. Therefore, cloning projects can be executed from start to finish, without the client ever having to touch a pipette! Records of all jobs and samples are permanently stored in the Aquarium inventory database, eliminating the need for messy lab notebooks and complex inventory systems.

     

  • Services

    Plasmid Construction and Verification

    Using Aquarium, the BIOFAB team can build plasmids and E. coli strains from scratch. Our cloning workflow includes:

    • Primer ordering via IDT
    • PCRs
    • Gel electrophoresis
    • DNA isolation and purification
    • Plasmid assemblies using Gibson and Golden Gate methods
    • Electrocompetent E. coli transformations
    • Sanger sequencing verification via Genewiz

    Yeast Strain Construction and Verification

    With the BIOFAB, it is easy to create novel yeast strains for experiments. Our yeast workflow includes:

    • Preparation of competent yeast cells
    • Yeast transformations
    • Strain verification via colony PCR and QIAxcel Bioanalyzer
    • Yeast mating available upon request

    Media and Reagent Preparation

    To support DNA, E. coli and yeast protocols. Available upon request.

    Yeast Media

    • Liquid/plates: YPAD, Synthetic Complete (SC), Synthetic Drop Out (SDO), SGCAA
    • Yeast selective media:  SDO –Histidine, SDO –Tryptophan, SDO –Uracil, SDO –Leucine, SDO –Lysine
    • Yeast antibiotics: Geneticin (Kan/G418), Bleomycin (Bleo/Zeocin), Hygromycin (Hyg), and Nourseothricin (Nat/ClonNat)
    Bacterial Media
    • Liquid/plates: LB, TB
    • Bacterial antibiotics: Ampicillin, Kanamycin, Chloramphenicol, Spectinomycin  

    Protein Engineering and Cell Sorting

    The BIOFAB can assist with yeast surface display experiments, including:

    • DNA library amplification and assembly
    • Preparation and transformation of electrocompetent yeast cells
    • De novo protein stability assays (using Rocklin et al. 2017 workflow)
    • High-throughput protein binder and small molecule binding assays
    • Cell sorting (FACS)
    • Amplicon NGS prep and Illumina sequencing
  • Getting Started

    1. Contact us (biofab@uw.edu) to express your interest.
    2. Schedule and attend a BIOFAB Workshop.
    3. Set up an Aquarium account (at the workshop).
    4. Link a UW budget number with your Aquarium account.
    5. Start submitting jobs!

  • Help

    How do I get started with the BIOFAB?

    1. Contact us (biofab@uw.edu) to express your interest.
    2. Schedule and attend a BIOFAB Workshop.
    3. Set up an Aquarium account (at the workshop).
    4. Link a UW budget number with your Aquarium account.
    5. Start submitting jobs!

    When are staff in the lab?

    8:00 AM - 5:00 PM Monday through Friday

    9:00 AM - 3:00 PM Saturday and Sunday

    Why isn’t my task moving forward?

    In general, the first thing to do is to check to make sure that all of the inputs for the given task are correct. Many times tasks get stuck in waiting status purely because the inputs are defined incorrectly. The other thing to keep in mind is the notifications on the home page. Tasks will update you as they proceed forward and sometimes these can take a few days.

    My PCR/Yeast Transformation/Yeast QC/Gibson is not working, what should I do?

    Most of the time tasks fail due to biological reasons. It’s up to you as the scientist to troubleshoot your experiments. The BIOFAB will just perform the tasks as you submit them.

    All my inputs are correct but my stuff isn’t moving forward.

    BIOFAB managers sometimes cap the amount of items in a given task daily. So if there are a large number of requests for a certain task one day your task may be delayed until the next day. Task priority is first submitted first served.

    I submitted a Yeast Mating Task or a Cytometry Task and it hasn’t been run, why?

    These two tasks aren’t in the normal workflow. To run them you must communicate with a BIOFAB manager in order to work it into that days schedule. These requests must be cleared with a BIOFAB manager the day before you want the protocol run.

    What is the correct way to remove a sample from the lab or add a sample to the lab?

    Delete items when they physically leave the lab. Add a new version of the item when an item returns or is created. Make sure it’s physically in the lab before being instantiated.

  • People

    Management and Admin

    Eric Klavins

    Director

    Aza Allen

    Lab Manager

  • Software Engineers

    William Bach
    Allison Li
    Wendi Ma
    Caroline Freer
    Jared Yen

    Technicians

    Hannah Park
    Nicole Roullier
    Ryan Luedtke
    Saeed Mahamood
    Sarah Mahan
    Sasha Kravchuk

  • Alumni

    Asmaa El-Ghazali, Technician (2014-2016)
    Ernesto Coronado, Manager (2015-2016)
    Nathan Hwang, Technician (2014-2016)
    Lindsay Ng, Technician (2014-2016)
    Delaney Orcutt, Technician (2015-2016)
    Jack Lee, Software Engineer (2015-2016)
    Yaoyu Yang, Software Engineer (2014-2017)
    Yue Shi, Project Consultant (2017)
    Aza Allen, Technician (2016-2017)
    Paige Almond, Technician (2015-2017)
    Muhammad Halimun, Technician (2016-2017)
    Michelle Parks, Manager (2013-2017)
    Brenda Robles, Technician (2016-2017)
    Marielle Summers, Technician (2013-2018)
    Ayesha Saleem, Technician/Software Engineer (2016-2018)
    Garrett Newman, Software Engineer (2015-2018)
    Lana Alabyeva, Technician (2017-2018)
    Gabriella Fier, Technician (2018-2018)
    James Leinas, Technician (2017-2018)
    Xavaar Quaranto, Technician (2017-2018)
    Sophia D'atri, Technician (2017-2018)
    Abraham Miller, Software Engineer (2017-2018)
    Luana Paleologu​, Technician (2017-2019)
    Aria Tornabene, Technician (2018-2019)
    Jon Luntzel. Software Engineer (2018-2019)
    Shamey Kassim, Technician (2018-2020)
    Yokesh Jayakumar, Software Engineer (2018-2020)
    Halie Borror, Technician (2017-2020)
    Margarita Ankoudinova, Technician (2018-2020)
    Aidan Cowles, Technician (2018-2020)
    Noah Baker, Technician (2019-2020)
    Andrew Olander, Technician (2018-2020)
    Paursa Kamalian, Technician (2019-2021)
    Sofia Shirley, Technician (2018-2021)
    Samer Halabiya, DNA Assembly & Sequencing Specialist
    Justin Vrana, Scientific Consultant
    Yokesh Jayakumar, Software Engineer
    Jon Luntzel, Software Engineer
    Jacqueline McAleer, Technician
    Izzy Shaquer, Technician
    Mimi McMurray, Technician
    Cami Cordray, Manager (2016-2021)
     

  • Contact Us

    University of Washington NanoEngineering and Sciences, Room 380
    Seattle, WA 98195
    (206) 221-0941