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      Principles of open source bioinstrumentation applied to the poseidon syringe pump system

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          Abstract

          The poseidon syringe pump and microscope system is an open source alternative to commercial systems. It costs less than $400 and can be assembled in under an hour using the instructions and source files available at https://pachterlab.github.io/poseidon. We describe the poseidon system and use it to illustrate design principles that can facilitate the adoption and development of open source bioinstruments. The principles are functionality, robustness, safety, simplicity, modularity, benchmarking, and documentation.

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          Single-cell barcoding and sequencing using droplet microfluidics.

          Rapolas Zilionis, Juozas Nainys, Adrian Veres … (2017)
          Single-cell RNA sequencing has recently emerged as a powerful tool for mapping cellular heterogeneity in diseased and healthy tissues, yet high-throughput methods are needed for capturing the unbiased diversity of cells. Droplet microfluidics is among the most promising candidates for capturing and processing thousands of individual cells for whole-transcriptome or genomic analysis in a massively parallel manner with minimal reagent use. We recently established a method called inDrops, which has the capability to index >15,000 cells in an hour. A suspension of cells is first encapsulated into nanoliter droplets with hydrogel beads (HBs) bearing barcoding DNA primers. Cells are then lysed and mRNA is barcoded (indexed) by a reverse transcription (RT) reaction. Here we provide details for (i) establishing an inDrops platform (1 d); (ii) performing hydrogel bead synthesis (4 d); (iii) encapsulating and barcoding cells (1 d); and (iv) RNA-seq library preparation (2 d). inDrops is a robust and scalable platform, and it is unique in its ability to capture and profile >75% of cells in even very small samples, on a scale of thousands or tens of thousands of cells.
          Article 0 comments Cited 269 times – based on 0 reviews     Review now
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            Materials science. Building research equipment with free, open-source hardware.

            Joshua Pearce (2012)
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              Open-Source Syringe Pump Library

              Bas Wijnen, Emily Hunt, Gerald C. Anzalone … (2014)
              This article explores a new open-source method for developing and manufacturing high-quality scientific equipment suitable for use in virtually any laboratory. A syringe pump was designed using freely available open-source computer aided design (CAD) software and manufactured using an open-source RepRap 3-D printer and readily available parts. The design, bill of materials and assembly instructions are globally available to anyone wishing to use them. Details are provided covering the use of the CAD software and the RepRap 3-D printer. The use of an open-source Rasberry Pi computer as a wireless control device is also illustrated. Performance of the syringe pump was assessed and the methods used for assessment are detailed. The cost of the entire system, including the controller and web-based control interface, is on the order of 5% or less than one would expect to pay for a commercial syringe pump having similar performance. The design should suit the needs of a given research activity requiring a syringe pump including carefully controlled dosing of reagents, pharmaceuticals, and delivery of viscous 3-D printer media among other applications.
              Article 0 comments Cited 89 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Jase Gehring: jgehring@caltech.edu
                Lior Pachter:
                ORCID: http://orcid.org/0000-0002-9164-6231
                lpachter@caltech.edu
                Journal
                Journal ID (nlm-ta): Sci Rep
                Journal ID (iso-abbrev): Sci Rep
                Title: Scientific Reports
                Publisher: Nature Publishing Group UK (London )
                ISSN (Electronic): 2045-2322
                Publication date (Electronic): 27 August 2019
                Publication date PMC-release: 27 August 2019
                Publication date Collection: 2019
                Volume: 9
                Electronic Location Identifier: 12385
                Affiliations
                [1 ]ISNI 0000000107068890, GRID grid.20861.3d, Department of Mechanical Engineering, , California Institute of Technology, ; Pasadena, CA 91125 USA
                [2 ]ISNI 0000000107068890, GRID grid.20861.3d, Department of Biology & Biological Engineering, , California Institute of Technology, ; Pasadena, CA 91125 USA
                [3 ]ISNI 0000000107068890, GRID grid.20861.3d, Department of Computing & Mathematical Sciences, , California Institute of Technology, ; Pasadena, CA 91125 USA
                Author information
                http://orcid.org/0000-0002-6442-4502
                http://orcid.org/0000-0002-1529-9207
                http://orcid.org/0000-0002-9164-6231
                Article
                Publisher ID: 48815
                DOI: 10.1038/s41598-019-48815-9
                PMC ID: 6711986
                PubMed ID: 31455877
                SO-VID: d10e0d1a-70fb-4fab-bd4a-117bb35c00ae
                Copyright © © The Author(s) 2019
                License:

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 7 February 2019
                Date accepted : 8 August 2019
                Categories
                Subject: Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2019

                ScienceOpen disciplines: Uncategorized
                Keywords: lab-on-a-chip,mechanical engineering
                Data availability:
                ScienceOpen disciplines: Uncategorized
                Keywords: lab-on-a-chip, mechanical engineering

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