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      Open Source Software to Control Bioflo Bioreactors

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      PLoS ONE
      Public Library of Science

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          Abstract

          Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW.

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          A system for optical high resolution screening of electrical excitable cells.

          The application of primary excitable cells for high content screening (HCS) requires a multitude of novel developments including cell culture and multi-well plates. Here we introduce a novel system combining optimised culture conditions of primary adult cardiomyocytes with the particular needs of excitable cells for arbitrary field stimulation of individual wells. The major advancements of our design were tested in calcium imaging experiments and comprise (i) each well of the plate can be subjected to individual pulse protocols, (ii) the software driving electrical stimulation can run as a stand-alone application but also as a plug-in in HCS software packages, (iii) the optical properties of the plastic substrate (foil) resemble those of glass coverslips fostering high resolution immersion-based microscopy, (iv) the bottom of the foil is coated with an oleophobic layer that prevents immersion oil from sticking, (v) the top of the foil is coated with an elastic film. The latter enables cardiomyocytes to display loaded contractions by mimicking the physiologically occurring local elastic network (e.g. extracellular matrix) and results in significantly increased contractions (with identical calcium transients) when compared to non-elastic substrates. Thus, our novel design and culture conditions represent an essential further step towards the application of primary cultured adult cardiomyocytes for HCS applications. 2009 Elsevier Ltd. All rights reserved.
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            Closed-loop control of bacterial high-cell-density fed-batch cultures: production of mcl-PHAs by Pseudomonas putida KT2442 under single-substrate and cofeeding conditions.

            Pseudomonas putida KT2442 is able to accumulate medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHAs) as intracellular inclusions on a variety of fatty acids and many other carbon sources. Some of these substrates, such as octanoic acid, alkenoic acids, and halogenated derivatives, are toxic when present in excess. Efficient production of mcl-PHAs on such toxic substrates therefore requires control of the carbon source concentration in the supernatant. In this study, we develop a closed-loop control system based on on-line gas chromatography to maintain continuously fed substrates at desired levels. We used the graphical programming environment LABVIEW to set up a flexible process control system that allows users to perform supervisory process control and permits remote access to the fermentation system over the Internet. Single-substrate supernatant concentration in a high-cell-density fed-batch fermentation process was controlled by a proportional (P) controller (P = 50%) acting on the substrate pump feed rate. Na-octanoate concentrations oscillated around the setpoint of 10 mM and could be maintained between 0 and 25 mM at substrate uptake rates as high as 90 mmol L(-1) h(-1). Under cofeeding conditions Na-10-undecenoate and Na-octanoate could be individually controlled at 2.5 mM and 9 mM, respectively, by applying a proportional integral (PI) controller for each substrate. The resulting copolymer contained 43.5 mol% unsaturated monomers and reflected the ratio of 10-undecenoate in the feed. It was suggested that both substrates were consumed at similar rates. These results show that this control system is suitable for avoiding substrate toxicity and supplying carbon substrates for growth and mcl-PHA accumulation. Copyright 1999 John Wiley & Sons, Inc.
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              Closed-loop control of fed-batch cultures of recombinant Escherichia coli using on-line HPLC.

              This article describes a fully automated system for the on-line monitoring and closed-loop control of a fed-batch fermentation of recombinant Escherichia coli, and presents two case studies of its used in limiting production of unwanted byproducts such as acetic in fed-batch fermentations. The system had two components. The first components, on-line monitoring, comprised an aseptic sampling device, a microcentrifuge, and HPLC System. These instruments removed a Sample from a fermentor, spun it at high speed to separate solid and liquid components, and then automatically injected the supernatant onto an HPLC column for analysis. The second component consisted of control algorithms programmed using the LabView visual programming environment in a control computer that was linked via a remote components were linked so that results from the on-line HPLC were captured and used by the control algorithm was designed to demonstrate coarse feedback control to confirm the operability of the controller. The second case study showed how the system could be used in a more sophisticated feedings strategy providing fine control and limiting acetate concentration to a low level throughout the fermentation. (c) 1994 John Wiley & Sons, Inc.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2014
                25 March 2014
                : 9
                : 3
                : e92108
                Affiliations
                [1 ]Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
                [2 ]Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
                CSIR Institute of Genomics and Integrative Biology, India
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: DB IL. Performed the experiments: DB. Analyzed the data: DB IL. Wrote the paper: DB IL.

                Article
                PONE-D-13-51915
                10.1371/journal.pone.0092108
                3965399
                b7775d93-fd42-4890-bf6b-170346c17e3d
                Copyright @ 2014

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 9 December 2013
                : 4 February 2014
                Page count
                Pages: 8
                Funding
                IGLL received funding support from: NSF(NSF/MCB-1042335), and ONR (N000141310552). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Biotechnology
                Applied Microbiology
                Bioengineering
                Microbiology
                Computer and Information Sciences
                Software Engineering
                Software Design
                Software Tools
                Engineering and Technology
                Control Engineering

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                Uncategorized

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