Principles of open source bioinstrumentation applied to the poseidon syringe pump system.
Ontology highlight
ABSTRACT:
SUBMITTER: Booeshaghi AS
PROVIDER: S-EPMC6711986 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description: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.
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Project description:OTTO is an open-source automated liquid handler that can be fabricated at a cost of $1,500 using off-the-shelf and 3D-printable parts as an alternative to commercial devices. Open-source approaches have been applied to build syringe pumps, centrifuges, and other laboratory equipment. These devices are affordable but generally rely on a single motor to perform simple operations and thus do not fully utilize the potential of the Maker Movement. Open-source linear actuators and microcontrollers enable the fabrication of more complex laboratory instruments that rely on 3D positioning and accurate dispensing of fluids, such as automated liquid handlers. These instruments can be built rapidly and affordably, thereby providing access to highly reproducible sample preparation for common biological assays such as qPCR. We applied the design principles of speed and accuracy, unattended automation, and open-source components to build an automated liquid handler that controls micropipetting of liquids in 3D space at speeds and positional resolutions required for qPCR. In benchmarking studies, OTTO showed accuracy and sample preparation times comparable to manual qPCR. The ability to control linear motion and liquid dispensing using affordable off-the-shelf and 3D-printable parts can facilitate the adoption of open-source automated liquid handlers for qPCR, bioplotting, and other bioinstrumentation applications.
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Project description:Recent advances in embedded 3D bioprinting have significantly improved the resolution of individual filaments to below 100 μm; however, printing with such small filaments requires accurate extrusion of nanoliter volumes of bioink. Commercially available bioprinters and extruders are expensive and most utilize pneumatic control, which limits the minimum extrusion volume and prevents retraction (pulling bioink back into the reservoir), which is essential to printing high resolution features and complex internal geometry. Here we present a new generation of our open-source syringe pump designed for extrusion-based 3D bioprinting of soft materials: the Replistruder 4. The Replistruder 4 takes advantage of the geometry customizability and ease of 3D plastic printing while improving performance by integrating mass produced high-precision linear motion components. Simultaneously this new syringe pump remains compact and lightweight enough for several to be utilized on a 3D bioprinter for multimaterial bioprinting. To facilitate multiple use cases the Replistruder 4 is compatible with a range of syringes including disposable BD and Hamilton gastight syringes. In addition, we describe the process of designing clamps for other syringes. We demonstrate the performance of a Replistruder 4 with a 2.5 mL Hamilton gastight syringe by printing collagen type I constructs with individual filaments comprising 3.35 nL and patent channels down to 300 μm in width. With smaller volume Hamilton gastight syringes this performance can be further improved. Thus, the Replistruder 4 provides an open-source solution to print soft materials at the resolution limits of current embedded bioprinting platforms.
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Project description:Syringe pump extruders are required for a wide range of 3D printing applications, including bioprinting, embedded printing, and food printing. However, the mass of the syringe becomes a major challenge for most printing platforms, requiring compromises in speed, resolution and/or volume. To address these issues, we have designed a syringe pump large volume extruder (LVE) that is compatible with low-cost, open source 3D printers, and herein demonstrate its performance on a PrintrBot Simple Metal. Key aspects of the LVE include: (1) it is open source and compatible with open source hardware and software, making it inexpensive and widely accessible to the 3D printing community, (2) it utilizes a standard 60 mL syringe as its ink reservoir, effectively increasing print volume of the average bioprinter, (3) it is capable of retraction and high speed movements, and (4) it can print fluids using nozzle diameters as small as 100 µm, enabling the printing of complex shapes/objects when used in conjunction with the freeform reversible embedding of suspended hydrogels (FRESH) 3D printing method. Printing performance of the LVE is demonstrated by utilizing alginate as a model biomaterial ink to fabricate parametric CAD models and standard calibration objects.
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Project description:Nitrate, the most oxidized form of nitrogen, is regulated to protect people and animals from harmful levels as there is a large over abundance due to anthropogenic factors. Widespread field testing for nitrate could begin to address the nitrate pollution problem, however, the Cadmium Reduction Method, the leading certified method to detect and quantify nitrate, demands the use of a toxic heavy metal. An alternative, the recently proposed Environmental Protection Agency Nitrate Reductase Nitrate-Nitrogen Analysis Method, eliminates this problem but requires an expensive proprietary spectrophotometer. The development of an inexpensive portable, handheld photometer will greatly expedite field nitrate analysis to combat pollution. To accomplish this goal, a methodology for the design, development, and technical validation of an improved open-source water testing platform capable of performing Nitrate Reductase Nitrate-Nitrogen Analysis Method. This approach is evaluated for its potential to i) eliminate the need for toxic chemicals in water testing for nitrate and nitrite, ii) reduce the cost of equipment to perform this method for measurement for water quality, and iii) make the method easier to carryout in the field. The device is able to perform as well as commercial proprietary systems for less than 15% of the cost for materials. This allows for greater access to the technology and the new, safer nitrate testing technique.
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Project description:JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter sets, and for making comparisons among different models running simultaneously or separately. Interactive use is supported by a large collection of graphical user interfaces for model writing and compilation diagnostics, defining input functions, model runs, selection of algorithms solving ordinary and partial differential equations, run-time multidimensional graphics, parameter optimization (8 methods), sensitivity analysis, and Monte Carlo simulation for defining confidence ranges. JSim uses Mathematical Modeling Language (MML) a declarative syntax specifying algebraic and differential equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc.) are accessed through procedure calls. MML syntax is simple, basically defining the parameters and variables, then writing the equations in a straightforward, easily read and understood mathematical form. This makes JSim good for teaching modeling as well as for model analysis for research. For high throughput applications, JSim can be run as a batch job. JSim can automatically translate models from the repositories for Systems Biology Markup Language (SBML) and CellML models. Stochastic modeling is supported. MML supports assigning physical units to constants and variables and automates checking dimensional balance as the first step in verification testing. Automatic unit scaling follows, e.g. seconds to minutes, if needed. The JSim Project File sets a standard for reproducible modeling analysis: it includes in one file everything for analyzing a set of experiments: the data, the models, the data fitting, and evaluation of parameter confidence ranges. JSim is open source; it and about 400 human readable open source physiological/biophysical models are available at http://www.physiome.org/jsim/.
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Project description:The causes of epilepsy are incompletely understood, and rodent models enable valuable mechanistic investigations. Synchronized video-electroencephalography (video-EEG) data is critical for clinical assessment of seizure events and is similarly important in basic research on epilepsy, but commercial packages offer limited flexibility and are costly. We've developed and here make freely available OpenVEEG, fully open-source software for millisecond-synchronized video-EEG. With only hardware costs, the system price is approximately one-fifth that of a commercial system with similar capabilities. It is straightforward to use, readily extensible, and records robustly on the time scale of weeks.
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Project description:BACKGROUND:MR-guided focused ultrasound or high-intensity focused ultrasound (MRgFUS/MRgHIFU) is a non-invasive therapeutic modality with many potential applications in areas such as cancer therapy, drug delivery, and blood-brain barrier opening. However, the large financial costs involved in developing preclinical MRgFUS systems represent a barrier to research groups interested in developing new techniques and applications. We aim to mitigate these challenges by detailing a validated, open-source preclinical MRgFUS system capable of delivering thermal and mechanical FUS in a quantifiable and repeatable manner under real-time MRI guidance. METHODS:A hardware and software package was developed that includes closed-loop feedback controlled thermometry code and CAD drawings for a therapy table designed for a preclinical MRI scanner. For thermal treatments, the modular software uses a proportional integral derivative controller to maintain a precise focal temperature rise in the target given input from MR phase images obtained concurrently. The software computes the required voltage output and transmits it to a FUS transducer that is embedded in the delivery table within the magnet bore. The delivery table holds the FUS transducer, a small animal and its monitoring equipment, and a transmit/receive RF coil. The transducer is coupled to the animal via a water bath and is translatable in two dimensions from outside the magnet. The transducer is driven by a waveform generator and amplifier controlled by real-time software in Matlab. MR acoustic radiation force imaging is also implemented to confirm the position of the focus for mechanical and thermal treatments. RESULTS:The system was validated in tissue-mimicking phantoms and in vivo during murine tumor hyperthermia treatments. Sonications were successfully controlled over a range of temperatures and thermal doses for up to 20 min with minimal temperature overshoot. MR thermometry was validated with an optical temperature probe, and focus visualization was achieved with acoustic radiation force imaging. CONCLUSIONS:We developed an MRgFUS platform for small-animal treatments that robustly delivers accurate, precise, and controllable sonications over extended time periods. This system is an open source and could increase the availability of low-cost small-animal systems to interdisciplinary researchers seeking to develop new MRgFUS applications and technology.
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