POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer.
Ontology highlight
ABSTRACT:
SUBMITTER: Lausted C
PROVIDER: S-EPMC507883 | biostudies-other | 2004
REPOSITORIES: biostudies-other
Publications
POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer.
Lausted Christopher C Dahl Timothy T Warren Charles C King Kimberly K Smith Kimberly K Johnson Michael M Saleem Ramsey R Aitchison John J Hood Lee L Lasky Stephen R SR
Genome biology 20040727 8
DNA arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo. We describe here an open-source inkjet arrayer capable of rapidly producing sets of unique 9,800-feature arrays. ...[more]
Similar Datasets
Project description:We present the open-source AiZynthFinder software that can be readily used in retrosynthetic planning. The algorithm is based on a Monte Carlo tree search that recursively breaks down a molecule to purchasable precursors. The tree search is guided by an artificial neural network policy that suggests possible precursors by utilizing a library of known reaction templates. The software is fast and can typically find a solution in less than 10 s and perform a complete search in less than 1 min. Moreover, the development of the code was guided by a range of software engineering principles such as automatic testing, system design and continuous integration leading to robust software with high maintainability. Finally, the software is well documented to make it suitable for beginners. The software is available at http://www.github.com/MolecularAI/aizynthfinder .
| S-EPMC7672904 | biostudies-literature
Project description:Herein we present TmPrime, a computer program to design oligonucleotide sets for gene assembly by both ligase chain reaction (LCR) and polymerase chain reaction (PCR). TmPrime offers much flexibility with no constraints on the gene and oligonucleotide lengths. The program divides the long input DNA sequence based on the input desired melting temperature, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences and potential formation of secondary structures. Our program also provides functions on sequence pooling to separate long genes into smaller pieces for multi-pool assembly and codon optimization for expression. The software has been successfully used in the design and synthesis of green fluorescent protein fragment (GFPuv) (760 bp), human protein kinase B-2 (PKB2) (1446 bp) and the promoter of human calcium-binding protein A4 (S100A4) (752 bp) using real-time PCR assembly with LCGreen I, which offers a novel approach to compare the efficiency of gene synthesis. The purity of assembled products is successfully estimated with the use of melting curve analysis, which would potentially eliminate the necessity for agarose gel electrophoresis. This program is freely available at http://prime.ibn.a-star.edu.sg.
| S-EPMC2703938 | biostudies-literature
Project description:Our understanding of complex living systems is limited by our capacity to perform experiments in high throughput. While robotic systems have automated many traditional hand-pipetting protocols, software limitations have precluded more advanced maneuvers required to manipulate, maintain, and monitor hundreds of experiments in parallel. Here, we present Pyhamilton, an open-source Python platform that can execute complex pipetting patterns required for custom high-throughput experiments such as the simulation of metapopulation dynamics. With an integrated plate reader, we maintain nearly 500 remotely monitored bacterial cultures in log-phase growth for days without user intervention by taking regular density measurements to adjust the robotic method in real-time. Using these capabilities, we systematically optimize bioreactor protein production by monitoring the fluorescent protein expression and growth rates of a hundred different continuous culture conditions in triplicate to comprehensively sample the carbon, nitrogen, and phosphorus fitness landscape. Our results demonstrate that flexible software can empower existing hardware to enable new types and scales of experiments, empowering areas from biomanufacturing to fundamental biology.
| S-EPMC7993322 | biostudies-literature
Project description:There is a need for flexible and affordable plant phenotyping solutions for basic research and plant breeding. We demonstrate our open source plant imaging and processing solution ('PhenoBox'/'PhenoPipe') and provide construction plans, source code and documentation to rebuild the system. Use of the PhenoBox is exemplified by studying infection of the model grass Brachypodium distachyon by the head smut fungus Ustilago bromivora, comparing phenotypic responses of maize to infection with a solopathogenic Ustilago maydis (corn smut) strain and effector deletion strains, and studying salt stress response in Nicotiana benthamiana. In U. bromivora-infected grass, phenotypic differences between infected and uninfected plants were detectable weeks before qualitative head smut symptoms. Based on this, we could predict the infection outcome for individual plants with high accuracy. Using a PhenoPipe module for calculation of multi-dimensional distances from phenotyping data, we observe a time after infection-dependent impact of U. maydis effector deletion strains on phenotypic response in maize. The PhenoBox/PhenoPipe system is able to detect established salt stress responses in N. benthamiana. We have developed an affordable, automated, open source imaging and data processing solution that can be adapted to various phenotyping applications in plant biology and beyond.
| S-EPMC6485332 | biostudies-literature
Project description:FiberSim is a flexible open-source model of myofilament-level contraction. The code uses a spatially explicit technique, meaning that it tracks the position and status of each contractile molecule within the lattice framework. This allows the model to simulate some of the mechanical effects modulated by myosin-binding protein C, as well as the dose dependence of myotropes and the effects of varying isoform expression levels. This paper provides a short introduction to FiberSim and presents simulations of tension-pCa curves with and without regulation of thick and thin filament activation by myosin-binding protein C. A myotrope dose-dependent response as well as slack/re-stretch maneuvers to assess rates of tension recovery are also presented. The software was designed to be flexible (the user can define their own model and/or protocol) and computationally efficient (simulations can be performed on a regular laptop). We hope that other investigators will use FiberSim to explore myofilament level mechanisms and to accelerate research focusing on the contractile properties of sarcomeres.
| S-EPMC8790209 | biostudies-literature
Project description:The human pupil behavior has gained increased attention due to the discovery of the intrinsically photosensitive retinal ganglion cells and the afferent pupil control path's role as a biomarker for cognitive processes. Diameter changes in the range of 10-2 mm are of interest, requiring reliable and characterized measurement equipment to accurately detect neurocognitive effects on the pupil. Mostly commercial solutions are used as measurement devices in pupillometry which is associated with high investments. Moreover, commercial systems rely on closed software, restricting conclusions about the used pupil-tracking algorithms. Here, we developed an open-source pupillometry platform consisting of hardware and software competitive with high-end commercial stereo eye-tracking systems. Our goal was to make a professional remote pupil measurement pipeline for laboratory conditions accessible for everyone. This work's core outcome is an integrated cross-platform (macOS, Windows and Linux) pupillometry software called PupilEXT, featuring a user-friendly graphical interface covering the relevant requirements of professional pupil response research. We offer a selection of six state-of-the-art open-source pupil detection algorithms (Starburst, Swirski, ExCuSe, ElSe, PuRe and PuReST) to perform the pupil measurement. A developed 120-fps pupillometry demo system was able to achieve a calibration accuracy of 0.003 mm and an averaged temporal pupil measurement detection accuracy of 0.0059 mm in stereo mode. The PupilEXT software has extended features in pupil detection, measurement validation, image acquisition, data acquisition, offline pupil measurement, camera calibration, stereo vision, data visualization and system independence, all combined in a single open-source interface, available at https://github.com/openPupil/Open-PupilEXT.
| S-EPMC8249868 | biostudies-literature
Project description:The study of mouse lung mechanics provides essential insights into the physiological mechanisms of pulmonary disease. Consequently, investigators assemble custom systems comprising infusion-withdrawal syringe pumps and analog pressure sensors to investigate the lung function of these animals. But these systems are expensive and require ongoing regulation, making them challenging to use. Here I introduce LungElast, an open-source, inexpensive, and self-contained instrument that can experimentally determine lung elasticity and volumes even in immature mice. It is assembled using custom 3D printed parts and readily available or easily constructed components. In this device, a microprocessor-controlled stepper motor automatically regulates lung volume by precisely driving a syringe piston whose position is determined using time-of-flight LIDAR technology. The airway pressures associated with the lung volumes are determined using compact sensor-on-chip technology, retrieved in a digital format, and stored by the microcontroller. The instrument software is modular, which eases device testing, calibration, and use. Data are also provided here that specify the accuracy and precision of the elastometer's sensors and volume delivery and demonstrate its use with lung models and mouse pups. This instrument has excellent potential for research and educational work.
| S-EPMC10338507 | biostudies-literature
Project description:BACKGROUND:Measuring food intake in rodents is a conceptually simple yet labor-intensive and temporally-imprecise task. Most commonly, food is weighed manually, with an interval of hours or days between measurements. Commercial feeding monitors are excellent, but are costly and require specialized caging and equipment. NEW METHOD:We have developed the Feeding Experimentation Device (FED): a low-cost, open-source, home cage-compatible feeding system. FED utilizes an Arduino microcontroller and open-source software and hardware. FED dispenses a single food pellet into a food well where it is monitored by an infrared beam. When the mouse removes the pellet, FED logs the timestamp to a secure digital (SD) card and dispenses a new pellet into the well. Post-hoc analyses of pellet retrieval timestamps reveal high-resolution details about feeding behavior. RESULTS:FED is capable of accurately measuring food intake, identifying discrete trends during light and dark-cycle feeding. Additionally, we show the utility of FED for measuring increases in feeding resulting from optogenetic stimulation of agouti-related peptide neurons in the arcuate nucleus of the hypothalamus. COMPARISON TO EXISTING METHODS:With a cost of ?$350 per device, FED is >10× cheaper than commercially available feeding systems. FED is also self-contained, battery powered, and designed to be placed in standard colony rack cages, allowing for monitoring of true home cage feeding behavior. Moreover, FED is highly adaptable and can be synchronized with emerging techniques in neuroscience, such as optogenetics, as we demonstrate here. CONCLUSIONS:FED allows for accurate, precise monitoring of feeding behavior in a home cage setting.
| S-EPMC4884551 | biostudies-literature
Project description:Forests, estimated to contain two thirds of the world's biodiversity, face existential threats due to illegal logging and land conversion. Efforts to combat illegal logging and to support sustainable value chains are hampered by a critical lack of affordable and scalable technologies for field-level inspection of wood and wood products. To meet this need we present the XyloTron, a complete, self-contained, multi-illumination, field-deployable, open-source platform for field imaging and identification of forest products at the macroscopic scale. The XyloTron platform integrates an imaging system built with off-the-shelf components, flexible illumination options with visible and UV light sources, software for camera control, and deep learning models for identification. We demonstrate the capabilities of the XyloTron platform with example applications for automatic wood and charcoal identification using visible light and human-mediated wood identification based on ultra-violet illumination and discuss applications in field imaging, metrology, and material characterization of other substrates.
| S-EPMC7366520 | biostudies-literature
Project description:Background Multiplexing tissue imaging is developing as a complement for single cell analysis, bringing the spatial information of cells in tissue in addition to multiple parameters measurements. More and more commercial or home-made systems are available. These techniques allow the imaging of tens of fluorescent reporters, where the spectral overlap is solved by imaging by cycles the fluorophores using microfluidics to change the reporters between each cycle. Methods For several systems, the acquisition system coupled to the microfluidic system is a wide field microscope, and the acquisition process is done by mosaicking to cover a large field of view, relying on image processing to obtain the data set to be analysed in intensity. The processed data set allows the identification of different populations, quite similarly to cytometry analysis, but with spatial information in addition. To obtain the final image for analysis from the raw acquisitions, several preprocessing steps are needed for inter-cycle registration, tissue autofluorescence correction or mosaicking. We propose a workflow for this preprocessing, implemented as an open source software (as a library, command line tool and standalone). Results We exemplify the workflow on the commercial system PhenoCycler TM (formerly named CODEX®) and provide a reduced size data set for testing. Conclusions We compare our processor with the commercially provided processor and show that we solve some problems also reported by other users.
| S-EPMC10799232 | biostudies-literature