scholarly journals An open source device for operant licking in rats

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2981 ◽  
Author(s):  
Matthew Longley ◽  
Ethan L. Willis ◽  
Cindy X. Tay ◽  
Hao Chen
Keyword(s):  
Open Source ◽  
Radio Frequency Identification ◽  
Source Code ◽  
Fixed Ratio ◽  
Progressive Ratio ◽  
Raspberry Pi ◽  
Motion Sensors ◽  
Environmental Sensors ◽  
3D Design ◽  
Behavioral Studies

We created an easy-to-use device for operant licking experiments and another device that records environmental variables. Both devices use the Raspberry Pi computer to obtain data from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors) and activate output devices (e.g., LED lights, syringe pumps) as needed. Data gathered from these devices are stored locally on the computer but can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the source code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. The source code can be found at http://github.com/chen42/openbehavior.

scholarly journals An open source device for operant licking in rats

2016 ◽  
Author(s):  
Matthew Longley ◽  
Ethan L Willis ◽  
Cindy X Tay ◽  
Hao Chen
Keyword(s):  
Open Source ◽  
Radio Frequency Identification ◽  
Credit Card ◽  
Fixed Ratio ◽  
Progressive Ratio ◽  
Complex Data ◽  
Motion Sensors ◽  
3D Design ◽  
Behavioral Studies ◽  
Complex Data Sets

Increasingly complex data sets are needed to fully understand the complexity in behavior. Credit card sized single-board computers with multi-core CPUs are an attractive platform for designing devices capable of collecting multi-dimensional behavioral data. To demonstrate this idea, we created an easy to-use device for operant licking experiments and another device that records environmental variables. These systems collect data obtained from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors) and activate output devices (e.g., LED lights, syringe pumps) as needed. Data gathered from these devices can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. http://github.com/chen42/openbehavior.

scholarly journals An open source device for operant licking in rats

2016 ◽  
Author(s):  
Matthew Longley ◽  
Ethan L Willis ◽  
Cindy X Tay ◽  
Hao Chen
Keyword(s):  
Open Source ◽  
Radio Frequency Identification ◽  
Credit Card ◽  
Fixed Ratio ◽  
Progressive Ratio ◽  
Complex Data ◽  
Motion Sensors ◽  
3D Design ◽  
Behavioral Studies ◽  
Complex Data Sets

Increasingly complex data sets are needed to fully understand the complexity in behavior. Credit card sized single-board computers with multi-core CPUs are an attractive platform for designing devices capable of collecting multi-dimensional behavioral data. To demonstrate this idea, we created an easy to-use device for operant licking experiments and another device that records environmental variables. These systems collect data obtained from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors) and activate output devices (e.g., LED lights, syringe pumps) as needed. Data gathered from these devices can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. http://github.com/chen42/openbehavior.

scholarly journals Ulyxes: an open source project for automation in engineering surveying

2018 ◽  
Author(s):  
Zoltan Siki ◽  
Bence Takács ◽  
Csaba Égető
Keyword(s):  
Open Source ◽  
Nuclear Power ◽  
Source Code ◽  
Raspberry Pi ◽  
Observation Data ◽  
Engineering Structures ◽  
Open Source Project ◽  
Monitoring Task ◽  
Server Side ◽  
Process Observation

Ulyxes is an open source project to drive robotic total stations as well as other sensors, collect their measurements in database and finally publish the results for authorized users on the web. On special requests the results are also presented with web based maps in the background. This project is like an instant coffee: three in one (coffee, sugar and milk). The coffee and the strongest part is the research and coding. The sugar is the application of the program in industrial environment and the milk on the top is the educational usage. The software development started in 2008 connected to a monitoring task in the Hungarian Nuclear Power Plant. Since then the development has been extended from total stations to different positioning capable sensors. In 2012 the development of a new Python based object oriented framework started. The code is based on the results of some other open source projects, Python, PySerial, GNUGama, SQLite, OpenCV, etc. After connecting to the international Geo4All network in 2014, Ulyxes became a project of our Geo4All Lab. The project has its own home page (http://www.agt.bme.hu/ulyxes) and the source code is available on the GitHub portal (https://github.com/zsiki/ulyxes). The code is maintained by the colleagues at the Department of Geodesy and Surveying at the Budapest University of Technology, volunteers from all over the World are welcome. BSc and MSc students are also involved in the development and testing. More theses were connected to this project in the recent five years. In the curriculum of an MSc subject called Surveying Automation, Ulyxes is used to demonstrate automatized tasks in engineering surveying. The system has been applied for several projects during the last 10+ years. Typical applications are the load tests of bridges and other engineering structures and on the other hand Ulyxes can be used to monitor the movements of buildings in the nearby of constructional works, like metro stations, underground garage and other buildings as well. Raspberry Pi small, single board computers are used with Raspbian operating system during on-site works. The source code is divided into three parts. The first one is the Ulyxes API which is the core of the system. The second one, Ulyxes Apps is a collection of applications based upon the API. Some of them were developed by our students. The third part is the server side scripts to publish observation results through the Internet. Moreover it is also planned to implement SOS standard using IstSOS. Our Geo4All Lab maintains another open source software, called GeoEasy to process observation data in engineering and land surveying. A closer cooperation is also planned between our two open source projects. In this paper the most important features of Ulyxes will be presented with examples, an actual monitoring project in Budapest and test loads of bridges and overpasses.

scholarly journals TailTimer: an open-source device for automating the rodent tail immersion assay

2020 ◽  
Author(s):  
Mallory E. Udell ◽  
Angel Garcia Martinez ◽  
Tengfei Wang ◽  
Jie Ni ◽  
Christian Hurt ◽  
...  
Keyword(s):  
User Interface ◽  
Water Temperature ◽  
Open Source ◽  
Radio Frequency Identification ◽  
Raspberry Pi ◽  
Thermal Pain ◽  
Withdrawal Latency ◽  
Tail Immersion ◽  
Two Factors ◽  
Thermal Pain Sensitivity

AbstractThe tail immersion assay is a widely used method for measuring acute thermal pain in a way which is quantifiable and reproducible. It is non-invasive and measures response to a stimulus that may be encountered by an animal in its natural environment. However, tail withdrawal latency data are usually collected manually, and precise temperatures of the water at the time of measurement are most often not recorded. These two factors can reduce the reproducibility of tail immersion assay data. We designed a device, TailTimer, which uses the Raspberry Pi single-board computer and a temperature sensor, to automatically record both tail withdrawal latency and water temperature. The device has a radio frequency identification (RFID) system that can record the ID of animals. Our software recognizes several specific RFID keys as user interface commands, which allows TailTimer to be operated via RFID fobs. We also programmed the device to only allow tests to be conducted when the water is within ± 0.25 °C of the target temperature. Data recorded using the TailTimer device showed a linear relationship between tail withdrawal latency and water temperature when tested between 47 - 50 °C. We also observed a profound effect of water mixing speed on tail withdrawal latency. Our data further revealed significant strain and sex differences, valorizing TailTimer in its ability to detect genetically-determined variations in thermal pain sensitivity.Significance StatementQuantification of tail withdrawal latency in response to thermal pain has essentially remained the same since the method was first introduced decades ago and relies on manual recording of water temperature and tail withdrawal latency. Such manual methods engender relatively substantial variability and are potential contributors to some of the discrepancies present among relevant research. The open source TailTimer device we report here is simple and inexpensive to manufacture. The RFID-based user interface is ergonomic, especially in animal facilities where space is limited and gloves are mandatory. We anticipate that the increased reproducibility of tail withdrawal latency provided by TailTimer will augment its utility in nociception and addiction research.

scholarly journals Early Detection of Apathetic Phenotypes in Huntington’s Disease Knock-in Mice Using Open Source Tools

2017 ◽  
Author(s):  
Shawn Minnig ◽  
Robert M. Bragg ◽  
Hardeep S. Tiwana ◽  
Wes T. Solem ◽  
William S. Hovander ◽  
...  
Keyword(s):  
Early Detection ◽  
Huntington's Disease ◽  
Open Source ◽  
Huntington’S Disease ◽  
Fixed Ratio ◽  
Noisy Data ◽  
Progressive Ratio ◽  
Phenotypic Rescue ◽  
Preclinical Work ◽  
Normal Performance

AbstractApathy is one of the most prevalent and progressive psychiatric symptom in Huntington’s disease (HD) patients. However, preclinical work in HD mouse models tend to focus on molecular and motor, rather than affective, phenotypes. Measuring behavior in mice often produces noisy data and requires large cohorts to detect phenotypic rescue with appropriate power. The operant equipment necessary for measuring affective phenotypes is typically expensive, proprietary to commercial entities, and bulky which can render adequately sized mouse cohorts as cost-prohibitive. Thus, we describe here a home-built open-source alternative to commercial hardware that is reliable, scalable, and reproducible. Using off-the-shelf hardware, we adapted and built several of the rodent operant buckets (ROBucket) designed to test HttQ111/+ mice for attention deficits in fixed ratio (FR) and progressive ratio (PR) tasks. We find that, despite normal performance in reward attainment in the FR task, HttQ111/+ mice exhibit reduced PR performance at 9-11 months of age, suggesting motivational deficits. We replicated this in two independent cohorts, which demonstrates the reliability and utility of both the apathetic phenotype, and these ROBuckets, for preclinical HD studies.

scholarly journals Ulyxes: an open source project for automation in engineering surveying

2018 ◽  
Author(s):  
Zoltan Siki ◽  
Bence Takács ◽  
Csaba Égető
Keyword(s):  
Open Source ◽  
Nuclear Power ◽  
Source Code ◽  
Raspberry Pi ◽  
Observation Data ◽  
Engineering Structures ◽  
Open Source Project ◽  
Monitoring Task ◽  
Server Side ◽  
Process Observation

Ulyxes is an open source project to drive robotic total stations as well as other sensors, collect their measurements in database and finally publish the results for authorized users on the web. On special requests the results are also presented with web based maps in the background. This project is like an instant coffee: three in one (coffee, sugar and milk). The coffee and the strongest part is the research and coding. The sugar is the application of the program in industrial environment and the milk on the top is the educational usage. The software development started in 2008 connected to a monitoring task in the Hungarian Nuclear Power Plant. Since then the development has been extended from total stations to different positioning capable sensors. In 2012 the development of a new Python based object oriented framework started. The code is based on the results of some other open source projects, Python, PySerial, GNUGama, SQLite, OpenCV, etc. After connecting to the international Geo4All network in 2014, Ulyxes became a project of our Geo4All Lab. The project has its own home page (http://www.agt.bme.hu/ulyxes) and the source code is available on the GitHub portal (https://github.com/zsiki/ulyxes). The code is maintained by the colleagues at the Department of Geodesy and Surveying at the Budapest University of Technology, volunteers from all over the World are welcome. BSc and MSc students are also involved in the development and testing. More theses were connected to this project in the recent five years. In the curriculum of an MSc subject called Surveying Automation, Ulyxes is used to demonstrate automatized tasks in engineering surveying. The system has been applied for several projects during the last 10+ years. Typical applications are the load tests of bridges and other engineering structures and on the other hand Ulyxes can be used to monitor the movements of buildings in the nearby of constructional works, like metro stations, underground garage and other buildings as well. Raspberry Pi small, single board computers are used with Raspbian operating system during on-site works. The source code is divided into three parts. The first one is the Ulyxes API which is the core of the system. The second one, Ulyxes Apps is a collection of applications based upon the API. Some of them were developed by our students. The third part is the server side scripts to publish observation results through the Internet. Moreover it is also planned to implement SOS standard using IstSOS. Our Geo4All Lab maintains another open source software, called GeoEasy to process observation data in engineering and land surveying. A closer cooperation is also planned between our two open source projects. In this paper the most important features of Ulyxes will be presented with examples, an actual monitoring project in Budapest and test loads of bridges and overpasses.

Impact of Clone Refactoring on External Quality Attributes of Open Source Softwares

2018 ◽  
pp. 86-94
Author(s):  
Himanshi Vashisht ◽  
Sanjay Bharadwaj ◽  
Sushma Sharma
Keyword(s):  
Open Source ◽  
Internal Structure ◽  
Software Quality ◽  
Source Code ◽  
Quality Attributes ◽  
Software Component ◽  
External Quality ◽  
Code Refactoring ◽  
Observable Behaviour

Code refactoring is a “Process of restructuring an existing source code.”. It also helps in improving the internal structure of the code without really affecting its external behaviour”. It changes a source code in such a way that it does not alter the external behaviour yet still it improves its internal structure. It is a way to clean up code that minimizes the chances of introducing bugs. Refactoring is a change made to the internal structure of a software component to make it easier to understand and cheaper to modify, without changing the observable behaviour of that software component. Bad smells indicate that there is something wrong in the code that have to refactor. There are different tools that are available to identify and emove these bad smells. A software has two types of quality attributes- Internal and external. In this paper we will study the effect of clone refactoring on software quality attributes.

AN OPEN-SOURCE CODE FOR NUMERICAL SIMULATION OF DRAINAGE BASIN DEVELOPMENT

2017 ◽  
Author(s):  
George H. Shaw ◽  
◽  
Howard D. Mooers ◽  
Josef Smrz ◽  
Zdenek Papez ◽  
...  
Keyword(s):  
Numerical Simulation ◽  
Open Source ◽  
Drainage Basin ◽  
Source Code ◽  
Open Source Code ◽  
Basin Development

scholarly journals Monitoring System for Tracking a PV Generator in an Experimental Smart Microgrid: An Open-Source Solution

2021 ◽  
Vol 13 (15) ◽  
pp. 8182
Author(s):  
José María Portalo ◽  
Isaías González ◽  
Antonio José Calderón
Keyword(s):  
Open Source ◽  
Monitoring System ◽  
Smart Grids ◽  
Raspberry Pi ◽  
Operator Interface ◽  
Open Source Hardware ◽  
Real Time Information ◽  
And Storage ◽  
Time Information ◽  
Pv Generator

Smart grids and smart microgrids (SMGs) require proper monitoring for their operation. To this end, measuring, data acquisition, and storage, as well as remote online visualization of real-time information, must be performed using suitable equipment. An experimental SMG is being deployed that combines photovoltaics and the energy carrier hydrogen through the interconnection of photovoltaic panels, electrolyser, fuel cell, and load around a voltage bus powered by a lithium battery. This paper presents a monitoring system based on open-source hardware and software for tracking the temperature of the photovoltaic generator in such an SMG. In fact, the increases in temperature in PV modules lead to a decrease in their efficiency, so this parameter needs to be measured in order to monitor and evaluate the operation. Specifically, the developed monitoring system consists of a network of digital temperature sensors connected to an Arduino microcontroller, which feeds the acquired data to a Raspberry Pi microcomputer. The latter is accessed by a cloud-enabled user/operator interface implemented in Grafana. The monitoring system is expounded and experimental results are reported to validate the proposal.

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