Towards Extracting the Role and Behavior of Contributors in Open-source Projects

2019 ◽  
Author(s):  
Michail Papamichail ◽  
Themistoklis Diamantopoulos ◽  
Vasileios Matsoukas ◽  
Christos Athanasiadis ◽  
Andreas Symeonidis
Keyword(s):  
Open Source ◽  
And Behavior

scholarly journals Open source modules for tracking animal behavior and closed-loop stimulation based on Open Ephys and Bonsai

2018 ◽  
Author(s):  
Alessio Paolo Buccino ◽  
Mikkel Elle Lepperød ◽  
Svenn-Arne Dragly ◽  
Philipp Häfliger ◽  
Marianne Fyhn ◽  
...  
Keyword(s):  
Open Source ◽  
Real Time ◽  
Closed Loop ◽  
Low Cost ◽  
Data Formats ◽  
Behavioral Tracking ◽  
Real Time Tracking ◽  
Set Up ◽  
And Behavior ◽  
Closed Loop Stimulation

AbstractObjectiveA major goal in systems neuroscience is to determine the causal relationship between neural activity and behavior. To this end, methods that combine monitoring neural activity, behavioral tracking, and targeted manipulation of neurons in closed-loop are powerful tools. However, commercial systems that allow these types of experiments are usually expensive and rely on non-standardized data formats and proprietary software which may hinder user-modifications for specific needs. In order to promote reproducibility and data-sharing in science, transparent software and standardized data formats are an advantage. Here, we present an open source, low-cost, adaptable, and easy to set-up system for combined behavioral tracking, electrophysiology and closed-loop stimulation.ApproachBased on the Open Ephys system (www.open-ephys.org) we developed multiple modules to include real-time tracking and behavior-based closed-loop stimulation. We describe the equipment and provide a step-by-step guide to set up the system. Combining the open source software Bonsai (bonsai-rx.org) for analyzing camera images in real time with the newly developed modules in Open Ephys, we acquire position information, visualize tracking, and perform tracking-based closed-loop stimulation experiments. To analyze the acquired data we provide an open source file reading package in Python.Main resultsThe system robustly visualizes real-time tracking and reliably recovers tracking information recorded from a range of sampling frequencies (30-1000Hz). We combined electrophysiology with the newly-developed tracking modules in Open Ephys to record place cell and grid cell activity in the hippocampus and in the medial entorhinal cortex, respectively. Moreover, we present a case in which we used the system for closed-loop optogenetic stimulation of entorhinal grid cells.SignificanceExpanding the Open Ephys system to include animal tracking and behavior-based closed-loop stimulation extends the availability of high-quality, low-cost experimental setup within standardized data formats serving the neuroscience community.

scholarly journals Toolkit for Oscillatory Real-time Tracking and Estimation (TORTE)

2021 ◽  
Author(s):  
Mark Schatza ◽  
Ethan Blackwood ◽  
Sumedh Nagrale ◽  
Alik S Widge
Keyword(s):  
Open Source ◽  
Real Time ◽  
Closed Loop ◽  
Brain Activity ◽  
Loop Control ◽  
Oscillatory Phase ◽  
Wide Range ◽  
Real Time Tracking ◽  
Therapeutic Tools ◽  
And Behavior

Closing the loop between brain activity and behavior is one of the most active areas of development in neuroscience. There is particular interest in developing closed-loop control of neural oscillations. Many studies report correlations between oscillations and functional processes. Oscillation-informed closed-loop experiments might determine whether these relationships are causal and would provide important mechanistic insights which may lead to new therapeutic tools. These closed-loop perturbations require accurate estimates of oscillatory phase and amplitude, which are challenging to compute in real time. We developed an easy to implement, fast and accurate Toolkit for Oscillatory Real-time Tracking and Estimation (TORTE). TORTE operates with the open-source Open Ephys GUI (OEGUI) system, making it immediately compatible with a wide range of acquisition systems and experimental preparations. TORTE efficiently extracts oscillatory phase and amplitude from a target signal and includes a variety of options to trigger closed-loop perturbations. Implementing these tools into existing experiments is easy and adds minimal latency to existing protocols. Most labs use in-house lab-specific approaches, limiting replication and extension of their experiments by other groups. Accuracy of the extracted analytic signal and accuracy of oscillation-informed perturbations with TORTE match presented results by these groups. However, TORTE provides access to these tools in a flexible, easy to use toolkit without requiring proprietary software. We hope that the availability of a high-quality, open-source, and broadly applicable toolkit will increase the number of labs able to perform oscillatory closed-loop experiments, and will improve the replicability of protocols and data across labs.

scholarly journals WormBot, an open-source robotics platform for survival and behavior analysis in C. elegans

GeroScience ◽  
2019 ◽  
Vol 41 (6) ◽  
pp. 961-973 ◽  
Author(s):  
Jason N. Pitt ◽  
Nolan L. Strait ◽  
Elena M. Vayndorf ◽  
Benjamin W. Blue ◽  
Christina H. Tran ◽  
...  
Keyword(s):  
Open Source ◽  
Behavior Analysis ◽  
C Elegans ◽  
And Behavior

scholarly journals CAVE: An Open-Source Tool for Combined Analysis of Head-Mounted Calcium Imaging and Behavior in MATLAB

2018 ◽  
Vol 12 ◽  
Author(s):  
Jennifer Tegtmeier ◽  
Marcel Brosch ◽  
Kathrin Janitzky ◽  
Hans-Jochen Heinze ◽  
Frank W. Ohl ◽  
...  
Keyword(s):  
Open Source ◽  
Calcium Imaging ◽  
Combined Analysis ◽  
Open Source Tool ◽  
And Behavior

scholarly journals BOLeRo: Behavior optimization and learning for robots

2020 ◽  
Vol 17 (3) ◽  
pp. 172988142091374
Author(s):  
Alexander Fabisch ◽  
Malte Langosz ◽  
Frank Kirchner
Keyword(s):  
Reinforcement Learning ◽  
Evolutionary Algorithms ◽  
Open Source ◽  
State Of The Art ◽  
Learning Algorithms ◽  
Robotic Systems ◽  
Policy Search ◽  
Behavior Learning ◽  
And Behavior

Reinforcement learning and behavior optimization are becoming more and more popular in the field of robotics because algorithms are mature enough to tackle real problems in this domain. Robust implementations of state-of-the-art algorithms are often not publicly available though, and experiments are hardly reproducible because open-source implementations are often not available or are still in a stage of research code. Consequently, often it is infeasible to deploy these algorithms on robotic systems. BOLeRo closes this gap for policy search and evolutionary algorithms by delivering open-source implementations of behavior learning algorithms for robots. It is easy to integrate in robotic middlewares and it can be used to compare methods and develop prototypes in simulation.

scholarly journals lab.js: A free, open, online study builder

2019 ◽  
Author(s):  
Felix Henninger ◽  
Yury Shevchenko ◽  
Ulf Kai Mertens ◽  
Pascal J. Kieslich ◽  
Benjamin E. Hilbig
Keyword(s):  
Data Collection ◽  
Open Source ◽  
Response Times ◽  
Laboratory Data ◽  
Web Based ◽  
Online Study ◽  
Extensive Documentation ◽  
Accuracy And Precision ◽  
And Behavior ◽  
Free Open Source

Web-based data collection is increasingly popular in both experimental and survey-based research, because it is flexible, efficient and location-independent. While dedicated software for laboratory-based experimentation and online surveys is commonplace, researchers looking to implement experiments in the browser have, heretofore, often had to manually construct their studies’ content and logic using code. We introduce lab.js, a free, open-source experiment builder that makes it easy to build experiments for both online and in-laboratory data collection. Through its visual interface, stimuli can be designed and combined into a study without programming, though studies’ appearance and behavior can be fully customized using HTML, CSS and JavaScript code if required. Presentation and response times are kept and measured with high accuracy and precision heretofore unmatched in browser-based studies. Experiments constructed with lab.js can be run directly on a local computer, and published online with ease, with direct deployment to cloud hosting, export to any web server, and integration with popular data collection tools. Studies can also be shared in an editable format, archived, re-used and adapted, enabling effortless, transparent replications, and thus facilitating open, cumulative science. The software is provided free of charge under an open-source license; further information, code and extensive documentation are available from https://lab.js.org/.

scholarly journals Visualizing habitat use and behavior of whale sharks using the open tag, applications for ecotourism regulation.

2013 ◽  
Author(s):  
Jacob J Levenson ◽  
Robert Cooper ◽  
Colin Ware ◽  
Jacqueline Sly ◽  
David Wise ◽  
...  
Keyword(s):  
Habitat Use ◽  
Open Source ◽  
High Speed ◽  
Sensor Data ◽  
Measurement Unit ◽  
Release Time ◽  
Whale Shark ◽  
Fine Scale ◽  
Whale Sharks ◽  
And Behavior

Background. The rapidly decreasing cost of components and growing open source electronics industry has enabled access to improved tools for monitoring the behavior of aquatic species on a fine scale never before achieved. We use the new Open Tag as a novel approach to visualizing feeding behavior of whale sharks. Methods. The Open Tag is a Arduino compatible open-source inertial measurement unit for recording high speed motion sensor data to a microSD memory card. A three dimensional gyroscope, accelerometer, and magnetometer allow for calculating pitch, yaw, and heading, while depth and temperature sample continuously. The rechargeable lithium battery allows for deployments up to 7 days sampling at 100Hz. The Open Tag is placed in a hydrodynamic syntactic foam float, with a band that stretches around the dorsal fin. A galvanic release incorporated into the tag allows for a release time to be programmed and a VHF tag (ATS) aids in recovery. Results. An Open Tag was successfully deployed on a whale shark for 101 hours in August of 2013 in Yucatan Mexico. Behaviors noted included frequent surface intervals, even during the night when previously believed whale sharks were normally in deeper waters. A maximum depth of 49 meters was observed, with dives to 25 meters recorded regularly. We were able to identify possible harassment at the surface and defecation events. Conclusion. The Open Tag fills a unique niche in whale shark studies as a useful tool to better understanding of fine scale habitat use and behavior. By incorporating these data into Trackplot with data on the position of ecotour vessels, we can visualize behavior and investigate potential erratic changes in depth, heading and lateral movement amplitude indicative of harassment

scholarly journals Towards a Technique for Extracting Relational Actors from Monolithic Applications

2019 ◽  
Author(s):  
Rodrigo Laigner ◽  
Sérgio Lifschitz ◽  
Marcos Kalinowski ◽  
Marcus Poggi ◽  
Marcos Antonio Vaz Salles
Keyword(s):  
Open Source ◽  
Relational Database ◽  
Data Model ◽  
Database Systems ◽  
Actor Model ◽  
Reactor Modeling ◽  
Relational Data Model ◽  
Relational Database Systems ◽  
And Behavior ◽  
Novel Model

Relational actors, or reactors for short, integrate the actor model with the relational data model, providing an abstraction for enabling actor-relational database systems. However, as a novel model of computation for databases, there is no extensive work on reasoning about reactor modeling. To close this gap, this paper aims to propose as well as evaluate a technique to extract reactors from a monolithic system. For evaluation, we selected a REST-based open-source OLTP system in which a decomposition to microservices was conducted and applied our technique on its predecessor monolithic version. Our technique led to the same set of decisions, regarding table and behavior selection, taken by experts when decomposing the same system into microservices. The proposed technique can be seen as a first step towards supporting practitioners in decomposing OLTP systems into reactors.

Trends in Free, Libre, Open Source Software Communities: From Volunteers to Companies

2013 ◽  
Vol 55 (5) ◽  
Author(s):  
Jesus M. Gonzalez-Barahona ◽  
Gregorio Robles
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Corporate Interests ◽  
And Behavior

AbstractThe first free/libre/open source software (FLOSS) development communities were composed almost exclusively of volunteers. They were individuals who, despite their affiliation, contributed to the project on their own. They decided which project to join, and their contributions were personal in nature, even when in some cases they were employees of companies with some interests in the project. GNU, the first of such communities, and some others that emerged during the late 1980s and 1990s, followed this pattern. During the 1990s corporate interests started to have a role in some FLOSS communities. Companies hired people from those communities to gain influence, or tasked their employees to contribute to them, again with the idea of influencing their decisions. During the 2000s, corporate communities, in which companies are first-class citizens, have emerged, changing the rules and redefining the role of volunteers and non-affiliated individuals. However, the role of developers, with independence of the company for which they work, is still important even in these communities. This paper addresses this transition from volunteer-based to company-based development communities, and explores the structure and behavior of the latter.

scholarly journals Rigbox: An Open-Source Toolbox for Probing Neurons and Behavior

eNeuro ◽  
2020 ◽  
Vol 7 (4) ◽  
pp. ENEURO.0406-19.2020 ◽  
Author(s):  
Jai Bhagat ◽  
Miles J. Wells ◽  
Kenneth D. Harris ◽  
Matteo Carandini ◽  
Christopher P. Burgess
Keyword(s):  
Open Source ◽  
And Behavior
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