scholarly journals ZAF, the first open source fully automated feeder for aquatic facilities

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Merlin Lange ◽  
AhmetCan Solak ◽  
Shruthi Vijay Kumar ◽  
Hirofumi Kobayashi ◽  
Bin Yang ◽  
...  
Keyword(s):  
Open Source ◽  
Food Distribution ◽  
Model Organisms ◽  
Precise Control ◽  
Automatic Feeder ◽  
Animal Feeding ◽  
Fully Automatic ◽  
Cost Efficient ◽  
User Friendly ◽  
Advanced Version

In the past few decades, aquatic animals have become popular model organisms in biology, spurring a growing need for establishing aquatic facilities. Zebrafish are widely studied and relatively easy to culture using commercial systems. However, a challenging aspect of maintaining aquatic facilities is animal feeding, which is both time- and resourceconsuming. We have developed an open-source fully automatic daily feeding system, Zebrafish Automatic Feeder (ZAF). ZAF is reliable, provides a standardized amount of food to every tank, is cost-efficient and easy to build. The advanced version, ZAF+, allows for the precise control of food distribution as a function of fish density per tank, and has a user-friendly interface. Both ZAF and ZAF+ are adaptable to any laboratory environment and facilitate the implementation of aquatic colonies. Here we provide all blueprints and instructions for building the mechanics, electronics, fluidics, as well as to setup the control software and its user-friendly graphical interface. Importantly, the design is modular and can be scaled to meet different user needs. Furthermore, our results show that ZAF and ZAF+ do not adversely affect zebrafish culture, enabling fully automatic feeding for any aquatic facility.

scholarly journals ZAF – An Open Source Fully Automated Feeder for Aquatic Facilities

2021 ◽  
Author(s):  
Merlin Lange ◽  
AhmetCan Solak ◽  
Shruthi Vijay Kumar ◽  
Hirofumi Kobayashi ◽  
Bin Yang ◽  
...  
Keyword(s):  
Open Source ◽  
Food Distribution ◽  
Model Organisms ◽  
Precise Control ◽  
Automatic Feeder ◽  
Animal Feeding ◽  
Fully Automatic ◽  
Cost Efficient ◽  
User Friendly ◽  
Advanced Version

In the past few decades, aquatic animals have become popular model organisms in biology, spurring a growing need for establishing aquatic facilities. Zebrafish are widely studied and relatively easy to culture using commercial systems. However, a challenging aspect of maintaining aquatic facilities is animal feeding, which is both time- and resource-consuming. We have developed an open-source fully automatic daily feeding system, Zebrafish Automatic Feeder (ZAF). ZAF is reliable, provides a standardized amount of food to every tank, is cost-efficient, easy to build, and has a user-friendly interface. The advanced version, ZAF+, allows for the precise control of food distribution as a function of fish density per tank. Both ZAF and ZAF+ are adaptable to any laboratory environment and can help facilitate the implementation of aquatic colonies. Here we provide all blueprints and instructions for building the mechanics, electronics, fluidics, as well as to setup the control software and its user-friendly graphical interface. Importantly, the design is modular and can be scaled to meet different user needs. Furthermore, our results show that ZAF and ZAF+ do not adversely affect zebrafish culture, enabling fully automatic feeding for any aquatic facility.

scholarly journals TGAC Browser: An open-source genome browser for non-model organisms

2019 ◽  
Author(s):  
Anil S. Thanki ◽  
Xingdong Bian ◽  
Robert P. Davey
Keyword(s):  
Open Source ◽  
Genomic Data ◽  
Vital Role ◽  
Genome Browser ◽  
Model Organisms ◽  
Genome Browsers ◽  
Public Repositories ◽  
Set Up ◽  
User Friendly ◽  
Ngs Data

Genome browsers play a vital role to provide visualisation for genomic data. It is often the case that bespoke genome browser customisations are required between different research groups, with an obvious necessity to update, upgrade and tailor tracks and features on a potentially frequent basis. However, most of the current genome browsers require highly curated data held in public repositories. Besides, these genome browsers often rely on particular dependencies, where writing plug-in or modifying existing code can be troublesome and resource expensive.We present TGAC Browser, a new open-source web-based genome browser designed to overcome shortcomings in available approaches. It uses a locally installed Ensembl Core Database schema and is also able to visualise data from well-known NGS data formats. We also added simple analysis functionality to perform BLAST searches within TGAC Browser. TGAC Browser also allows uploading your genomic data. TGAC Browser is an open-source, easy to set up, and user-friendly genome browser with minimal, lightweight configuration details.

MackDroid - An Android based Application to monitor devices

2016 ◽  
Vol 9 ◽  
pp. 1
Author(s):  
Maaz Sirkhot ◽  
Ekta Sirwani ◽  
Aishwarya Kourani ◽  
Akshit Batheja ◽  
Kajal Jethanand Jewani
Keyword(s):  
Operating System ◽  
Open Source ◽  
Vital Role ◽  
Mobile Users ◽  
Android Application ◽  
Web Page ◽  
Technological World ◽  
Monitoring Service ◽  
User Friendly

In this technological world, smartphones can be considered as one of the most far-reaching inventions. It plays a vital role in connecting people socially. The number of mobile users using an Android based smartphone has increased rapidly since last few years resulting in organizations, cyber cell departments, government authorities feeling the need to monitor the activities on certain targeted devices in order to maintain proper functionality of their respective jobs. Also with the advent of smartphones, Android became one of the most popular and widely used Operating System. Its highlighting features are that it is user friendly, smartly designed, flexible, highly customizable and supports latest technologies like IoT. One of the features that makes it exclusive is that it is based on Linux and is Open Source for all the developers. This is the reason why our project Mackdroid is an Android based application that collects data from the remote device, stores it and displays on a PHP based web page. It is primarily a monitoring service that analyzes the contents and distributes it in various categories like Call Logs, Chats, Key logs, etc. Our project aims at developing an Android application that can be used to track, monitor, store and grab data from the device and store it on a server which can be accessed by the handler of the application.

scholarly journals An Interactive WebGIS Framework for Coastal Erosion Risk Management

2021 ◽  
Vol 9 (6) ◽  
pp. 567
Author(s):  
Alessandra Capolupo ◽  
Cristina Monterisi ◽  
Alessandra Saponieri ◽  
Fabio Addona ◽  
Leonardo Damiani ◽  
...  
Keyword(s):  
Open Source ◽  
3D Visualization ◽  
Erosion Risk ◽  
Innovative Strategies ◽  
Web Mapping ◽  
Natural Processes ◽  
Multi Scale ◽  
Interactive Interface ◽  
Multi Temporal ◽  
User Friendly

The Italian coastline stretches over about 8350 km, with 3600 km of beaches, representing a significant resource for the country. Natural processes and anthropic interventions keep threatening its morphology, moulding its shape and triggering soil erosion phenomena. Thus, many scholars have been focusing their work on investigating and monitoring shoreline instability. Outcomes of such activities can be largely widespread and shared with expert and non-expert users through Web mapping. This paper describes the performances of a WebGIS prototype designed to disseminate the results of the Italian project Innovative Strategies for the Monitoring and Analysis of Erosion Risk, known as the STIMARE project. While aiming to include the entire national coastline, three study areas along the regional coasts of Puglia and Emilia Romagna have already been implemented as pilot cases. This WebGIS was generated using Free and Open-Source Software for Geographic information systems (FOSS4G). The platform was designed by combining Apache http server, Geoserver, as open-source server and PostgreSQL (with PostGIS extension) as database. Pure javascript libraries OpenLayers and Cesium were implemented to obtain a hybrid 2D and 3D visualization. A user-friendly interactive interface was programmed to help users visualize and download geospatial data in several formats (pdf, kml and shp), in accordance with the European INSPIRE directives, satisfying both multi-temporal and multi-scale perspectives.

scholarly journals BREC: an R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes

2021 ◽  
Vol 22 (S6) ◽  
Author(s):  
Yasmine Mansour ◽  
Annie Chateau ◽  
Anna-Sophie Fiston-Lavier
Keyword(s):  
Data Quality ◽  
Data Science ◽  
Fruit Fly ◽  
R Package ◽  
Model Organisms ◽  
Data Quality Control ◽  
Recombination Rates ◽  
Functional Dynamics ◽  
Shiny App ◽  
User Friendly

Abstract Background Meiotic recombination is a vital biological process playing an essential role in genome's structural and functional dynamics. Genomes exhibit highly various recombination profiles along chromosomes associated with several chromatin states. However, eu-heterochromatin boundaries are not available nor easily provided for non-model organisms, especially for newly sequenced ones. Hence, we miss accurate local recombination rates necessary to address evolutionary questions. Results Here, we propose an automated computational tool, based on the Marey maps method, allowing to identify heterochromatin boundaries along chromosomes and estimating local recombination rates. Our method, called BREC (heterochromatin Boundaries and RECombination rate estimates) is non-genome-specific, running even on non-model genomes as long as genetic and physical maps are available. BREC is based on pure statistics and is data-driven, implying that good input data quality remains a strong requirement. Therefore, a data pre-processing module (data quality control and cleaning) is provided. Experiments show that BREC handles different markers' density and distribution issues. Conclusions BREC's heterochromatin boundaries have been validated with cytological equivalents experimentally generated on the fruit fly Drosophila melanogaster genome, for which BREC returns congruent corresponding values. Also, BREC's recombination rates have been compared with previously reported estimates. Based on the promising results, we believe our tool has the potential to help bring data science into the service of genome biology and evolution. We introduce BREC within an R-package and a Shiny web-based user-friendly application yielding a fast, easy-to-use, and broadly accessible resource. The BREC R-package is available at the GitHub repository https://github.com/GenomeStructureOrganization.

Interactive Graphical Design of 3D Serious Neurorehabilitation Games

2012 ◽  
Vol 21 (1) ◽  
pp. 58-68 ◽  
Author(s):  
Sergio Moya ◽  
Dani Tost ◽  
Sergi Grau
Keyword(s):  
Virtual Environments ◽  
Serious Games ◽  
Task Environment ◽  
System Testing ◽  
3D Game ◽  
Fully Automatic ◽  
Graphical Design ◽  
User Friendly ◽  
3D Virtual Environments ◽  
Rehabilitation Tasks

We describe a graphical narrative editor that we have developed for the design of serious games for cognitive neurorehabilitation. The system is addressed to neuropsychologists. It is aimed at providing them an easy, user-friendly, and fast way of specifying the therapeutical contents of the rehabilitation tasks that constitute the serious games. The editor takes as input a description of the virtual task environment and the actions allowed inside. Therapists use it to describe the actions that they expect patients to do in order to fulfill the goals of the task and the behavior of the game if patients do not reach their goals. The output of the system is a complete description of the task logic. We have designed a 3D game platform that provides to the editor a description the 3D virtual environments, and that translates the task description created in the editor into the task logic. The main advantage of the system is that it is fully automatic, it allows therapists to interactively design the tasks and immediately validate them by realizing it virtually. We describe the design of the two applications and present the results of system testing.

scholarly journals Smart Secured Real Time Agriculture Monitoring System

2018 ◽  
Vol 7 (3.6) ◽  
pp. 281
Author(s):  
J Srirampavan
Keyword(s):  
Sensor Networks ◽  
Embedded Systems ◽  
Sensor Network ◽  
Mobile Device ◽  
Vital Role ◽  
Separate Entity ◽  
Cloud Data ◽  
Lcd Display ◽  
Cost Efficient ◽  
User Friendly

Embedded systems in Agriculture play a vital role in unifying the work involved and improve conservations. Designing a smart as well as a cost efficient and more user-friendly system will be idealistic challenge. The following system that has been proposed is designed with those ideal constraints in mind. It consists of a Raspberry pi3 as a gateway that links the sensor networks with the cloud. To improve security an MQTT protocol is used for cloud connectivity. The communication between the sensor networks is managed by NRF24L01. The Sensor network is a separate entity that can used like a plug and play device and is built by a micro controller with a LCD display and an interfaced GPS. Multicasting is also possible between sensor networks and the gateway. The processed data from the sensor networks is sent through NRF24L01 to the gateway. The gateway further processes and encapsulates the data and through MQTT the data gets stored on the cloud. This cloud data can be accessed through computer or mobile device  

scholarly journals Microvessel Chaste: An Open Library for Spatial Modelling of Vascularized Tissues

2017 ◽  
Author(s):  
J.A. Grogan ◽  
A.J. Connor ◽  
B. Markelc ◽  
R.J. Muschel ◽  
P.K. Maini ◽  
...  
Keyword(s):  
Open Source ◽  
Tumour Growth ◽  
Spatial Models ◽  
3D Models ◽  
Tissue Growth ◽  
Coronary Perfusion ◽  
Analysis Model ◽  
User Friendly

AbstractSpatial models of vascularized tissues are widely used in computational physiology, to study for example, tumour growth, angiogenesis, osteogenesis, coronary perfusion and oxygen delivery. Composition of such models is time-consuming, with many researchers writing custom software for this purpose. Recent advances in imaging have produced detailed three-dimensional (3D) datasets of vascularized tissues at the scale of individual cells. To fully exploit such data there is an increasing need for software that allows user-friendly composition of efficient, 3D models of vascularized tissue growth, and comparison of predictions with in vivo or in vitro experiments and other models. Microvessel Chaste is a new open-source library for building spatial models of vascularized tissue growth. It can be used to simulate vessel growth and adaptation in response to mechanical and chemical stimuli, intra- and extra-vascular transport of nutrient, growth factor and drugs, and cell proliferation in complex 3D geometries. The library provides a comprehensive Python interface to solvers implemented in C++, allowing user-friendly model composition, and integration with experimental data. Such integration is facilitated by interoperability with a growing collection of scientific Python software for image processing, statistical analysis, model annotation and visualization. The library is available under an open-source Berkeley Software Distribution (BSD) licence at https://jmsgrogan.github.io/MicrovesselChaste. This article links to two reproducible example problems, showing how the library can be used to model tumour growth and angiogenesis with realistic vessel networks.

scholarly journals RICOCHET: A quick-and-dirty approach to analyze μ-XRF synchrotron data using open-source utilities

2019 ◽  
Vol 23 ◽  
pp. 162
Author(s):  
E. Mitsi ◽  
T. J. Mertzimekis
Keyword(s):  
Open Source ◽  
Online Analysis ◽  
Synchrotron Facility ◽  
User Friendly

A semi-automated procedure based on open-source utilities was designed and built to analyze spectra collected at a synchrotron accelerator using the μ-XRF technique. The software (RICOCHET) has a fast, efficient and user-friendly design aimed at performing online analysis. A few examples of its application using recent μ-XRF data from the SUL-X beamline at ANKA Synchrotron Facility (KIT) are presented.

scholarly journals Covid19Risk.ai: An open source repository and online calculator of prediction models for early diagnosis and prognosis of Covid-19

2021 ◽  
Author(s):  
Iva Halilaj ◽  
Avishek Chatterjee ◽  
Yvonka van Wijk ◽  
Guangyao Wu ◽  
Brice van Eeckhout ◽  
...  
Keyword(s):  
Open Source ◽  
Predictive Models ◽  
Prediction Models ◽  
Patient Specific ◽  
Diagnosis And Prognosis ◽  
Online Calculator ◽  
User Friendly ◽  
Type 3 ◽  
Proof Of Principle

AbstractObjectiveThe current pandemic has led to a proliferation of predictive models being developed to address various aspects of COVID-19 patient care. We aimed to develop an online platform that would serve as an open source repository for a curated subset of such models, and provide a simple interface for included models to allow for online calculation. This platform would support doctors during decision-making regarding diagnoses, prognoses, and follow-up of COVID-19 patients, expediting the models’ transition from research to clinical practice.MethodsIn this proof-of-principle study, we performed a literature search in PubMed and WHO database to find suitable models for implementation on our platform. All selected models were publicly available (peer reviewed publications or open source repository) and had been validated (TRIPOD type 3 or 2b). We created a method for obtaining the regression coefficients if only the nomogram was available in the original publication. All predictive models were transcribed on a practical graphical user interface using PHP 8.0.0, and published online together with supporting documentation and links to the associated articles.ResultsThe open source website https://covid19risk.ai/ currently incorporates nine models from six different research groups, evaluated on datasets from different countries. The website will continue to be populated with other models related to COVID-19 prediction as these become available. This dynamic platform allows COVID-19 researchers to contact us to have their model curated and included on our website, thereby increasing the reach and real-world impact of their work.ConclusionWe have successfully demonstrated in this proof-of-principle study that our website provides an inclusive platform for predictive models related to COVID-19. It enables doctors to supplement their judgment with patient-specific predictions from externally-validated models in a user-friendly format. Additionally, this platform supports researchers in showcasing their work, which will increase the visibility and use of their models.

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