Open Source Resources Research Articles

Methodology for Bathymetric Mapping Using Open-Source Software

Abstract The modern technologies not only provide an opportunity to collect water depth data much more efficiently than in the past, but also there is a wide range of opportunities to process these data to develop bathymetric maps and perform various calculations in the computer environment. This research aims to construct a high-resolution bathymetric map by using open-source software. Lake Zebrus was selected as the study site, where fieldwork was performed to obtain the depth data and subsequently process to find optimal methodology for creating a bathymetric map. The methodology used in this research is modifiable for different purposes and is based on obtaining the best results from using open-source resources and knowledge of cartography. Lake Zebrus is an example how to perform accurate and state of the art bathymetric survey in a short time period. The area of Lake Zebrus is 417.57 ha. The lake has a small crooked coastline. Lake Zebrus has a maximum depth of 4.45 m and an average depth of 1.48 m. Results from the bathymetric survey can be used for further research based on depth data. The research tasks are accomplished as the methodology selected is repeatable in the other lakes. The research results prove that this methodology can be used for a bathymetric survey and it is possible to obtain high-definition results using open-source resources.

The Collective Leadership for Safety Culture (Co-Lead) Team Intervention to Promote Teamwork and Patient Safety.

Traditional hierarchical leadership has been implicated in patient safety failings internationally. Given that healthcare is almost wholly delivered by multidisciplinary teams, there have been calls for a more collective and team-based approach to the sharing of leadership and responsibility for patient safety. Although encouraging a collective approach to accountability can improve the provision of high quality and safe care, there is a lack of knowledge of how to train teams to adopt collective leadership. The Collective Leadership for Safety Cultures (Co-Lead) programme is a co-designed intervention for multidisciplinary healthcare teams. It is an open-source resource that offers teams a systematic approach to the development of collective leadership behaviours to promote effective teamworking and enhance patient safety cultures. This paper provides an overview of the co-design, pilot testing, and refining of this novel intervention prior to its implementation and discusses key early findings from the evaluation. The Co-Lead intervention is grounded in the real-world experiences and identified needs and priorities of frontline healthcare staff and management and was co-designed based on the evidence for collective leadership and teamwork in healthcare. It has proven feasible to implement and effective in supporting teams to lead collectively to enhance safety culture. This intervention overview will be of value to healthcare teams and practitioners seeking to promote safety culture and effective teamworking by supporting teams to lead collectively.

Generation of open-source genomics resources for African orphan tree crops by African Orphan Crops Consortium (AOCC), a public-private partnership for promoting food and nutritional security in Africa

Generation of open-source genomics resources for African orphan tree crops by African Orphan Crops Consortium (AOCC), a public-private partnership for promoting food and nutritional security in Africa

Mini Pinyin: A modified miniature language for studying language learning and incremental sentence processing.

Artificial grammar learning (AGL) paradigms are used extensively to characterise (neuro)cognitive bases of language learning. However, despite their effectiveness in characterising the capacity to learn complex structured sequences, AGL paradigms lack ecological validity and typically do not account for cross-linguistic differences in sentence comprehension. Here, we describe a new modified miniature language paradigm - Mini Pinyin - that mimics natural language as it is based on an existing language (Mandarin Chinese) and includes both structure and meaning. Mini Pinyin contains a number of cross-linguistic elements, including varying word orders and classifier-noun rules. To evaluate the effectiveness of Mini Pinyin, 76 (mean age = 24.9; 26 female) monolingual native English speakers completed a learning phase followed by a sentence acceptability judgement task. Generalised mixed effects modelling revealed that participants attained a moderate degree of accuracy on the judgement task, with performance scores ranging from 25% to 100% accuracy depending on the word order of the sentence. Further, sentences compatible with the canonical English word order were learned more efficiently than non-canonical word orders. We controlled for inter-individual differences in statistical learning ability, which accounted for ~20% of the variance in performance on the sentence judgement task. We provide stimuli and statistical analysis scripts as open-source resources and discuss how future research can utilise this paradigm to study the neurobiological basis of language learning. Mini Pinyin affords a convenient tool for improving the future of language learning research by building on the parameters of traditional AGL or existing miniature language paradigms.

An Assessment Method and Toolkit to Evaluate Keyboard Design on Smartphones.

Keyboard input has played an essential role in human-computer interaction with a vast user base, and the keyboard design has always been one of the fundamental objects of studies on smart devices. With the development of screen technology, more precise data and indicators could be collected by smartphones to in-depth evaluate the keyboard design. The enlargement of the phone screen has led to unsatisfactory input experience and finger pain, especially for one-handed input. The input efficiency and comfort have attracted the attention of researchers and designers, and the curved keyboard with size-adjustable buttons, which roughly accorded with the physiological structure of thumbs, was proposed to optimize the one-handed usage on large-screen smartphones. However, its real effects remained ambiguous. Therefore, this protocol demonstrated a general and summarized method to evaluate the effect of curved QWERTY keyboard design on a 5-inch smartphone through a self-developed software with detailed variables, including objective behavioral data, subjective feedback, and the coordinate data of each touchpoint. There is sufficient existing literature on evaluating virtual keyboards; however, only a few of them systematically summarized and took reflection on the evaluation methods and processes. Therefore, this protocol fills in the gap and presents a process and method of the systematic evaluation of keyboard design with available codes for analysis and visualization.It needs no additional or expensive equipmentand is easy to conduct and operate. In addition, the protocol also helps to get potential reasons for the disadvantages of the design and enlightens the optimization of designs. In conclusion, this protocol with the open-source resources could not only be an in-class demonstrative experiment to inspire the novice to start their studies but also contributes to improving the user experience and the revenue of input method editor companies.

Generation and validation of recombinant antibodies to study human aminoacyl-tRNA synthetases

Aminoacyl-tRNA synthetases (aaRSs) have long been viewed as mere housekeeping proteins and have therefore often been overlooked in drug discovery. However, recent findings have revealed that many aaRSs have noncanonical functions, and several of the aaRSs have been linked to autoimmune diseases, cancer, and neurological disorders. Deciphering these roles has been challenging because of a lack of tools to enable their study. To help solve this problem, we have generated recombinant high-affinity antibodies for a collection of thirteen cytoplasmic and one mitochondrial aaRSs. Selected domains of these proteins were produced recombinantly in Escherichia coli and used as antigens in phage display selections using a synthetic human single-chain fragment variable library. All targets yielded large sets of antibody candidates that were validated through a panel of binding assays against the purified antigen. Furthermore, the top-performing binders were tested in immunoprecipitation followed by MS for their ability to capture the endogenous protein from mammalian cell lysates. For antibodies targeting individual members of the multi-tRNA synthetase complex, we were able to detect all members of the complex, co-immunoprecipitating with the target, in several cell types. The functionality of a subset of binders for each target was also confirmed using immunofluorescence. The sequences of these proteins have been deposited in publicly available databases and repositories. We anticipate that this open source resource, in the form of high-quality recombinant proteins and antibodies, will accelerate and empower future research of the role of aaRSs in health and disease.

Machado: Open source genomics data integration framework.

BackgroundGenome projects and multiomics experiments generate huge volumes of data that must be stored, mined, and transformed into useful knowledge. All this information is supposed to be accessible and, if possible, browsable afterwards. Computational biologists have been dealing with this scenario for more than a decade and have been implementing software and databases to meet this challenge. The GMOD's (Generic Model Organism Database) biological relational database schema, known as Chado, is one of the few successful open source initiatives; it is widely adopted and many software packages are able to connect to it.FindingsWe have been developing an open source software package named Machado, a genomics data integration framework implemented in Python, to enable research groups to both store and visualize genomics data. The framework relies on the Chado database schema and, therefore, should be very intuitive for current developers to adopt it or have it running on top of already existing databases. It has several data-loading tools for genomics and transcriptomics data and also for annotation results from tools such as BLAST, InterproScan, OrthoMCL, and LSTrAP. There is an API to connect to JBrowse, and a web visualization tool is implemented using Django Views and Templates. The Haystack library integrated with the ElasticSearch engine was used to implement a Google-like search, i.e., single auto-complete search box that provides fast results and filters.ConclusionMachado aims to be a modern object-relational framework that uses the latest Python libraries to produce an effective open source resource for genomics research.

Open educational resources for computer networking

To reflect the importance of network technologies, networking courses are now part of the core materials of Computer Science degrees. We report our experience in jointly developing an open-source ebook for the introductory course, and a series of open educational resources for both the introductory and advanced networking courses. These ensure students actively engage with the course materials, through a hands-on approach; and scale to the larger classrooms and limited teaching staff, by leveraging open-source resources and an automated grading platform to provide feedback. We evaluate the impact of these pedagogical innovations by surveying the students, who indicated that these were helpful for them to master the course materials.

An Overview of the Relevance Ranking Based Open Source Resource Discovery Interface (VuFind) for Library and Information Services

An Overview of the Relevance Ranking Based Open Source Resource Discovery Interface (VuFind) for Library and Information Services

Information systems for creating e-learning resources for realization of resource-based learning aimed at students majoring in Economics

The authors have examined and analysed information systems (Constructor Electronic books 1.1.3, SunRav, Webnode, Google Classroom) in terms of functionality, which will allow creating electronic educational resources for introduction of the resource-based learning for students in higher school. It has been proven that Constructor Electronic books 1.1.3 and SunRav provide the creation of online tutorials that are run using an exe-file. Webnode Website Designer enables the creation of open-source electronic educational resources that are freely available on the World Wide Web (teacher's personal sites, discipline study site, e-learning teaching / learning support of disciplines, etc.). These electronic educational resources effectively and fully function in any modern browser: Google Chrome, Opera, Mozilla Firefox, Internet Explorer, etc., and also provide the opportunity to work online with students. Using Google Classroom is appropriate when you need to organise full-time online (virtual) online distance learning. For the resource-based learning of the students majoring in Economics, the authors have developed and presented an electronic manual "Higher Mathematics for Economists" in the Designer of Electronic Textbooks (N. Kononets); an educational and methodological complex of the discipline "Economic Informatics" in the environment of SunRav IS (N. Kononets); a site of study studio "Digital Technologies in the Economist's Work", created at Webnode (V. Baliuk); a Virtual Classroom "Educational practice in information systems and technologies in Economics" in Google Classroom (N. Kononets and V. Baliuk).

An agile and parsimonious approach to data management in groundwater science using open-source resources

National governments and international organizations such as the European Commission, are promoting the increased use of information and communication technologies to assist scientists in the “mining” of knowledge. A typical workflow for a hydrogeologist consists of investigating and reporting hydrogeological processes in a study area, from data collection to model-based analysis. While hydrogeologists may feel insufficiently skilled to undertake the self-automatizing and digitizing process, the digitalization of the aforementioned workflow can be easily obtained by means of agile and parsimonious methodologies based on free and open-source software, and by using existing standards. This route is demonstrated for the digitalization of a vadose-zone monitoring system, where a large number of raw data related to water infiltration through the vadose zone are collected. The main aspects of the proposed methodology are a structured database (DB) where field data are stored, and a Python script to manage and process the available data. The structured DB was designed to store data recorded by field sensors and to generate inputs to run a transfer-function-based model to simulate percolation to the water table. Field data and model outputs were also exploited to automatically generate summary reports, like plots and table statistics. The proposed methodology can be generalized to other hydrogeological processes and case studies, as it is based on commonly available standards, basic knowledge of data-storage and data-management, and elementary programming skills to connect the different components of its suite.

Exploiting the Capabilities of Surfcam for Coastal Morphodynamic Analysis

Valentini, N.; Balouin, Y., and Bouvier, C., 2020. Exploiting the capabilities of Surfcam for coastal morphodynamic analysis. In: Malvárez, G. and Navas, F. (eds.), Global Coastal Issues of 2020. Journal of Coastal Research, Special Issue No. 95, pp. 1333–1338. Seville (Spain), ISSN 0749-0208.A free webcam network is used in this study, operated by ©Viewsurf, a European company with more than 1200 stations in France, among beaches, urban and mountain areas in order to assess the capabilities of surfcam for coastal morphodynamics analysis. Four representative coastal sites, with different tidal range and wave energy are monitored in order to extract optical signatures for morphodynamic analysis: three in the Atlantic and a gravel beach in the Mediterranean area. A representative site is here documented, Hendaye beach, which is characterized by a meso-tidal environment, with highly energetic waves often present, which makes the image processing challenging. Shoreline detections for beach width and intertidal area calculation are accomplished by using a new image segmentation algorithm, based on a framework, derived by opportunely coupling a superpixels algorithm and a Deep-Conditional-Neural-Network DCNN model. Aiming to exploit the capabilities of cBathy algorithm (Holman, Plant, and Holland, 2013), a version of the open-source methodology (https://coastal-imaging-research-network.github.io), is employed for bathymetry reconstruction. A coupled bathymetry by merging cBathy depth estimate and intertidal reconstructed depth from automatically extracted shorelines is accomplished, which is compared with survey and lead to an RMS error of 0.43 m. Discussions are given with respect to this new potential open-source resource and its limitations.

Influence of important environmental parameters on the spread and severity of COVID-19: Part 1

In the absence of the detailed COVID-19 epidemiological data or large benchmark studies, an effort has been made to explore and correlate the relation of parameters like environment, economic indicators, and the large scale exposure of different prevalent diseases, with COVID-19 spread and severity amongst the different countries affected by COVID-19. Data for environmental, socio-economic and others important infectious diseases were collected from reliable and open source resources like World Health Organization, World Bank, etc. Further, this large data set is utilized to understand the COVID-19 worldwide spread using simple statistical tools. Important observations that are made in this study are the high degree of resemblance in the pattern of temperature and humidity distribution among the cities severely affected by COVID-19. Further, It is surprising to see that in spite of the presence of many environmental parameters that are considered favorable (like clean air, clean water, EPI, etc.), many countries are suffering with the severe consequences of this disease. Lastly a noticeable segregation among the locations affected by different prevalent diseases (like Malaria, HIV, Tuberculosis, and Cholera) was also observed. Among the considered environmental factors, temperature, humidity and EPI should be an important parameter in understanding and modelling COVID-19 spreads. Further, contrary to intuition, countries with strong economies, good health infrastructure and cleaner environment suffered disproportionately higher with the severity of this disease. Therefore, policymaker should sincerely review their country preparedness toward the potential future contagious diseases, weather natural or manmade.

Determination of the Normalized Difference Vegetation Index (NDVI) with Top-of-Canopy (TOC) Reflectance from a KOMPSAT-3A Image Using Orfeo ToolBox (OTB) Extension

Surface reflectance data obtained by the absolute atmospheric correction of satellite images are useful for land use applications. For Landsat and Sentinel-2 images, many radiometric processing methods exist, and the images are supported by most types of commercial and open-source software. However, multispectral KOMPSAT-3A images with a resolution of 2.2 m are currently lacking tools or open-source resources for obtaining top-of-canopy (TOC) reflectance data. In this study, an atmospheric correction module for KOMPSAT-3A images was newly implemented into the optical calibration algorithm in the Orfeo Toolbox (OTB), with a sensor model and spectral response data for KOMPSAT-3A. Using this module, named OTB extension for KOMPSAT-3A, experiments on the normalized difference vegetation index (NDVI) were conducted based on TOC reflectance data with or without aerosol properties from AERONET. The NDVI results for these atmospherically corrected data were compared with those from the dark object subtraction (DOS) scheme, a relative atmospheric correction method. The NDVI results obtained using TOC reflectance with or without the AERONET data were considerably different from the results obtained from the DOS scheme and the Landsat-8 surface reflectance of the Google Earth Engine (GEE). It was found that the utilization of the aerosol parameter of the AERONET data affects the NDVI results for KOMPSAT-3A images. The TOC reflectance of high-resolution satellite imagery ensures further precise analysis and the detailed interpretation of urban forestry or complex vegetation features.

Many hands make light work, or too many cooks spoil the soup? Lessons from the development of the BASIL biochemistry laboratory curriculum through a diverse multi‐institutional collaboration.

The BASIL (Biochemistry Authentic Scientific Investigation Laboratory) curriculum is driven by a consortium of biochemistry and computational instructors. BASIL is a protein biochemistry Course‐based Undergraduate Research Experience (CURE) in which students discover enzymatic function of previously uncharacterized proteins. It combines computational and wet‐lab protein science to deliver foundational concepts within the undergraduate biochemistry teaching lab. BASIL came together in 2015 as instructors sought to integrate genuine research into the biochemistry laboratory course to broaden the impact of teaching through research.In order to maximize impact, BASIL has been intentionally developed as a collaborative effort across institutions diverse in type, size, and location nationwide. This presentation summarizes lessons learned from building this collaboration, including the following aspects. (1) Establishing the group: Participants were identified and recruited for the most part at national meetings such as Experimental Biology/ASBMB and others. (2) Funding: Development of the BASIL curriculum was supported by NSF IUSE as a collaborative research proposal. (3) Communication: Group members interact through videoconferencing on a weekly basis, and at national/regional meetings. (4) Teaching resources: The BASIL curriculum has been published as a free and open‐source resource, supplemented by online teaching suggestions. (5) Assessment: The effectiveness of this curriculum has been assessed through student surveys shared across campuses and surveys of faculty to monitor success of (and obstacles to) implementation at each home campus. (7) Dissemination and recruitment: Availability of the BASIL resources has been published, and additional faculty/campuses continue to join as BASIL implementors.These are presented with the goal of sharing successful (and not‐so‐successful) strategies for collaborating across campuses as a way to stimulate effective student learning while promoting faculty development and well‐being through this team model.Support or Funding InformationNSF IUSE 1709278

Exercising with Baxter: preliminary support for assistive social-physical human-robot interaction

BackgroundThe worldwide population of older adults will soon exceed the capacity of assisted living facilities. Accordingly, we aim to understand whether appropriately designed robots could help older adults stay active at home.MethodsBuilding on related literature as well as guidance from experts in game design, rehabilitation, and physical and occupational therapy, we developed eight human-robot exercise games for the Baxter Research Robot, six of which involve physical human-robot contact. After extensive iteration, these games were tested in an exploratory user study including 20 younger adult and 20 older adult users.ResultsOnly socially and physically interactive games fell in the highest ranges for pleasantness, enjoyment, engagement, cognitive challenge, and energy level. Our games successfully spanned three different physical, cognitive, and temporal challenge levels. User trust and confidence in Baxter increased significantly between pre- and post-study assessments. Older adults experienced higher exercise, energy, and engagement levels than younger adults, and women rated the robot more highly than men on several survey questions.ConclusionsThe results indicate that social-physical exercise with a robot is more pleasant, enjoyable, engaging, cognitively challenging, and energetic than similar interactions that lack physical touch. In addition to this main finding, researchers working in similar areas can build on our design practices, our open-source resources, and the age-group and gender differences that we found.

Forensic Technical Process by E-Mail

Forensic mail network were based more on the e-mail message structure, whereas email content was rarely used. In different security extension schemes, cyber criminals tend to make use of email protocols by multiple producers over the course of a year for illegal purposes, for example send emails have become the most important digital platform for communication, file transfer and transactions and use not only laptops but also many other electronic gadgets including mobile phones.In this context, a number of forensics open source resources were frequently used by professionals. Furthermore, the misuse of Internet infrastructure by denial of service, storage waste and computer resources costs every internet user directly or indirectly. E-mail forensic is used to the origin and the content of e-mail as evidence, to determine the actual sender, the recipient, and when and how it was sent, etc. These instruments were nevertheless developed in isolation rather than in cooperation. Since forensic email users have to know the utility of a method for forensics research in their own situations. This paper is intended to illustrate the email system architecture from a forensic perspective. It describes the email partners ' roles and responsibilities, the metadata in the email headers

Technological Structure for Technology Integration in the Classroom, Inspired by the Maker Culture

Technological Structure for Technology Integration in the Classroom, Inspired by the Maker Culture

Process selection methodology for near net shape manufacturing

This paper presents a new selection methodology that for the first time supports the identification of Near Net Shape (NNS) processes. The methodology, known as “Product, Geometry, Manufacturing and Materials Matching” (ProGeMa3), is composed of four steps, which aim to minimize raw material usage and machining by adopting a NNS approach. A key component of the methodology is the Process Selection Matrix (ProSMa) that associates a component’s shape and production volume with its material requirements to reduce the number of candidate NNS processes. A final selection is then made from this shortlist by using fuzzy logic and considering other constraints and functional requirements. The ProGeMa3 selection process is illustrated by its application to an industrial component that resulted in changes to the processes used for its commercial manufacture. The ProGeMa3 and ProSMa presented in this paper aspires to be current and comprehensive for solid metallic components produced by casting, forging and additive technologies. However, ProSMa is also accessible as an open source resource available for other researcher to extend and adapt.

Continuous Digital Monitoring of Walking Speed in Frail Elderly Patients: Noninterventional Validation Study and Longitudinal Clinical Trial.

BackgroundDigital technologies and advanced analytics have drastically improved our ability to capture and interpret health-relevant data from patients. However, only limited data and results have been published that demonstrate accuracy in target indications, real-world feasibility, or the validity and value of these novel approaches.ObjectiveThis study aimed to establish accuracy, feasibility, and validity of continuous digital monitoring of walking speed in frail, elderly patients with sarcopenia and to create an open source repository of raw, derived, and reference data as a resource for the community.MethodsData described here were collected as a part of 2 clinical studies: an independent, noninterventional validation study and a phase 2b interventional clinical trial in older adults with sarcopenia. In both studies, participants were monitored by using a waist-worn inertial sensor. The cross-sectional, independent validation study collected data at a single site from 26 naturally slow-walking elderly subjects during a parcours course through the clinic, designed to simulate a real-world environment. In the phase 2b interventional clinical trial, 217 patients with sarcopenia were recruited across 32 sites globally, where patients were monitored over 25 weeks, both during and between visits.ResultsWe have demonstrated that our approach can capture in-clinic gait speed in frail slow-walking adults with a residual standard error of 0.08 m per second in the independent validation study and 0.08, 0.09, and 0.07 m per second for the 4 m walk test (4mWT), 6-min walk test (6MWT), and 400 m walk test (400mWT) standard gait speed assessments, respectively, in the interventional clinical trial. We demonstrated the feasibility of our approach by capturing 9668 patient-days of real-world data from 192 patients and 32 sites, as part of the interventional clinical trial. We derived inferred contextual information describing the length of a given walking bout and uncovered positive associations between the short 4mWT gait speed assessment and gait speed in bouts between 5 and 20 steps (correlation of 0.23) and longer 6MWT and 400mWT assessments with bouts of 80 to 640 steps (correlations of 0.48 and 0.59, respectively).ConclusionsThis study showed, for the first time, accurate capture of real-world gait speed in slow-walking older adults with sarcopenia. We demonstrated the feasibility of long-term digital monitoring of mobility in geriatric populations, establishing that sufficient data can be collected to allow robust monitoring of gait behaviors outside the clinic, even in the absence of feedback or incentives. Using inferred context, we demonstrated the ecological validity of in-clinic gait assessments, describing positive associations between in-clinic performance and real-world walking behavior. We make all data available as an open source resource for the community, providing a basis for further study of the relationship between standardized physical performance assessment and real-world behavior and independence.