Free Open Software Research Articles

CaptuRING: A do‐it‐yourself tool for wood sample digitization

Abstract Standard procedures to obtain high‐quality images of wood samples have become a bottleneck in the digitization of dendrochronology. Digitization is currently dominated by flatbed scanners, but the use of these devices is limited by sample length and surface flatness. Although several solutions based on digital photography have been published, they lack effective digitization processes or are too expensive to be widely adopted. Free open‐source software and hardware has emerged as an alternative to create research tools that combine reduced costs with high reliability. Here we present CaptuRING, an open‐source tool for wood sample digitization combining a do‐it‐yourself hardware based on Arduino® with a DSLR camera and a free open‐source software with an easy‐to‐use graphical user interface. We compared CaptuRing with image acquisition from a standard flatbed scanner Epson® V750PRO. CaptuRING outperforms scanner image resolution and sharpness, while it removes sample size limitations. Moreover, CaptuRing performs this task in less than half of the time needed by Epson® V750PRO flatbed scanner. CaptuRING emerges as a reliable and low‐cost tool to capture high‐resolution images of wood samples boosting current digitization processes. The combination of free open software and hardware empowers dendrochronology to advance in wood sample digitization.

POS0322 CORRELATION BETWEEN QUANTITATIVE COMPUTED TOMOGRAPHY AND DISEASE ACTIVITY IN SYSTEMIC SCLEROSIS

Background:High Resolution Computed Tomography (HRCT) is the gold standard to evaluate Interstitial Lung Diseases (ILDs) extent and severity. Quantitative Computed Tomography (QCT) is a promising tool as it provides an operator-independent assessment of ILD extent. Even if there are emerging data on QCT in Systemic Sclerosis (SSc), its correlation with disease activity (DA) has not been yet studied.Objectives:To evaluate the correlation between QCT score and DA in an Italian cohort of SSc patients.Methods:A multicentric, observational study was conducted in three Italian rheumatological centers.Adult SSc patients classified according to the ACR/EULAR 2013 criteria [1] were assessed with pulmonary function tests, HRCT and for DA. CT images were analyzed quantitatively with the densitometric radiomic data obtained through a free open software – Mean lung attenuation (MLA), Standard Deviation (SD), Kurtosis, Skewness and Lung volume. DA assessment was conducted according to EUSTAR index [2]: a score ≥2.5 was considered indicative of high disease activity.Age below 18 and pregnancy were considered exclusion criteria. We used Student’s T test to evaluate the means of the parameters, Pearson’s r test for correlations, receiver operating characteristics curve to define the cutoff values of the significant details, and linear regression with collinearity test to define the role of the details. P value <0.05 was considered statistically significant.Results:Sixty patients were enrolled (male 8, female 52), with mean age 53.2 years (SD 15.6) and mean disease duration 5.3 years (SD 4.2). QCT indexes distribution was different in high DA vs low DA SSc patients. In particular mean lung attenuation (MLA, -834.7 vs -812.1, p =0.03), standard deviation (95.9 vs 102, p =0.03), skewness (2.2 vs 1.7, P =0.006) and kurtosis (5.5 vs 3.3, p =0.009) of the parenchymal lung and skewness (3.1 vs 2.8, p =0.03) of the whole lung were statistically different. DA correlates with MLA (r =0.28, p =0.003), standard deviation (r =0.21, p =0.02), skewness (r =-0.32, p =0.001) and kurtosis (r =-0.29, p =0.001) of the parenchymal lung and MLA (r =0.25, p =0.006), skewness (R =-0.27, p =0.003), kurtosis (r =-0.21, P =0.02) of the whole lung. The skewness of the parenchymal lung was the QCT index with the best performance in identifying high DA SSc patients (cutoff value ≤1.85; area under the curve 0.74, p =0.005; sensitivity 79.5%, specificity 68.7% accuracy 76.6%).Conclusion:To our knowledge, this is the first study which correlate the QCT score with DA in SSc patients. Our results suggest that QCT can identify SSc patients with high DA score. This could open a scenario of new applications as an operator-independent contribution in DA scores with a potential role in clinical practice. Further studies are needed to confirm the data and to better identify the most suitable parameters for the purpose.

Continuing and online education for health professionals in Brazil: Results from UNA-SUS

Abstract UNA-SUS System was established to enforce the National Policy of Continuing Education in Health, and it is composed of a Network of 34 public institutions (mostly Universities), responsible for online educational offerings, in response to the demands generated by the Ministry of Health. The system produces courses that are committed to the 2030 Agenda for Sustainable Development (specially Goals 3, 4, 5, 10, and 16). Objectives to verify the profile of users and the penetrance of UNA-SUS online courses and their contribution to the democratization of Continuing Education of health workers. Methods Data were collected from Arouca Platform and statistical analysis was performed by the Open Free Software R 3.6. Results There were more than 2.8 million enrollments, counting more than 1 million students, from every SUS health regions, Brazilian municipalities and states. Courses with the greatest demands were related to important clinical situations faced by the Primary Care professionals in Brazil. There was a predominance of women (80%), whites (36%), followed by browns (33%), singles (57%) and in the age group of 21 to 40 years (70%). Nurses, doctors and dentists were the professionals who most sought courses at UNA-SUS. No relationship was found between enrollment in population-weighted self-instructional courses and the Brazilian State HDI, but a negative relationship was established between the Gini coefficient and enrollment in courses, showing that the more unequal the region, the fewer enrolled students it had. Conclusions The UNA-SUS is effective in providing continuing education through free, online course offerings, reaching users from different Brazilian geographic regions, including those leaving in areas with few presential or free educational opportunities, contributing to improve the service offered by the Brazilian Public Health System. Key messages Continuing education for Health Professionals in Brazil using online education courses is democratic. UNA-SUS is an effective system to consolidate the National Policy of Continuing Education.

New Software for Gluten-Free Diet Evaluation and Nutritional Education.

Following a gluten-free diet (GFD) is the only treatment for celiac disease. This diet must ensure the absence of gluten but also needs to be nutritionally balanced. Dietitians working in this field cannot properly evaluate energy and nutrient intake of celiac people because dietary programs available on the market do not contain the nutritional composition of gluten-free products (GFP). Here we present a new GFD evaluation software that contains more than 700 gluten-free rendered foodstuffs and their macronutrient composition. Apart from diet evaluation and design, the software represents a tool for nutritional education as well, since it shows diet appropriacy and indicates how to promote balanced self-care. Moreover, anthropometric and biochemical data or symptoms presence and diet adherence can be recorded and evaluated. This open free software, can be downloaded in its app format for mobiles and tablets. Software evaluation indicated its correct functionality and the importance of assessing a GFD with GFP instead of with their gluten-containing analogues. Thus, this software represents an essential e-Health tool, not only for proper GFD evaluation, but also for improving life quality of celiac and gluten sensitive people.

A Study of Knowledge From Closed and Open System That Affect the Innovation Capability of Employees in the Thai Automotive Industry

The objective of this research was to investigate the knowledge from closed and open systems that affect the innovation capability of employees in the Thai automotive industry. The study was conducted by reviewing related literature and theories and holding a small group meeting with experts in the automotive industry to review the research model and factors obtained from this study. This research is only part of the main research that we are currently studying. The results from this research have led to the research model. According to the research results, knowledge from a closed system can be divided into two types: 1) Knowledge from on-the-job training that consists of six factors; i.e. Coaching, Mentoring, Job rotation, Job instruction, Apprenticeship, and Understudy, and 2) Knowledge from off-the-job training that consist of one factor, i.e. Conference and seminar. In addition, knowledge from an open system can be divided into five factors, i.e. Free open software, Business partnership, Customer knowledge, Supplier knowledge, and University knowledge. The results obtained from this research will be used to additionally expand the development of research model in order to study the population, collect data, and extend results of the next research.

Towards a methodology to build virtual reality manufacturing systems based on free open software technologies

Virtual reality and augmented reality are being increasingly used in the manufacturing field for different purposes. As a result, these technologies seem to have a very promising future in the manufacturing industry. However, most of the current applications are based on the use of expensive proprietary software packages (such as specific CAD modules). This work presents a methodology that helps programmers to build virtual and augmented reality systems, which is valid for a broad number of industrial plants. Differently to other approaches, ours is based on open technologies, most of them free of cost. The technologies proposed to build the virtual worlds are already mature at the entertainment industry. The presented approach opens new possibilities for creating virtual reality models aimed at two major directions: (1) pure simulation of real processes and products for different purposes (e.g. staff training; prototype designing; manufacturing optimization; marketing) and (2) teleoperation of real processes (e.g. in dangerous environments or in micro and macro scale manufacturing). The application of the methodology is illustrated by means of the creation of a non-immersive virtual world which represents a part-classifying station, allowing both the simulation of the real plant as well as its remote operation.

A modular CPS architecture design based on ROS and Docker

In this paper a modular generic architecture for cyber-physical systems based on free open software components is presented. The architecture is implemented over inexpensive components frequently found in information and communication technology contexts. More specifically, the robot operating system middleware abstracts communication among multiple networked modules, whereas the Docker lightweight virtualization container is proposed to wrap up software modules. Focus is on mobile robotics in production systems and industrial automation environments. Actually, an automated guided vehicle problem is demonstrated by means of a proof of concept aimed at industrial automation applications illustrating the potential of the proposed architecture and its implementation, built with low cost hardware modules.

Análisis e influencia de los sistemas de referencia en la cinemática del hombro

The shoulder is one of the most complex systems in the human body. To know how its work is essential to understand the biomechanics of the body. The purpose of this study was to analyze the influence of Local Coordinate Systems in the kinematic analysis of GlenoHumeral joint. The motion tracking was performed using passive sensors attached to pins. Trabecular pins were placed on the shoulder and scapula. The data processing was performed using the free open software pyFormex. The joint displacements were determined by two different variants of Coordinate Systems, being detected a difference from 2 to 12 degrees.

Automatic Germination Evaluation and Qualitative Analysis of Essential Oil of <i>Mentha × piperita</i> L. under the Influence of High Frequency Pulsatile Electromagnetic and Ultrasound Pulsatile Fields

The study illustrates the influence of high frequency pulsatile electromagnetic fields and ultrasound pulsatile fields on Mentha × piperita L. seed germination and the quality of its essential oil. The physiological role of the above mentioned experimental factors was considered to be a catalyticall base point, improving germination percent, SVI (seedling vigor index), GVI (germination velocity index). All the biometric aspects of the germination process (seed area, seed perimeter, seed development on x and y radius, radicele length, hypocotyl length) where determined using open free software, consolidating the general idea that scientific communities can improve and perfect open source projects. High frequency pulsatile electromagnetic fields (91.75%) and ultrasound pulsatile fields (64.75%) experimental variants gave higher germination percent compared to control (47.00%). Following the main terpenes determination, the same experimental variants obtained high accumulations of menthol, eugenol, thymol, eucalyptol, linalool and other components. These aspects can be scientifically sustained by the seedling vigor index marks obtained at high frequency pulsatile electromagnetic fields (1985.47) and ultrasound pulsatile fields (1480.09), creating the general premises for better development stages in the nursery sector. Raised accumulation of main therapeutical terpenes in Mentha × piperita L. must be supervised in further studies, when microscopically imagery of glandular trichomes and their density may lead to more profound conclusions.

Численное моделирование сверхзвукового обтекания клина с применением свободного открытого программного кода OpenFOAM

Численное моделирование сверхзвукового обтекания клина с применением свободного открытого программного кода OpenFOAM

Book Review: Coding Freedom: The Ethics and Aesthetics of Hacking, by E. Gabriella Coleman

Coding Freedom: The Ethics and Aesthetics of Hacking. E. Gabriella Coleman. Princeton, NJ: Princeton University Press, 2013. 254 pp. $24.95 pbk.The image of the computer hacker, for many, may be forged by pop culture and news mediathink - think Matthew Broderick's underachieving high school computer whizz who nearly brought the world to thermo nuclear war by hacking into the government's computers in the 1983 movie War Games.News accounts also depict the hacker as a brilliant pirate intent on flouting the law either for political or economic gain or just plain fun. Contemporary news accounts of stolen credit card data from big box retailers, identity theft, and other cybercriminal activities are also closely identified with hackers.Perhaps the computer hacker's image, self-image, and identity itself are due for a bit of reverence if not respect. E. Gabriella Coleman's book, Coding Freedom: The Ethics and Aesthetics of Hacking may be just the document for that image overhaul. In fact, Coleman, the Wolfe Chair in Scientific and Technological Literacy at McGill University, holds computer hackers as well as creators of free open software as pillars of democracy.Coleman, a cultural anthropologist, takes a look at the hacker and coder as the subject of her study. Hackers, she writes, sit simultaneously at the center and the margins of liberal This study is her ethnography of the computer world and the underworld where hackers and coders both collaborate and compete. She names a handful of coding pioneers and hackers and explains some of their motivations to break the codes and share these crown jewel algorithms that make computers the tools that regular people can operate. She even points to a loose code of ethics among hackers.The book draws on her extensive study of hackers, coders, moguls, and even politicians. Coleman's intricate knowledge of her topic, its doctrines, players, and existing scholarship also brings meaning to the alphabet soup of acronyms, abbreviations and computer terms. She literally opens her book by defining free and open-source software (F/OSS), which is similarly woven throughout as sort of a democratized principle which challenges our conception of both the purpose of computer programs and the role of intellectual property law.She writes,I argue that F/OSS draws from and also rearticulates elements of the liberal tradition. Rather than designating only a set of explicitly held political, economic, or legal views, I treat liberalism in its cultural registers. Free software hackers culturally concretize a number of liberal themes and sensibilities-for example, through their competitive mutual aid, avid free speech principles, and implementation of meritocracy along with their frequent challenge to intellectual property provisions.While detail-oriented with an insider's understanding of the computer world, Coding Freedom becomes relevant for lay people thanks to the mass market personal and home computing explosion developing in the 1970s and 80s, the dotcom and Silicon Valley boom from the 1990s, and the social media revolution from the past decade. …

Português

The settlement of the National Infrastructure for Spatial Data (Infraestrutura Nacional de Dados Espaciais - INDE) is an initiative to help organizing the generation, storage, access, sharing, dissemination and use of geographic data about the Brazilian territory. Now-a-days, there are several initiatives of implementation and management of Spatial Data Infrastructures. However, only a few organizations are really documenting the metadata in their geospatial databases. This is mainly due to the fact that the process of documenting data is time consuming and complex, requiring training on the part of data producers. This paper discusses an alternative process for the extraction and documentation of metadata using free open software to increase efficiency and providing incentive to the generation of metadata for the data produced in Brazil. We performed the customization of the MGB profile using CatMDEdit software for viewing and editing the metadata in this profile. This tool was also used to extract and document metadata from files in shapefile format and to edit metadata fields after extraction. The file generated in XML was imported and converted to an MGB profile contained in the application Geonetwork. Results show that it is possible to extract information contained in the data and easily and quickly generate metadata in MGB profile, if the activity is well planned and supported by model files (templates).

Next-generation scholarly communication: a researcher's perspective.

This article was previously published in INTERNATIONAL MICROBIOLOGY [Int Microbiol 16:253-257].

BioMAJ: a flexible framework for databanks synchronization and processing

Large- and medium-scale computational molecular biology projects require accurate bioinformatics software and numerous heterogeneous biological databanks, which are distributed around the world. BioMAJ provides a flexible, robust, fully automated environment for managing such massive amounts of data. The JAVA application enables automation of the data update cycle process and supervision of the locally mirrored data repository. We have developed workflows that handle some of the most commonly used bioinformatics databases. A set of scripts is also available for post-synchronization data treatment consisting of indexation or format conversion (for NCBI blast, SRS, EMBOSS, GCG, etc.). BioMAJ can be easily extended by personal homemade processing scripts. Source history can be kept via html reports containing statements of locally managed databanks.Availability: http://biomaj.genouest.org. BioMAJ is free open software. It is freely available under the CECILL version 2 license.Contact: biomaj@genouest.org

Patient Record Information System (PaRIS) for primary health care centers in Indonesia

This study explores the Patient Record Information System (PaRIS) for primary health care centers in a developing country such as Indonesia. The specific geography of the thousand islands country Indonesia is the reason for transportation difficulties as well as communication problems. This causes a serious adverse effect on the public healthcare service especially in the rural area within the country. Hence, a sustainable system is required that makes use of appropriate Information and Communication Technology (ICT). We developed a clinical information system with modest communication technology combined with a unique database distribution system. The Internet and its free software are the main tools for this system. It is a good opportunity for a developing country such as Indonesia to apply open free software in regard to the healthcare sector. This cost effective and sustainable system can enhance the work of physicians in order to provide better and applicable public health care service.

9A13 Sustainable Patient Information Network for Primary Care Health Center in Thousand Islands Country

Sustainable Patient Information Network for primary care health center is needed for Indonesia. There are many of remote, isolated and urban area, which causes transportation problems and telecommunication problems, for example : necessity of wireless infrastructure. We develop low speed communication system to access the Internet using Internet radio packet and used PostgreSQL database server on Linux machines. This system connects every health center to each other and avoid central data storage which common use in this day. It is a good opportunity for developing country such as Indonesia to use open free software. And radio packet communication uses radio media is no connection charge like telephone line for data communication. The study opens perspective for a further data storage, distribution, synchronizing, maintenance and security.