Open-source Web Platform Research Articles

THE DEVELOPMENT OF A 2D/3D BIM-GIS WEB PLATFORM FOR PLANNED MAINTENANCE OF BUILT AND CULTURAL HERITAGE: THE MAIN10ANCE PROJECT

Abstract. The integration of Building Information Modeling (BIM), or Historic BIM (HBIM), and Geographic Information Systems (GIS) has assumed a crucial role not only in the management of smart cities or urban districts, as well as in the construction sector or infrastructures but also in the management, conservation and safeguarding of cultural heritage. This integration opens up new opportunities for decision-makers to assess the impact of interventions on heritage sites, evaluate preservation strategies, and facilitate informed decision-making processes. This contribution presents and describes the open-source web platform developed within the Interreg MAIN10ANCE project. The project aims to promote a common methodology for the cooperation and collaboration of the various stakeholders involved in the restoration, management and maintenance activities of built and cultural heritage sites. This objective has been pursued by creating a BIM-GIS database, focused on the definition of planned maintenance activities, whose data has been made available to professionals and management bodies by means of a shared web platform, usable directly in situ on a tablet or portable devices. The paper highlights the key components of the web platform, including the BIM, GIS, and artifact Viewers, the Planner, and the overall Dashboard. The platform's multiscale and multi-source approach makes it extensible to various cultural assets, whether environmental, architectural, or movable. By integrating historical and geometric information and planning maintenance activities, the web platform thus supports public administrations and professionals, amending existing state-of-the-art solutions.

Linked Open Images: Visual similarity for the Semantic Web

This paper presents ArtVision, a Semantic Web application that integrates computer vision APIs with the ResearchSpace platform, allowing for the matching of similar artworks and photographs across cultural heritage image collections. The field of Digital Art History stands to benefit a great deal from computer vision, as numerous projects have already made good progress in tackling issues of visual similarity, artwork classification, style detection, gesture analysis, among others. Pharos, the International Consortium of Photo Archives, is building its platform using the ResearchSpace knowledge system, an open-source semantic web platform that allows heritage institutions to publish and enrich collections as Linked Open Data through the CIDOC-CRM, and other ontologies. Using the images and artwork data of Pharos collections, this paper outlines the methodologies used to integrate visual similarity data from a number of computer vision APIs, allowing users to discover similar artworks and generate canonical URIs for each artwork.

Luox: validated reference open-access and open-source web platform for calculating and sharing physiologically relevant quantities for light and lighting.

Light exposure has a profound impact on human physiology and behaviour. For example, light exposure at the wrong time can disrupt our circadian rhythms and acutely suppress the production of melatonin. In turn, appropriately timed light exposure can support circadian photoentrainment. Beginning with the discovery that melatonin production is acutely suppressed by bright light more than 40 years ago, understanding which aspects of light drive the 'non-visual' responses to light remains a highly active research area, with an important translational dimension and implications for "human-centric" or physiologically inspired architectural lighting design. In 2018, the International Commission on Illumination (CIE) standardised the spectral sensitivities for predicting the non-visual effects of a given spectrum of light with respect to the activation of the five photoreceptor classes in the human retina: the L, M and S cones, the rods, and the melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs). Here, we described a novel, lean, user-friendly, open-access and open-source platform for calculating quantities related to light. The platform, called luox, enables researchers and research users in vision science, lighting research, chronobiology, sleep research and adjacent fields to turn spectral measurements into reportable quantities. The luox code base, released under the GPL-3.0 License, is modular and therefore extendable to other spectrum-derived quantities. luox calculations of CIE quantities and indices have been endorsed by the CIE following black-box validation.

Flukebook: an open-source AI platform for cetacean photo identification

Determining which species are at greatest risk, where they are most vulnerable, and what are the trajectories of their communities and populations is critical for conservation and management. Globally distributed, wide-ranging whales and dolphins present a particular challenge in data collection because no single research team can record data over biologically meaningful areas. Flukebook.org is an open-source web platform that addresses these gaps by providing researchers with the latest computational tools. It integrates photo-identification algorithms with data management, sharing, and privacy infrastructure for whale and dolphin research, enabling the global collaborative study of these global species. With seven automatic identification algorithms trained for 15 different species, resulting in 37 species-specific identification pipelines, Flukebook is an extensible foundation that continually incorporates emerging AI techniques and applies them to cetacean photo identification through continued collaboration between computer vision researchers, software engineers, and biologists. With over 2.0 million photos of over 52,000 identified individual animals submitted by over 250 researchers, the platform enables a comprehensive understanding of cetacean populations, fostering international and cross-institutional collaboration while respecting data ownership and privacy. We outline the technology stack and architecture of Flukebook, its performance on real-world cetacean imagery, and its development as an example of scalable, extensible, and reusable open-source conservation software. Flukebook is a step change in our ability to conduct large-scale research on cetaceans across biologically meaningful geographic ranges, to rapidly iterate population assessments and abundance trajectories, and engage the public in actions to protect them.

Accessible from the open web: a qualitative analysis of the available open-source information involving cyber security and critical infrastructure

Abstract In order to efficiently manage and operate industrial-level production, an increasing number of industrial devices and critical infrastructure (CI) are now connected to the internet, exposed to malicious hackers and cyberterrorists who aim to cause significant damage to institutions and countries. Throughout the various stages of a cyber-attack, Open-source Intelligence (OSINT) tools could gather data from various publicly available platforms, and thus help hackers identify vulnerabilities and develop malware and attack strategies against targeted CI sectors. The purpose of the current study is to explore and identify the types of OSINT data that are useful for malicious individuals intending to conduct cyber-attacks against the CI industry. Applying and searching keyword queries in four open-source surface web platforms (Google, YouTube, Reddit, and Shodan), search results published between 2015 and 2020 were reviewed and qualitatively analyzed to categorize CI information that could be useful to hackers. Over 4000 results were analyzed from the open-source websites, 250 of which were found to provide information related to hacking and/or cybersecurity of CI facilities to malicious actors. Using thematic content analysis, we identified three major types of data malicious attackers could retrieve using OSINT tools: indirect reconnaissance data, proof-of-concept codes, and educational materials. The thematic results from this study reveal an increasing amount of open-source information useful for malicious attackers against industrial devices, as well as the need for programs, training, and policies required to protect and secure industrial systems and CI.

Metabolite profiling and antiprotozoal activity of three endemic Iranian Helichrysum species

Tropical diseases such as leishmaniosis constitute a major health concern in developing countries. Multiresistance of pathogens against classical antibiotics is a growing problem in treating infectious diseases. Thus, the search for new antibiotics is an urgent challenge. Helichrysum spp., mainly distributed in African countries, have been used in traditional and folk medicine for the treatment of several disorders including infectious diseases such as protozoal problems. In an ongoing project on the beneficial effects of Helichrysum spp., we aim to investigate and compare the anti-protozoal activities and phytochemical components of Helichrysum oligocephalum DC. and Helichrysum leucocephalum Ausfeld. Previously, we discovered pyrone and phloroglucinol derivatives as the active anti-protozoal components in Helichrysum oocephalum Boiss. [IC50 values 5.08 µg/mL and 4.01 µg/mL against Leishmania donovani and Plasmodium falciparum, respectively for dichloromethane (DCM) fraction]. As the former plants also showed similar activities to some extent [IC50 values 5.19 µg/mL and 5.42 µg/mL against L. donovani and P. falciparum respectively for DCM fraction of H. oligocephalum, IC50 value 3.8 µg/mL against P. falciparum for DCM fraction of H. leucocephalum], we decided to compare the metabolite profiles of those plants with H. oocephalum for dereplication purposes. A sensitive method coupling high-performance liquid chromatography with a photodiode-array detector (PDA) and electrospray ionization mass spectrometry (ESIMS) was optimized for separation and metabolite profiling. The LC-ESIMS metabolite profiles of the fractions from the plants were compared by applying a two-step workflow using an ACD/MS workbook suite add-in, and data clustering on an open-source web platform freeclust. The metabolites were identified by NMR and LC-PDA-ESIMS techniques. The metabolites can be categorized into major types namely flavonoids, phenolic acids, pyrone, and phloroglucinol derivatives. Phloroglucinol derivatives were mainly present in DCM fractions. DCM extract of H. oligocephalum showed the most similar profile to our previously studied extract of H. oocephalum and seems to be even much richer in pyrone and phloroglucinol derivatives. The data could emphasize the potential of Helichrysum spp. for the treatment of infectious diseases. However, more studies on the other species around the world are needed to have a much better insight.

A Finite Element Modeling and Simulation of Human Temporomandibular Joint with and Without TM Disorders: An Indian Experience

Temporomandibular joint (TMJ) is anatomically the most intricate joint which connects the lower jaw to the upper jaw and regulates jaw movements. It significantly deals with mastication and speech. It is hence imperative to study the mechanics and functioning of the jaw joint to devise alternative solutions for its replacement whenever required. Further, human skulls are anthropologically categorized into three types – African, Asian and European. Out of these, the Indian skull is also a bit different than its Asian counterparts because of its osteology and skeletal biology. Hence, a comprehensive biomechanical and computational study is essential to provide customized solutions. For the present study, four different loading conditions are selected to perform finite element analysis on the human skull, Anonymized and unidentifiable CT scan data sets from open-source web platforms are converted to STL and then 3D models using 3D slicer. Finite element analysis of jaw joint is carried out. Results based on Von Mises stress studies show significant behavioral differences under varying load conditions. Hence, it is crucial to identify solutions for TMJ disorders of the Indian population.

Luox: novel validated open-access and open-source web platform for calculating and sharing physiologically relevant quantities for light and lighting

Light exposure has a profound impact on human physiology and behaviour. For example, light exposure at the wrong time can disrupt our circadian rhythms and acutely suppress the production of melatonin. In turn, appropriately timed light exposure can support circadian photoentrainment. Beginning with the discovery that melatonin production is acutely suppressed by bright light more than 40 years ago, understanding which aspects of light drive the 'non-visual' responses to light remains a highly active research area, with an important translational dimension and implications for "human-centric" or physiologically inspired architectural lighting design. In 2018, the International Commission on Illumination (CIE) standardised the spectral sensitivities for predicting the non-visual effects of a given spectrum of light with respect to the activation of the five photoreceptor classes in the human retina: the L, M and S cones, the rods, and the melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs). Here, we described a novel, lean, user-friendly, open-access and open-source platform for calculating quantities related to light. The platform, called luox, enables researchers and research users in chronobiology, sleep research and adjacent field to turn spectral measurements into reportable quantities. The luox code base, released under the GPL-3.0 License, is modular and therefore extendable to other spectrum-derived quantities. luox has been endorsed by the CIE following black-box validation.

Luox: novel validated open-access and open-source web platform for calculating and sharing physiologically relevant quantities for light and lighting

Light exposure has a profound impact on human physiology and behaviour. For example, light exposure at the wrong time can disrupt our circadian rhythms and acutely suppress the production of melatonin. In turn, appropriately timed light exposure can support circadian photoentrainment. Beginning with the discovery that melatonin production is acutely suppressed by bright light more than 40 years ago, understanding which aspects of light drive the 'non-visual' responses to light remains a highly active research area, with an important translational dimension and implications for "human-centric" or physiologically inspired architectural lighting design. In 2018, the International Commission on Illumination (CIE) standardised the spectral sensitivities for predicting the non-visual effects of a given spectrum of light with respect to the activation of the five photoreceptor classes in the human retina: the L, M and S cones, the rods, and the melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs). Here, we described a novel, lean, user-friendly, open-access and open-source platform for calculating quantities related to light. The platform, called luox, enables researchers and research users in chronobiology, sleep research and adjacent field to turn spectral measurements into reportable quantities. The luox code base, released under the GPL-3.0 License, is modular and therefore extendable to other spectrum-derived quantities. luox has been endorsed by the CIE following black-box validation.

Luox: novel open-access and open-source web platform for calculating and sharing physiologically relevant quantities for light and lighting.

Light exposure has a profound impact on human physiology and behaviour. For example, light exposure at the wrong time can disrupt our circadian rhythms and acutely suppress the production of melatonin. In turn, appropriately timed light exposure can support circadian photoentrainment. Beginning with the discovery that melatonin production is acutely suppressed by bright light more than 40 years ago, understanding which aspects of light drive the 'non-visual' responses to light remains a highly active research area, with an important translational dimension and implications for "human-centric" or physiologically inspired architectural lighting design. In 2018, the International Commission on Illumination (CIE) standardised the spectral sensitivities for predicting the non-visual effects of a given spectrum of light with respect to the activation of the five photoreceptor classes in the human retina: the L, M and S cones, the rods, and the melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs). Here, we described a novel, lean, user-friendly, open-access and open-source platform for calculating quantities related to light. The platform, called luox, enables researchers and research users in chronobiology, sleep research and adjacent field to turn spectral measurements into reportable quantities. The luox code base, released under the GPL-3.0 License, is modular and therefore extendable to other spectrum-derived quantities.

VocBench 3: A collaborative Semantic Web editor for ontologies, thesauri and lexicons

VocBench is an open source web platform for the collaborative development of datasets complying with Semantic Web standards. Since its public release – five years ago – as an open source platform, VocBench has attracted a growing user community consi

BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations.

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE) is an open-source web platform developed with the aim to provide an environment for the design of reliable methods to conduct reproducible biomolecular simulations. It is built on the well-known Galaxy bioinformatics platform. Through this, BRIDGE hosts computational chemistry tools on public web servers for internet use and provides machine- and operating-system-independent portability using the Docker container platform for local use. This construction improves the accessibility, shareability, and reproducibility of computational methods for molecular simulations. Here we present integrated free energy tools (or apps) to calculate absolute binding free energies (ABFEs) and relative binding free energies (RBFEs), as illustrated through use cases. We present free energy perturbation (FEP) methods contained in various software packages such as GROMACS and YANK that are independent of hardware configuration, software libraries, or operating systems when ported in the Galaxy-BRIDGE Docker container platform. By performing cyclin-dependent kinase 2 (CDK2) FEP calculations on geographically dispersed web servers (in Africa and Europe), we illustrate that large-scale computations can be performed using the exact same codes and methodology by collaborating groups through publicly shared protocols and workflows. The ease of public sharing and independent reproduction of simulations via BRIDGE makes possible an open review of methods and complete simulation protocols. This makes the discovery of inhibitors for drug targets accessible to nonexperts and the computer experiments that are used to arrive at leads verifiable by experts and reviewers. We illustrate this on β-galactoside α-2,3-sialyltransferase I (ST3Gal-I), a breast cancer drug target, where a combination of RBFE and ABFE methods are used to compute the binding free energies of three inhibitors.

An Open-Source Web Platform to Share Multisource, Multisensor Geospatial Data and Measurements of Ground Deformation in Mountain Areas

Nowadays, the increasing demand to collect, manage and share archives of data supporting geo-hydrological processes investigations requires the development of spatial data infrastructure able to store geospatial data and ground deformation measurements, also considering multisource and heterogeneous data. We exploited the GeoNetwork open-source software to simultaneously organize in-situ measurements and radar sensor observations, collected in the framework of the HAMMER project study areas, all located in high mountain regions distributed in the Alpines, Apennines, Pyrenees and Andes mountain chains, mainly focusing on active landslides. Taking advantage of this free and internationally recognized platform based on standard protocols, we present a valuable instrument to manage data and metadata, both in-situ surface measurements, typically acquired at local scale for short periods (e.g., during emergency), and satellite observations, usually exploited for regional scale analysis of surface displacement. Using a dedicated web-interface, all the results derived by instrumental acquisitions and by processing of remote sensing images can be queried, analyzed and downloaded from both expert users and stakeholders. This leads to a useful instrument able to share various information within the scientific community, including the opportunity of reprocessing the raw data for other purposes and in other contexts.

Aplicación de la secuenciación masiva y la bioinformática al diagnóstico microbiológico clínico

Massive parallel sequencing (High-Throughput Sequencing [HTS]) allows to read millions or billions of DNA sequences or fragments (reads) in parallel and is revolutionizing microbiology research, moving from laboratory methods to computed-assisted analyses, with the compelling use of Bioinformatics. The time and cost reduction in studies on the microbiota, microbiome and metagenome, allows to rapidly progress in diagnosis, taxonomy, epidemiology, comparative genomics, virulence, discovery of genes or variants of interest and the association of microorganisms with traditionally considered non-microbial diseases. In this review, the terminology, the sequencing technologies and their applications are described for microbial analysis using open-source bioinformatics software, analysis pipelines, databases and web platforms that allow a user-friendly bioinformatics approach affordable by the clinical microbiologist and infectious disease practitioners.

OSGEO UN COMMITTEE EDUCATIONAL CHALLENGE: A USE CASE OF SHARING SOFTWARE AND EXPERIENCE FROM ALL OVER THE WORLD

Abstract. The paper presents the outcomes of an Educational Challenge launched by the OSGeo (Open Source Geospatial Foundation) United Nations (UN) Committee in 2018. The Committee promotes the development and use of open source software that meets UN needs and supports the aims of the UN. The Challenge supported the UN OpenGIS Initiative, a project “... to identify and develop an Open Source GIS bundle that meets the requirements of UN operations, taking full advantage of the expertise of mission partners including partner nations, technology contributing countries, international organizations, academia, NGOs, private sector”. The UN OpenGIS Initiative is organized into working groups, called ‘Spirals’. The OSGeo UN Challenge called for the development of training material that can be used for training UN staff working on Spirals 1 and 3. Spiral 1 focuses on a new open source web platform for data collection and Spiral 3 is related to new functionalities needed by UN staff during their field operations. The material developed for the challenges is now openly available for anybody, reaching a wider audience than only UN staff members. This paper describes the challenges and the training material developed for them. Expertise from all over the world was pulled together in designing, mentoring and developing the material.

Evaluation of Password Hashing Schemes in Open Source Web Platforms

Evaluation of Password Hashing Schemes in Open Source Web Platforms

Evaluation of password hashing schemes in open source web platforms

Nowadays, the majority of web platforms in the Internet originate either from CMS to easily deploy websites or by web applications frameworks that allow developers to design and implement web applications. Considering the fact that CMS are intended to be plug and play solutions and their main aim is to allow even non-developers to deploy websites, we argue that the default hashing schemes rarely are modified. Also, recent studies suggest that even developers do not use appropriate hash functions to protect passwords, since they may not have adequate security expertise. Therefore, the default settings of CMS and web applications frameworks play an important role in the security of password storage. This paper evaluates the default hashing schemes of popular CMS and web application frameworks. First, we formulate the cost time of password guessing attacks and next we investigate the default hashing schemes of popular CMS and web applications frameworks. We then apply our framework to perform a comparative analysis of the cost time of password guessing attacks between the various CMS and web application frameworks. Finally, considering that intensive hash functions consume computational resources, we analyze hashing schemes from a different perspective. That is, we investigate if it is feasible and under what conditions to perform slow rate denial of service attacks from concurrent login attempts. Through our study we have derived a set of critical observations. We have discovered that many CMS and web application frameworks use outdated hash functions, arbitrary number of hash iterations, while there is a lack of password policies and salt. Notably, the popular WordPress still uses MD5 with low number of hash iterations. Overall, we believe that the security status of the hashing schemes of CMS and web application frameworks calls for changes to the default settings from an opt-in to an opt-out security policy. More security audits and official library implementations are also required to accelerate the adoption of memory hard functions both by policy makers and the industry.

A system for profiling the IXPs in a region and monitoring their growth: Spotlight at the internet frontier

SummaryThis work aims at designing and implementing a system able to profile and help manage the set of Internet eXchange Points (IXPs) in an Internet region. As part of the Internet Society's strategy to help monitor and understand the evolution of IXPs in a particular region, a route‐collector data analyzer tool was developed before being deployed and tested in AfriNIC. In fact, traffic localization efforts in the African peering ecosystem would be more sustained, and their efficacy assessed if they were supported by a platform, which evaluates and reports in real time about their impact on the Internet. We, thus, built the “African” Route‐collectors Data Analyzer (ARDA), an open source web platform for analyzing publicly available routing information collected since 2005, by local route‐collectors. ARDA evaluates predefined metrics that picture the status of the interconnection at local, national, and regional levels. It shows that a small proportion of AfriNIC ASes (roughly 17%) are peering in the region. Through them, 58% of all African networks are visible at one IXP or more. These have been static from April to September 2017, and even February 2018, underlining the need for increased efforts to improve local interconnectivity. We show how ARDA can help detect the impact of policies on the growth of local IXPs or continually provide the community with up‐to‐date empirical data on the evolution of the IXP substrate. Given its features, this tool will be a helpful compass for stakeholders in the quest for better traffic localization and new interconnection opportunities in the targeted region.

Open Source Web Platform for the Analysis of Academic Spin-offs

Universities have assumed an increasingly important role in transferring technology to society with a strong economic impact. The companies originated from the academic environment, called academic spin-offs, have fostered the appearance of new projects based on emerging technologies and knowledge, created by young students and researchers who seek to launch their own business and generate new jobs in society. However, the number of existing studies on academic spin-offs is limited and restricted to the specific national realities, and the results of these studies are typically incorporated only in scientific manuscripts. In this sense, this study proposes a web platform that allows the analysis of academic spin-offs according to multiple dimensions, such as firm, institutions, individual, localization, science parks, financial data and corporate actions. The application is built exclusively in open source technologies and allows data to be explored in real-time and interactively. The results obtained allow us to evaluate the behavior of the application regarding fundamental elements in the success of the adoption of a Web application, such as usability, security, interoperability and portability.

A scalable online tool for quantitative social network assessment reveals potentially modifiable social environmental risks

Social networks are conduits of support, information, and health behavior flows. Existing measures of social networks used in clinical research are typically summative scales of social support or artificially truncated networks of ≤ 5 people. Here, we introduce a quantitative social network assessment tool on a secure open-source web platform, readily deployable in large-scale clinical studies. The tool maps an individual’s personal network, including specific persons, their relationships to each other, and their health habits. To demonstrate utility, we used the tool to measure the social networks of 1493 persons at risk of multiple sclerosis. We examined each person’s social network in relation to self-reported neurological disability. We found that the characteristics of persons surrounding the participant, such as negative health behaviors, were strongly associated with the individual’s functional disability. This quantitative assessment reveals the key elements of individuals’ social environments that could be targeted in clinical trials.