Automated landmarking via multiple templates.

This chapter describes a pragmatic approach to using open source and free software tools as valuable resources to affect learning of software industry practices using iterative and incremental development methods. The authors discuss how the above resources are used in teaching undergraduate Software Engineering (SE) courses. More specifically, they illustrate iterative and incremental development, documenting software requirements, version control and source code management, coding standards compliance, design visualization, software testing, software metrics, release deliverables, software engineering ethics, and professional practices. The authors also present how they positioned the activities of this course to qualify it for writing intensive designation. End of semester course evaluations and anecdotal evidence indicate that the proposed approach is effective in educating students in software industry practices.

Dendrochronological techniques are paramount in forest research. The current climate change scenario and the central role of forests in biogeophysical cycles enforce the importance of novel techniques to get accurate data from trees and their relationship with the environment in faster ways. Recent technological advances and the place of open source software and hardware are making free, user-developed tools for forest research available to the research community. The aim of this Ph.D. thesis is the development of tools for image acquisition and data collection in dendrochronology based on open source software and hardware. Thus, four different tools for dendrochronological research are presented in five different chapters. The first chapter focuses on the development of a do-it-yourself tool based on open source hardware for image acquisition and wood sample digitization at high resolution. We used open hardware equipment from Arduino and Python programming to develop CaptuRING and published the entire free open source tool as: "CaptuRING: A Do-It-Yourself tool for wood sample digitization" in Methods in Ecology and Evolution, 2022; 13:1185-1191. Furthermore, the original software was registered in the Registro General de Propiedad Intelectual (00/2022/737) of Ministerio de Cultura y Deporte (Spain). The second chapter presents "How to build and install your own CaptuRING". This contribution presents a series of videos with a step-by-step guide to promote the use of CaptuRING in the research community. The manuscript and related videos have been submitted for publication. The third chapter describes ρ-MtreeRing. This free and open-source software, which is written in R, analyzes X-ray films from dendrochronological samples to get microdensity values automatically segmented through a graphical user interface. The open source tool and manuscript are published as: "ρ-MtreeRing. A graphical user interface for X-ray microdensity analysis" in Forests. 2021; 12(10):1405. The fourth chapter describes the potential of deep learning methods to automatically segment xylem vessels. We trained three different convolutional neural networks to segment vessels in stained wood microsections using the Keras framework in Python. Our results demonstrate the potential of these techniques to automatically segment xylem vessels and overcome derived problems from image illumination, which hamper segmentation using classical image segmentation methods. The manuscript is published as "Convolutional neural networks for segmenting xylem vessels in stained cross-sectional images" in: Neural Computing & Applications, 2020; 32:17927-17939. The fifth chapter develops an algorithm to delineate annual ring limits in stained wood microsections of a species with diffuse porous wood using convolutional neural networks. We used Python for image processing and the Keras framework for the algorithm training. The results show the ability of this techniques to obtain accurate tree ring segmentation for quantitative wood anatomy, reaching similar or even outperforming conventional manual delimitation in most of the evaluated cases. The results of this chapter will be presented in the manuscript "Deep Learning for ring bordering in stained cross-sectional images". This PhD Thesis presents four open source tools to get accurate information from wood features to unveil how trees respond to the environment. From digitization at macroscopic perspective, automatic data collection and the development of feature segmentation on microscopic samples. The presented four novel dendrochronological tools based on open source software facilitates forest research in the current climate change scenario.

The development of open-source FPGA CAD tools is challenging. Vendor CAD tools exist but are closed-source and specific to each FPGA family. These tools give limited opportunity for customizing and also have the disadvantage of long compile times. Several open source tools have been built, but the quality of results from these tools is still far behind commercial tools. This research is aimed at bridging some of the gap between commercial and open-source FPGA CAD tools by tuning policies of existing implementation algorithms. We build a set of synthetic benchmarks to identify the mapping between input circuit patterns and policies of a given CAD algorithm and architecture. This work discusses the framework for policy tuning and is aimed at showing that algorithm policies need to adapt to the input circuit. We demonstrate our framework with the packing step of the FPGA CAD flow and show how our approach can be used to improve the quality of results in open-source tools.

The software industry has evolved toward complex supplier-user networks that cooperate and collaborate in many ways. We hardly see any longer the traditional way of software development in which one company handles design, production, sales, delivery, and service. Business models, engineering life cycles, distribution channels, and services have changed dramatically. A key driver in these new value networks is open source software (OSS). Open source refers to software that we may freely use, modify, or distribute, provided we observe certain restrictions with respect to copyright and protection of its open source status. OSS is not freeware and generally has a copyright. IEEE Software, through this paper, has assembled this minitheme to provide a glimpse of where OSS is heading.

The Move to the Middle: Convergence of the Open-Source and Proprietary Software Industries

With forensics playing such a crucial role in today's data-driven world, this paper addresses the need to explore the different mobile device forensic tools available. Open Source and Commercial tools are two domains in close contention, with contrasting considerations such as accessibility and security. This paper aims at performing a comparative analysis of the various commercial and open source mobile device forensic tools, with respect to predefined software parameters and by employing a cross-device and test-driven approach. The test scenarios are structured to assess whether the selected tools possess the capabilities of a holistic one, while responding to threats and scenarios pertaining to the digital realm. The Commercial Tools under consideration are MOBILedit! Forensic (including Phone Forensics Express) and Cellebrite's UFED Physical Analyzer, while the Open Source Tools are — The Sleuth Kit (including Autopsy) and SANS SIFT. The result of this paper is a comparison matrix, which could help in identifying the best-fit solution as per the need of the investigation. It could also indicate the degree to which open source tools are comparable to (or better than) their commercial counterparts, and answer questions like — Can open source tools be a suitable replacement for the proprietary tools? Can this in reality, be a feasible shift for the forensic industry?

Digital Systems plays an important role in today’s modern technology. The practical implementation of digital circuits in laboratories leads to a complex wired circuits and testing finds difficult. The damage of ICs, breadboards due to complexity needs replacement. This paper disseminates the virtual use of all the components using an open source tool. Digital circuits are of combinational logic circuits and sequential circuits. Implementation of combinational circuits using logic gates in virtual mode is described. Autodesk Tinkercad is an open-source software tool for the development of system. The design of combinational circuits such as Adder, Subtractor, Encoder, Decoder, Code converters are implemented with ICs using Tinkercad tool.

Chapter 1 - Digital Forensics with Open Source Tools

Over the past decade, numerous computer-assisted retrosynthesis reaction prediction methods have been reported in the chemical literature, several of which are also shared as open-source code. Reports of integrating these modern open-source retrosynthetic prediction techniques into the chemical education classroom, however, is largely absent. This article describes our efforts to teach a computer-assisted retrosynthesis workshop series using open-source reaction prediction software and methods. In addition to three workshops on selected open-source reaction prediction methods, the series included workshops on Python programming and introductory cheminformatics using the RDKit cheminformatics toolkit. A pre and post survey was distributed to better understand participant familiarity and workshop outcomes. Participants indicated that they had minimal experience with cheminformatics, and open-source retrosynthesis software, however after the workshop series they indicated increased familiarity, interest, and desire to pursue additional training related to open-source retrosynthesis software and methods. We conclude this article with our experiences and ideas for future improvements. The workshop materials and code are available with an open source license, and educators are encouraged to adapt and improve the lessons (https://github.com/UA-Libraries-Research-Data-Services/retrosynthesis).

Three-dimensional (3D) shape lies at the core of understanding the physical objects that surround us. In the biomedical field, shape analysis has been shown to be powerful in quantifying how anatomy changes with time and disease. The Shape AnaLysis Toolbox (SALT) was created as a vehicle for disseminating advanced shape methodology as an open source, free, and comprehensive software tool. We present new developments in our shape analysis software package, including easy-to-interpret statistical methods to better leverage the quantitative information contained in SALT's shape representations. We also show SlicerPipelines, a module to improve the usability of SALT by facilitating the analysis of large-scale data sets, automating workflows for non-expert users, and allowing the distribution of reproducible workflows.

Open source software is becoming increasingly prominent, and the economic structure of open-source development is changing. In recent years, firms motivated by revenues from software services markets have become the primary contributors to open-source development. In this paper we study the role of services in open source software development and explore the choice between open source and proprietary software. Specifically, our economic model jointly analyzes the investment and pricing decisions of the originators of software and of subsequent open-source contributors. We find that if a contributor is efficient in software development, the originator should adopt an open-source strategy, allowing the contributor to offer higher total quality and capture the higher end of the market while the originator focuses on providing software services to lower end consumers. Conversely, if the contributor is not efficient in development, the originator should adopt a proprietary software development strategy, gaining revenue from software sales and squeezing the contributor out of the services market. In certain cases an increase in originator development efficiency can result in increased contributor profits. Finally, we find that, somewhat counterintuitively, an increase in contributor development efficiency can reduce overall social welfare.

The Norwegian Water Resources and Energy Directorate (NVE) is tasked with management of water- and energy resources in Norway, as well as reducing the risk of damages associated with landslides and flooding. Copernicus satellite data can provide valuable insight for those tasks. The vast amount of Copernicus data however requires scalable and robust solutions for processing. Standardized and modular workflows help safeguarding maintainability and efficiency of service delivery. In order to implement operational Copernicus services at NVE, the Open Source OSGeo Community project actinia was introduced together with the Open Source Apache Airflow software as a platform for delivering operational Copernicus services at national scale. actinia (https://actinia-org.github.io/) is a REST API for scalable, distributed, and high performance processing of time series of satellite images, as well as geographical raster and vector data. It is a modular system that uses mainly GRASS GIS for computational tasks. Apache Airflow (https://airflow.apache.org/) is an orchestration solution that allows to programmatically author, schedule and monitor workflows. In the presentation, we will illustrate how Apache Airflow and actinia work together and present selected examples of current and future applications operationalized on the platform. Those applications cover currently: Avalanches Flooding snow cover lake ice More services related to NVE`s area of responsibility are being investigated, like landslides, slush flows, glacier lake outburst floods, and specific land cover changes... Finally, we discuss challenges and opportunities of using Open Source Software tools and collaborative science approaches at NVE in national, operational services.

New and rapid political and economic changes in Myanmar are increasing the pressures on the country’s forests. Yet, little is known about the past and current condition of these forests and how fast they are declining. We mapped forest cover in Myanmar through a consortium of international organizations and environmental non-governmental groups, using freely-available public domain data and open source software tools. We used Landsat satellite imagery to assess the condition and spatial distribution of Myanmar’s intact and degraded forests with special focus on changes in intact forest between 2002 and 2014. We found that forests cover 42,365,729 ha or 63% of Myanmar, making it one of the most forested countries in the region. However, severe logging, expanding plantations, and degradation pose increasing threats. Only 38% of the country’s forests can be considered intact with canopy cover >80%. Between 2002 and 2014, intact forests declined at a rate of 0.94% annually, totaling more than 2 million ha forest loss. Losses can be extremely high locally and we identified 9 townships as forest conversion hotspots. We also delineated 13 large (>100,000 ha) and contiguous intact forest landscapes, which are dispersed across Myanmar. The Northern Forest Complex supports four of these landscapes, totaling over 6.1 million ha of intact forest, followed by the Southern Forest Complex with three landscapes, comprising 1.5 million ha. These remaining contiguous forest landscape should have high priority for protection. Our project demonstrates how open source data and software can be used to develop and share critical information on forests when such data are not readily available elsewhere. We provide all data, code, and outputs freely via the internet at (for scripts: https://bitbucket.org/rsbiodiv/; for the data: http://geonode.themimu.info/layers/geonode%3Amyan_lvl2_smoothed_dec2015_resamp)

Open-source software abbreviated as OSS is computer software that is available with source code and is provided under a software license that permits users to study, change, and improve the software. For the commercial software the source code and certain other rights are normally reserved for copyright holders,i.e. the company who developes the software. A group of people in a collaborative manner often developes the Open source software, not under the roof of a large organization. This strategy makes open source software cheap, reliable and modifiable if needed. In this context we shall discuss mainly the features of Open Source Software, differences of open source and free software and open source software movement in Indian perspective.

A lot misinformation and mystery surrounds the topic of Open Source software. The conceptual misunderstanding of software is fostered, in some respects, by a lack of understanding within the professional ranks of the computer field. There are many different views of Open Source software today, based upon ones perspective. After about 20 years of evolution, the position of Open Source in our economy still has not coalesced. Few seems to understand whether Open Source is free software for running a computer (i.e., Linux) or just a way to obtain some software products without giving Microsoft ones money. “There is one thing stronger than all the armies in the world and that is an idea whose time has come” - Victor Hugo any view Open Source (OS) software as just a free alternative to proprietary software. The term does not mean that there is no cost associated with its procurement, although some vendors do provide free versions. The word “free” usually means the freedom to copy, modify, or distribute the software. One must be very careful when applying this broad, general meaning to Open Source software. There are many different Open Source licenses in use and it is imperative that users acquaint themselves with the legal ramifications of dealing with intellectual property rights. ` Open Source software should be viewed as a viable alternative in many software selection processes. Recently, the news has portrayed the report of India's Kerala state moving to Linux and OpenOffice for its 2,724 high schools. Likewise, OpenOffice is replacing Microsoft Office in many schools districts around the US. With tight school budgets, school superintendents are realizing significant cost savings by using the OpenOffice products for their campuses. Products such as OpenOffice may not be 100% compatible with their current proprietary counterpart, but for many applications, compatibility is not the issue. The price and the software license management of proprietary packages may be overwhelming.