BACKGROUND: Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α- & β-diversity. Feature subset selection - a sub-field of machine learning - can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate between age groups in the human gut microbiome. RESULTS: We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. CONCLUSIONS: We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.

This research provides a detailed account of Open Source Software (OSS) development in the context of developing countries (DCs) by exploring the specific case of Chinese indigenous Linux design and development. It builds an interdisciplinary, socio-technical, analytical framework from the perspective of science and technology studies (STS), in particular the social shaping of technology (SST), infrastructural studies and international technology transfer. It also covers the fields of economic analysis, policy studies and development studies. The research investigates the adaptation process of a unique OSS with infrastructural features – Linux in the context of China by conducting case studies on both embedded Linux and platform Linux products developed by two Chinese Linux providers. Drawing upon the concepts developed in the SST perspective and infrastructural studies, this research addresses both the dynamism and continuity of OSS. In order to avoid the shortcomings of existing social scientific study on OSS, we applied social and biography of artefacts (BoA) approaches to examine the evolution of Chinese Linux by mapping out the key actors, investigating the linkages between them, and probing deeply into the intricate interplays among these actors over time. A detailed longitudinal and contextual analysis has been undertaken through a qualitative historical case study of the evolution of both Chinese embedded Linux and platform Linux from 1998-2008. The empirical data reveals that the local adaptation and further innovation of Chinese Linux is a ‘generification’ process, i.e. a process of design and developing generic Linux solutions for diverse local users. Theoretically, the understanding of the socio-technical interfaces of the software (seeking, identifying, categorising local users/intermediaries, as well as collaborating with key players associated with the particular software) are central elements for software technology transfer and local technological capabilities building. The findings also throw the light on the crucial importance of government role in providing incentives and institutional measures for Linux adaptation in China. In particular, it highlights the challenges concerning the socio-technical specificities of infrastructural software, like Linux OS (operating system) and the particular relevance to DCs as technology adapters. Finally, this study throws light on the policy and practice for China’s future Linux development, and the implications for other DCs.

Releasing software is challenging. To decide when to release software, developers may consider a deadline, a set of features or quality attributes. Yet, there are many stories of software that is not released on time. In large-scale software development, release management requires significant communication and coordination. It is particularly challenging in Free and Open Source Software (FOSS) ecosystems, in which hundreds of loosely connected developers and their projects are coordinated for releasing software according to a schedule. In this work, we investigate the release management process in two large-scale FOSS development projects. In particular, our focus is the communication in the whole release management process in each ecosystem across multiple releases. The main research questions addressed in this dissertation are: (1) How do developers in these FOSS ecosystems communicate and coordinate to build and release a common product based on different projects? (2) What are the release management tasks in a FOSS ecosystem? and (3) What are the challenges that release managers face in a FOSS ecosystem? To understand this process and its challenges better, we used a multiple case study methodology, and colleced evidence from a combination of the following sources: documents, archival records, interviews, direct observation, participant observation, and physical artifacts. We conducted the case studies on two FLOSS software ecosystems: GNOME and OpenStack. We analyzed over two and half years of communication in each ecosystem and studied developers’ interactions. GNOME is a collection of libraries, system services, and end-user applications; together, these projects provide a unified desktop —the GNOME desktop. OpenStack is a collection of software tools for building and managing cloud computing platforms for public and private clouds. We catalogued communication channels, categorized coordination activities in one channel, and triangulated our results by interviewing key developers identified through social network analysis. We found factors that impact the release process in a software ecosystem, including a release schedule positively, influence instead of direct control, and diversity. The release schedule drives most of the communication within an ecosystem. To achieve a concerted release, a Release Team helps developers reach technical consensus through influence rather than direct control. The diverse composition of the Release Team might increase its reach and influence in the ecosystem. Our results can help organizations build better large-scale teams and show that software engineering research focused on individual projects might miss important parts of the picture. The contributions of this dissertation are: (1) an empirical study of release management in two FOSS ecosystems (2) a set of lessons learned from the case studies, and (3) a theory of release management in FOSS ecosystems. We summarize our theory that explains our understanding of release management in FOSS ecosystems as three statements: (1) the size and complexity of the integrated product is constrained by the release managers capacity, (2) release management should be capable of reaching the whole ecosystem, and (3) the release managers need social and technical skills. The dissertation discusses this theory in the light of the case studies, other research efforts, and its implications. / Graduate / 0984 / gpoo+proquest@calcifer.org

The two most popular classification tree algorithms in machine learning and statistics - C4.5 and CART - are compared in a benchmark experiment together with two other more recent constant-fit tree learners from the statistics literature (QUEST, conditional inference trees). The study assesses both misclassification error and model complexity on bootstrap replications of 18 different benchmark datasets. It is carried out in the R system for statistical computing, made possible by means of the RWeka package which interfaces R to the open-source machine learning toolbox Weka. Both algorithms are found to be competitive in terms of misclassification error - with the performance difference clearly varying across data sets. However, C4.5 tends to grow larger and thus more complex trees. (author's abstract) / Series: Research Report Series / Department of Statistics and Mathematics

Today there is a heavy integration of information technology in almost every aspect of our lives and there is an increase in computer security that goes with it. To ensure this security, and that policies and procedures within an organisations related to this security are enforced; security audits are conducted. At the same time, use of open source software is also becoming increasingly common, becoming more a fact of life rather than an option. With these two trends in mind, this study analyses a selection of scientific literature on the topic and identifies the unique challenges a security audit in an open source environment faces, and aims to contribute on how to help alleviate the challenges. The study was performed in the form of a literature review, where the comparison and analysis revealed interesting information regarding the open source specific challenges, including both technical issues as well as challenges stemming from people’s perception and handling of open source software today. The answer to the question “What are the challenges when conducting security audits for open source systems and how can they be alleviated?” shows the main challenges to be too much trust is put in unverified binaries. The report offers suggestions and ideas on how to implement solutions in order to help diminish this challenge through the use and integration of Reproducible Builds, answering the second part of the question.

Programmers often have to choose components online for reuse based on software quality. To help with this choice, most component repositories (SourceForge, CodeProject, etc.) provide information such as user ratings and reviews of components. However, the reusability of components is not immediately obvious from this material. To make things worse, reviews and other material could potentially contradict one another about reusability or any other issue. Moreover, there could be multiple components that claim to perform identical tasks in which case it becomes difficult to identify the most reusable component. This thesis presents the result of two studies aimed at discovering how to use material from a component repository to automatically characterize the reusability of components. It was found that two factors (out of three) were significant predictors of reusability. Additionally, a review summarizer was developed to summarize user reviews and return the overall opinion reflected by the comments. / Graduation date: 2013

Open Source Software (OSS) is widely used and is becoming a significant and irreplaceable part of the software engineering community. Today a huge number of OSS exist. This becomes a problem if one needs to choose from such a large pool of OSS candidates in the same category. An OSS maturity model that facilitates the software assessment and helps users to make a decision is needed. A few maturity models have been proposed in the past. However, the parameters in the model are assigned not based on experimental data but on human experiences, feelings and judgments. These models are subjective and can provide only limited guidance for the users at the best. This dissertation has proposed a quantitative and objective model which is built from the statistical perspective. In this model, seven metrics are chosen as criteria for OSS evaluation. A linear multiple-regression model is created to assign a final score based on these seven metrics. This final score provides a convenient and objective way for the users to make a decision. The coefficients in the linear multiple-regression model are calculated from 43 OSS. From the statistical perspective, these coefficients are considered random variables. The joint distribution of the coefficients is discussed based on Bayesian statistics. More importantly, an updating rule is established through Bayesian analysis to improve the joint distribution, and thus the objectivity of the coefficients in the linear multiple-regression model, according to new incoming data. The updating rule provides the model the ability to learn and improve itself continually.

Der Vortrag wurde zum UNIX-Stammtsich am 25.5.2010 gehalten.

Open source software are those which permit execution, copy, read, distribution and improvement of the software without any restrictions. Library Management Software (LMS), is an enterprise resource planning system for a library, used to track items owned, orders made, bills paid, and patrons who have borrowed. Commercial library management software are very expensive. Therefore, open source library management system can be appropriate alternatives for automatic library systems. This paper discusses features of open source library management software, criteria of selection of best open source library management software, their, advantages and limitations. Open source library management software is a solution to reduce that cost. The paper describes in brief about the feature of some of the open source library management software like Koha, NewGenlib, Evergreen, SENAYAN, ABCD, and BiblioteQ.

Softwares now-a-days have become the life line of modern day organizations. Organizations cannot think of doing their tasks effectively and efficiently without softwares. The extremely competitive environment, zero deficiency and enhanced productivity has made it mandatory for the organizations to carefully choose the appropriate software after comprehensive needs assessment. Softwares simply their tasks and saves a lot of precious time which can be utilized in managing other important issues. Libraries also need softwares if they want to create a parallel digital library with features which we may not find in a traditional library. There are several open source softwares available to create a digital library. For this, firstly the library professionals should be aware of the advantages of open source software and should involve in their development. They should have basic knowledge about the selection, installation and maintenance. Open source software requires a greater degree of computing responsibility than commercial software. Digitization involves huge money to create and maintain and the OSS appears to be a means to reduce it. Among these, DSpace and Greenstone are becoming more popular in India and abroad. This paper deals with the comparison of these two popular OSS from various points of view. The comparative table may help the professionals who are planning to create a digital library.