Developing semantic pathway comparison methods for systems biology

Systems biology is an emerging multi-disciplinary field in which the behaviour of complex biological systems is studied by considering the interaction of many cellular and molecular constituents rather than using a “traditional” reductionist approach where constituents are studied individually. Systems are often studied over time with the ultimate goal of developing models which can be used to understand and predict complex biological processes, such as human diseases. To support systems biology, a large number of biological pathways are being derived for many different organisms, and these are stored in various databases. This pathway collection presents an opportunity to compare and contrast pathways, and to utilise the knowledge they represent. This thesis presents some of the first algorithms that are designed to explore this opportunity. It is argued that the methods will be useful to biologists in order to assess the biological plausibility of derived pathways, compare different biological pathways for semantic similarities, and to derive putative pathways that are semantically similar to documented biological pathways. The methods will therefore extend the systems biology toolbox that biologists can use to make new biological discoveries.Knowledge Foundation. Grant No. 2003/0215Information Fusion Research Program (University of Skovde, Sweden) Grant No 2003/010

Invisible Pixels Are Dead, Long Live Invisible Pixels!

Privacy has deteriorated in the world wide web ever since the 1990s. The tracking of browsing habits by different third-parties has been at the center of this deterioration. Web cookies and so-called web beacons have been the classical ways to implement third-party tracking. Due to the introduction of more sophisticated technical tracking solutions and other fundamental transformations, the use of classical image-based web beacons might be expected to have lost their appeal. According to a sample of over thirty thousand images collected from popular websites, this paper shows that such an assumption is a fallacy: classical 1 x 1 images are still commonly used for third-party tracking in the contemporary world wide web. While it seems that ad-blockers are unable to fully block these classical image-based tracking beacons, the paper further demonstrates that even limited information can be used to accurately classify the third-party 1 x 1 images from other images. An average classification accuracy of 0.956 is reached in the empirical experiment. With these results the paper contributes to the ongoing attempts to better understand the lack of privacy in the world wide web, and the means by which the situation might be eventually improved.Comment: Forthcoming in the 17th Workshop on Privacy in the Electronic Society (WPES 2018), Toronto, AC

Public Sector Open Source Software Projects -- How is development organized?

Background: Open Source Software (OSS) started as an effort of communities of volunteers, but its practices have been adopted far beyond these initial scenarios. For instance, the strategic use of OSS in industry is constantly growing nowadays in different verticals, including energy, automotive, and health. For the public sector, however, the adoption has lagged behind even if benefits particularly salient in the public sector context such as improved interoperability, transparency, and digital sovereignty have been pointed out. When Public Sector Organisations (PSOs) seek to engage with OSS, this introduces challenges as they often lack the necessary technical capabilities, while also being bound and influenced by regulations and practices for public procurement. Aim: We aim to shed light on how public sector OSS projects, i.e., projects initiated, developed and governed by public sector organizations, are developed and structured. We conjecture, based on the challenges of PSOs, that the way development is organized in these type of projects to a large extent disalign with the commonly adopted bazaar model (popularized by Eric Raymond), which implies that development is carried out collaboratively in a larger community. Method: We plan to contrast public sector OSS projects with a set of earlier reported case studies of bazaar OSS projects, including Mockus et al.'s reporting of the Apache web server and Mozilla browser OSS projects, along with the replications performed on the FreeBSD, JBossAS, JOnAS, and Apache Geronimo OSS projects. To enable comparable results, we will replicate the methodology used by Mockus et al. on a purposefully sampled subset of public sector OSS projects. The subset will be identified and characterized quantitatively by mining relevant software repositories, and qualitatively investigated through interviews with individuals from involved organizations.Comment: Registered Report accepted at MSR'2

Adopting Open Source IT Certification in Higher Education: Lessons from the Field

This paper suggests areas of good practice and considerations based upon the experience of embedding an open source information technology (IT) certification into a UK higher education program. Academically, open source is used as a vehicle for teaching general academic skills and values, but also as a collection of marketable skills. IT certification is used to further develop and signpost these skills to employers. This paper critically reviews literature in the fields of open source software in education and IT certification. A case study then discusses the methods used to embed such certification at Birmingham City University in the UK. Key barriers are reviewed along with a summary of lessons learned for the benefit of those considering similar actions

Propagating semantic information in biochemical network models

<p>Abstract</p> <p>Background</p> <p>To enable automatic searches, alignments, and model combination, the elements of systems biology models need to be compared and matched across models. Elements can be identified by machine-readable biological annotations, but assigning such annotations and matching non-annotated elements is tedious work and calls for automation.</p> <p>Results</p> <p>A new method called "semantic propagation" allows the comparison of model elements based not only on their own annotations, but also on annotations of surrounding elements in the network. One may either propagate feature vectors, describing the annotations of individual elements, or quantitative similarities between elements from different models. Based on semantic propagation, we align partially annotated models and find annotations for non-annotated model elements.</p> <p>Conclusions</p> <p>Semantic propagation and model alignment are included in the open-source library semanticSBML, available on sourceforge. Online services for model alignment and for annotation prediction can be used at <url>http://www.semanticsbml.org</url>.</p

An empirically-based characterization and quantification of information seeking through mailing lists during Open Source developers' software evolution

Context Several authors have proposed information seeking as an appropriate perspective for studying software evolution. Empirical evidence in this area suggests that substantial time delays can accrue, due to the unavailability of required information, particularly when this information must travel across geographically distributed sites. Objective As a first step in addressing the time delays that can occur in information seeking for distributed Open Source (OS) programmers during software evolution, this research characterizes the information seeking of OS developers through their mailing lists. Method A longitudinal study that analyses 17 years of developer mailing list activity in total, over 6 different OS projects is performed, identifying the prevalent information types sought by developers, from a qualitative, grounded analysis of this data. Quantitative analysis of the number-of-responses and response time-lag is also performed. Results The analysis shows that Open Source developers are particularly implementation centric and team focused in their use of mailing lists, mirroring similar findings that have been reported in the literature. However novel findings include the suggestion that OS developers often require support regarding the technology they use during development, that they refer to documentation fairly frequently and that they seek implementation-oriented specifics based on system design principles that they anticipate in advance. In addition, response analysis suggests a large variability in the response rates for different types of questions, and particularly that participants have difficulty ascertaining information on other developer's activities. Conclusion The findings provide insights for those interested in supporting the information needs of OS developer communities: They suggest that the tools and techniques developed in support of co-located developers should be largely mirrored for these communities: that they should be implementation centric, and directed at illustrating "how" the system achieves its functional goals and states. Likewise they should be directed at determining the reason for system bugs: a type of question frequently posed by OS developers but less frequently responded to

Trademarks, Certification Marks and Technical Standards

The names of many technical standards such as Wi-Fi, Bluetooth and DVD have become household terms known throughout the developed world. This chapter describes different approaches that have been taken with respect to the naming and legal protection of technical standards, ranging from those that are wholly unregulated to those that are administered under strict certification and compliance regimes. It concludes by questioning the need for aggressive protection of marks that exist largely to inform consumers about technical product features rather than the source of standards themselves