Collecting data from distributed FOSS projects

A key trait of Free and Open Source Software (FOSS) development is its distributed nature. Nevertheless, two project-level operations, the fork and the merge of program code, are among the least well understood events in the lifespan of a FOSS project. Some projects have explicitly adopted these operations as the primary means of concurrent development. In this study, we examine the effect of highly distributed software development, is found in the Linux kernel project, on collection and modelling of software development data. We find that distributed development calls for sophisticated temporal modelling techniques where several versions of the source code tree can exist at once. Attention must be turned towards the methods of quality assurance and peer review that projects employ to manage these parallel source trees. Our analysis indicates that two new metrics, fork rate and merge rate, could be useful for determining the role of distributed version control systems in FOSS projects. The study presents a preliminary data set consisting of version control and mailing list data.

Combined Tevatron upper limit on gg->H->W+W- and constraints on the Higgs boson mass in fourth-generation fermion models

We combine results from searches by the CDF and D0 collaborations for a standard model Higgs boson (H) in the process gg->H->W+W- in p=pbar collisions at the Fermilab Tevatron Collider at sqrt{s}=1.96 TeV. With 4.8 fb-1 of integrated luminosity analyzed at CDF and 5.4 fb-1 at D0, the 95% Confidence Level upper limit on \sigma(gg->H) x B(H->W+W-) is 1.75 pb at m_H=120 GeV, 0.38 pb at m_H=165 GeV, and 0.83 pb at m_H=200 GeV. Assuming the presence of a fourth sequential generation of fermions with large masses, we exclude at the 95% Confidence Level a standard-model-like Higgs boson with a mass between 131 and 204 GeV.

Collecting data from distributed FOSS projects

A key trait of Free and Open Source Software (FOSS) development is its distributed nature. Nevertheless, two project-level operations, the fork and the merge of program code, are among the least well understood events in the lifespan of a FOSS project. Some projects have explicitly adopted these operations as the primary means of concurrent development. In this study, we examine the effect of highly distributed software development, is found in the Linux kernel project, on collection and modelling of software development data. We find that distributed development calls for sophisticated temporal modelling techniques where several versions of the source code tree can exist at once. Attention must be turned towards the methods of quality assurance and peer review that projects employ to manage these parallel source trees. Our analysis indicates that two new metrics, fork rate and merge rate, could be useful for determining the role of distributed version control systems in FOSS projects. The study presents a preliminary data set consisting of version control and mailing list data.

Optimization of sample preparation for next-generation sequencing with Illumina Genome Analyzer II

The growing interest for sequencing with higher throughput in the last decade has led to the development of new sequencing applications. This thesis concentrates on optimizing DNA library preparation for Illumina Genome Analyzer II sequencer. The library preparation steps that were optimized include fragmentation, PCR purification and quantification. DNA fragmentation was performed with focused sonication in different concentrations and durations. Two column based PCR purification method, gel matrix method and magnetic bead based method were compared. Quantitative PCR and gel electrophoresis in a chip were compared for DNA quantification. The magnetic bead purification was found to be the most efficient and flexible purification method. The fragmentation protocol was changed to produce longer fragments to be compatible with longer sequencing reads. Quantitative PCR correlates better with the cluster number and should thus be considered to be the default quantification method for sequencing. As a result of this study more data have been acquired from sequencing with lower costs and troubleshooting has become easier as qualification steps have been added to the protocol. New sequencing instruments and applications will create a demand for further optimizations in future.

Exact bounds for distributed graph colouring

A distributed system is a collection of networked autonomous processing units which must work in a cooperative manner. Currently, large-scale distributed systems, such as various telecommunication and computer networks, are abundant and used in a multitude of tasks. The field of distributed computing studies what can be computed efficiently in such systems. Distributed systems are usually modelled as graphs where nodes represent the processors and edges denote communication links between processors. This thesis concentrates on the computational complexity of the distributed graph colouring problem. The objective of the graph colouring problem is to assign a colour to each node in such a way that no two nodes connected by an edge share the same colour. In particular, it is often desirable to use only a small number of colours. This task is a fundamental symmetry-breaking primitive in various distributed algorithms. A graph that has been coloured in this manner using at most k different colours is said to be k-coloured. This work examines the synchronous message-passing model of distributed computation: every node runs the same algorithm, and the system operates in discrete synchronous communication rounds. During each round, a node can communicate with its neighbours and perform local computation. In this model, the time complexity of a problem is the number of synchronous communication rounds required to solve the problem. It is known that 3-colouring any k-coloured directed cycle requires at least ½(log* k - 3) communication rounds and is possible in ½(log* k + 7) communication rounds for all k ≥ 3. This work shows that for any k ≥ 3, colouring a k-coloured directed cycle with at most three colours is possible in ½(log* k + 3) rounds. In contrast, it is also shown that for some values of k, colouring a directed cycle with at most three colours requires at least ½(log* k + 1) communication rounds. Furthermore, in the case of directed rooted trees, reducing a k-colouring into a 3-colouring requires at least log* k + 1 rounds for some k and possible in log* k + 3 rounds for all k ≥ 3. The new positive and negative results are derived using computational methods, as the existence of distributed colouring algorithms corresponds to the colourability of so-called neighbourhood graphs. The colourability of these graphs is analysed using Boolean satisfiability (SAT) solvers. Finally, this thesis shows that similar methods are applicable in capturing the existence of distributed algorithms for other graph problems, such as the maximal matching problem.

Tsoi Yuen Resistance and Post-80s Generation: A new wave of domestic social movement

Hong Kong was once a British colony and has been under the sovereignty of People’s Republic of China (PRC) since 1997. However, some of the unjust practices and colonial legacies are infiltrated into the development ideology as well as the social structures. The construction of intercity express railway project announced in 2008 causing the demolishment of Tsoi Yuen Tsuen, a “non-indigenous” agricultural village in Hong Kong, was one of the current examples. Tsoi Yuen village was established under the former colonial sovereignty sixty years ago. Approximately 450 populations were affected that they had to relocate their homeland involuntarily. However, these villagers were very attached to their homelands and were unwilling to move, and meanwhile they found that they were absent in the government’s consultation and decision-making process. Soon they began their resistance and demanded for “No Move! No Demolish!”. Their movement was strongly supported by a group of “Post-80s generation” and turned into the most important social movement of the city in recent years. In fact, demolition of Tsoi Yuen Village for city development is not an isolated case in the city. Meanwhile the situation is getting worse in Mainland China. I chose the case study of Tsoi Yuen Resistance from 2008 to 2011 for revelation of the complicated colonial history and postcolonial era of Hong Kong. I focused on discussing the Tsoi Yuen Resistance and the Post-80s movement, and how they have exposed the tension between top-down urban planning and development and public movements fighting for a more democratic process in choosing their way of living. Through the study of a village movement which as well as the rationale behind the Post-80s’ support, I hoped to illustrate how this movement has awaken a different sense of living for the new generations in the midst of the high-sounding urban development. It is an opportunity to examine Hong Kong’s colonial epoch in a different perspective: through studying the Tsoi Yuen Village, let them (subalterns) speak for themselves. Furthermore, the significance of this resistance, taking place eleven years after the handover to the PRC, is an important fact that I shall not miss in later discussion. Last but not least, during the resistance, advanced technology and social networks such as Facebook, Twitter, iPhone were used by Post 80s generation to spread the latest information in order to attract public’s concern and participation. Therefore, apart from studying Tsoi Yuen Resistance as a local social movement, I also regard it as a part of the global movement in perusing ecological lifestyle and civil society. How Post 80s’ generation manipulates the global idea in a local context will also be examined.