PSAMM: A Portable System for the Analysis of Metabolic Models

The genome-scale models of metabolic networks have been broadly applied in phenotype prediction, evolutionary reconstruction, community functional analysis, and metabolic engineering. Despite the development of tools that support individual steps along the modeling procedure, it is still difficult to associate mathematical simulation results with the annotation and biological interpretation of metabolic models. In order to solve this problem, here we developed a Portable System for the Analysis of Metabolic Models (PSAMM), a new open-source software package that supports the integration of heterogeneous metadata in model annotations and provides a user-friendly interface for the analysis of metabolic models. PSAMM is independent of paid software environments like MATLAB, and all its dependencies are freely available for academic users. Compared to existing tools, PSAMM significantly reduced the running time of constraint-based analysis and enabled flexible settings of simulation parameters using simple one-line commands. The integration of heterogeneous, model-specific annotation information in PSAMM is achieved with a novel format of YAML-based model representation, which has several advantages, such as providing a modular organization of model components and simulation settings, enabling model version tracking, and permitting the integration of multiple simulation problems. PSAMM also includes a number of quality checking procedures to examine stoichiometric balance and to identify blocked reactions. Applying PSAMM to 57 models collected from current literature, we demonstrated how the software can be used for managing and simulating metabolic models. We identified a number of common inconsistencies in existing models and constructed an updated model repository to document the resolution of these inconsistencies

The Changing Economic Geography of Globalization

The process of globalization has had profound, often destabilizing, effects on space, at all levels (i.e. local, regional, national, international). This revealing book analyzes, both theoretically and empirically, the effects of globalization over space. It considers, through a dialogue among different paradigms, the ways in which space has become more important in the global economy. Globalization has been advocated as a way of shrinking time and space which will lead to a homogenized global market; a suggestion challenged in differing ways and with a variety of approaches by all the contributors to this volume. Leading authorities from a range of disciplines are represented amongst this impressive list of contributors, including Eric Sheppard, Bjørn Asheim, Richard Walker and Peter Swann. The chapters demonstrate persuasively the continuing, and even increasing, role of space in the global economy, and throughout, the book covers viewpoints from the fields of: international political economy economic geography regional and local economics. This impressive volume, which contains a selection of the best in contemporary scholarship, will be of interest to the international arena of academicians, policy makers and professionals in these or related fields

Algorithmic problems in analysis of real time system specifications

I uppsatsen studeras representationen av William Shakespeares pjäs Hamlet i affischsammanhang. Ett antal Hamletaffischer från 1900-talet framtill 2008 beskrivs, tolkas och analyseras. Fokus ligger främst på det aktuella anslaget från 2008 års produktion på Dramaten i Stockholm. Bakgrunden innehåller kortare teoriavsnitt om klassisk och visuell retorik, bildstruktur, semiotik samt affischens historia och roll i dag. En kortare beskrivning av pjäsens handling ger en naturlig ingång till den kortare presentationen av samtliga affischer som följer. I analysen studeras Hamlet från 2008 i en djupare dimension, där en analysmodell av Roland Barthes tillämpas på ett detaljerat plan. Därefter följer en jämförande analys med tidigare affischer, vilket avslutningsvis följs av en sammanfattande diskussion kring tidigare affischer och hur dess framtida representation kan tänkas ta form.

Einstein vs. Bergson

On 6 April 1922, Einstein met Bergson to debate the nature of time: is the time the physicist calculates the same time the philosopher reflects on? Einstein claimed that only scientific time is real, while Bergson argued that scientific time always presupposes a living and perceiving subject. On that day, nearly 100 years ago, conflict was inevitable. Is it still inevitable today? How many kinds of time are there

NEPAD, narrative and African integration.

Thesis (M.A.)-University of KwaZulu-Natal, Durban, 2009.The untenable inequalities and suffering experienced by Africans blatantly exposes that a lot more than simple developmental ‘lag’, lack of economic ‘growth’, ‘governance’, or a shaky ‘investment climate’ inhibits Africa’s legitimately progressive human development. This dissertation calls for and probes a serious reflection on the roots of the concepts broadly understood as ‘African Integration’ and ‘African Renaissance’ in light of how the space we call Africa has been constructed across centuries, serving very particular interests to effect modernity’s meta-narrative into reality, subsequently positioning Africa at the periphery of the periphery of its hierarchical ordering. Narratives, defined as a distinct form of discourse as retrospective meaning-making are effective stories manifesting the conscious experience of every ‘thing’ in the universe. How Africa’s ‘story’ has been constructed, and how its actual story diverges from the convergence theories of the colonial-imperial-globalisation project are this dissertation’s major focus. It deeply mines what Foucault exposed as global technologies-of-power, to elucidate the negative impacts of northern-centric discourses on Africa’s ‘self’, from individuated to collective aspects of that ‘self’. This dissertation draws attention to how Africa’s eco-social justice practices vindicate particular scientific, cultural, and social emancipatory discourses, and democratic theories emphatic that the monumental task of de-colonising Africa’s minds from meta-narrative constructions should prioritise, and inform developmental continental policy design

Einstein vs. Bergson

On 6 April 1922, Einstein met Bergson to debate the nature of time: is the time the physicist calculates the same time the philosopher reflects on? Einstein claimed that only scientific time is real, while Bergson argued that scientific time always presupposes a living and perceiving subject. On that day, nearly 100 years ago, conflict was inevitable. Is it still inevitable today? How many kinds of time are there

Decolonisation as a social change framework and its impact on the development of Indigenous-based curricula for Helping Professionals in mainstream Tertiary Education Organisations

This research examined the social and political approaches that Indigenous peoples undertook to situate Indigenous-based education programmes in mainstream post-secondary/tertiary education organisations. Indigenous-based helping programmes assist to progress Indigenous aspirations for self-determination and are sites that center Indigenous worldviews. A decolonisation analysis framework that is embedded in the curriculum deepens students’ understanding about the impacts of imperialism, colonisation and post colonial issues. This thesis involved researching two Indigenous-based programmes that are based within mainstream tertiary institutes. The first is the Te Whiuwhiu o te Hau Maori Counselling degree programme which is based at the Waikato Institute of Technology (WINTEC) in Hamilton, Aotearoa, New Zealand. The other is the Native Human Services Social Work degree programme which is based at Laurentian University in Sudbury, Ontario, Canada