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Institute
- Institut für Informatik und Computational Science (49) (remove)
Refined elasticity sampling for Monte Carlo-based identification of stabilizing network patterns
(2015)
Motivation: Structural kinetic modelling (SKM) is a framework to analyse whether a metabolic steady state remains stable under perturbation, without requiring detailed knowledge about individual rate equations. It provides a representation of the system's Jacobian matrix that depends solely on the network structure, steady state measurements, and the elasticities at the steady state. For a measured steady state, stability criteria can be derived by generating a large number of SKMs with randomly sampled elasticities and evaluating the resulting Jacobian matrices. The elasticity space can be analysed statistically in order to detect network positions that contribute significantly to the perturbation response. Here, we extend this approach by examining the kinetic feasibility of the elasticity combinations created during Monte Carlo sampling.
Results: Using a set of small example systems, we show that the majority of sampled SKMs would yield negative kinetic parameters if they were translated back into kinetic models. To overcome this problem, a simple criterion is formulated that mitigates such infeasible models. After evaluating the small example pathways, the methodology was used to study two steady states of the neuronal TCA cycle and the intrinsic mechanisms responsible for their stability or instability. The findings of the statistical elasticity analysis confirm that several elasticities are jointly coordinated to control stability and that the main source for potential instabilities are mutations in the enzyme alpha-ketoglutarate dehydrogenase.
Pervasive educational games have the potential to transfer learning content to real-life experiences beyond lecture rooms, through realizing field trips in an augmented or virtual manner. This article introduces the pervasive educational game "RouteMe" that brings the rather abstract topic of routing in ad hoc networks to real-world environments. The game is designed for university-level courses and supports these courses in a motivating manner to deepen the learning experience. Students slip into the role of either routing nodes or applications with routing demands. On three consecutive levels of difficulty, they get introduced with the game concept, learn the basic routing mechanisms and become aware of the general limitations and functionality of routing nodes. This paper presents the pedagogical and technical game concept as well as findings from an evaluation in a university setting.
Boolean networks provide a simple yet powerful qualitative modeling approach in systems biology. However, manual identification of logic rules underlying the system being studied is in most cases out of reach. Therefore, automated inference of Boolean logical networks from experimental data is a fundamental question in this field. This paper addresses the problem consisting of learning from a prior knowledge network describing causal interactions and phosphorylation activities at a pseudo-steady state, Boolean logic models of immediate-early response in signaling transduction networks. The underlying optimization problem has been so far addressed through mathematical programming approaches and the use of dedicated genetic algorithms. In a recent work we have shown severe limitations of stochastic approaches in this domain and proposed to use Answer Set Programming (ASP), considering a simpler problem setting. Herein, we extend our previous work in order to consider more realistic biological conditions including numerical datasets, the presence of feedback-loops in the prior knowledge network and the necessity of multi-objective optimization. In order to cope with such extensions, we propose several discretization schemes and elaborate upon our previous ASP encoding. Towards real-world biological data, we evaluate the performance of our approach over in silico numerical datasets based on a real and large-scale prior knowledge network. The correctness of our encoding and discretization schemes are dealt with in Appendices A-B. (C) 2014 Elsevier B.V. All rights reserved.
The growing impact of globalisation and the development of
a ‘knowledge society’ have led many to argue that 21st century skills are
essential for life in twenty-first century society and that ICT is central
to their development. This paper describes how 21st century skills, in
particular digital literacy, critical thinking, creativity, communication
and collaboration skills, have been conceptualised and embedded in the
resources developed for teachers in iTEC, a four-year, European project.
The effectiveness of this approach is considered in light of the data
collected through the evaluation of the pilots, which considers both the
potential benefits of using technology to support the development of
21st century skills, but also the challenges of doing so. Finally, the paper
discusses the learning support systems required in order to transform
pedagogies and embed 21st century skills. It is argued that support is
required in standards and assessment; curriculum and instruction; professional
development; and learning environments.
In the project MoKoM, which is funded by the German
Research Foundation (DFG) from 2008 to 2012, a test instrument
measuring students’ competences in computer science was developed.
This paper presents the results of an expert rating of the levels of
students’ competences done for the items of the instrument.
At first we will describe the difficulty-relevant features that were
used for the evaluation. These were deduced from computer science,
psychological and didactical findings and resources. Potentials and
desiderata of this research method are discussed further on. Finally
we will present our conclusions on the results and give an outlook on
further steps.
BugHunt
(2015)
Competencies related to operating systems and computer
security are usually taught systematically. In this paper we present
a different approach, in which students have to remove virus-like
behaviour on their respective computers, which has been induced by
software developed for this purpose. They have to develop appropriate
problem-solving strategies and thereby explore essential elements of
the operating system. The approach was implemented exemplarily in
two computer science courses at a regional general upper secondary
school and showed great motivation and interest in the participating
students.
The objectives of this study were to examine (a) the effect
of dynamic assessment (DA) in a 3D Immersive Virtual Reality
(IVR) environment as compared with computerized 2D and noncomputerized
(NC) situations on cognitive modifiability, and (b) the
transfer effects of these conditions on more difficult problem solving
administered two weeks later in a non-computerized environment. A
sample of 117 children aged 6:6-9:0 years were randomly assigned
into three experimental groups of DA conditions: 3D, 2D, and NC, and
one control group (C). All groups received the pre- and post-teaching
Analogies subtest of the Cognitive Modifiability Battery (CMB-AN).
The experimental groups received a teaching phase in conditions similar
to the pre-and post-teaching phases. The findings showed that cognitive
modifiability, in a 3D IVR, was distinctively higher than in the two
other experimental groups (2D computer group and NC group). It was
also found that the 3D group showed significantly higher performance
in transfer problems than the 2D and NC groups.
This article shows a discussion about the key competencies
in informatics and ICT viewed from a philosophical foundation presented
by Martha Nussbaum, which is known as ‘ten central capabilities’.
Firstly, the outline of ‘The Capability Approach’, which has been presented
by Amartya Sen and Nussbaum as a theoretical framework of
assessing the state of social welfare, will be explained. Secondly, the
body of Nussbaum’s ten central capabilities and the reason for being
applied as the basis of discussion will be shown. Thirdly, the relationship
between the concept of ‘capability’ and ‘competency’ is to be
discussed. After that, the author’s assumption of the key competencies
in informatics and ICT led from the examination of Nussbaum’s ten
capabilities will be presented.
This paper originated from discussions about the need for
important changes in the curriculum for Computing including two focus
group meetings at IFIP conferences over the last two years. The
paper examines how recent developments in curriculum, together with
insights from curriculum thinking in other subject areas, especially mathematics
and science, can inform curriculum design for Computing.
The analysis presented in the paper provides insights into the complexity
of curriculum design as well as identifying important constraints and
considerations for the ongoing development of a vision and framework
for a Computing curriculum.
Computational thinking is a fundamental skill set that is learned
by studying Informatics and ICT. We argue that its core ideas can
be introduced in an inspiring and integrated way to both teachers and
students using fun and contextually rich cs4fn ‘Computer Science for
Fun’ stories combined with ‘unplugged’ activities including games and
magic tricks. We also argue that understanding people is an important
part of computational thinking. Computational thinking can be fun for
everyone when taught in kinaesthetic ways away from technology.