PROM-OPEN: PROMOTING OPEN SCIENCE IN AN ON-LINE E-LEARNING ENVIRONMENT

Peer-reviewed

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

Identification of chemical compounds with specific biological activities is an important step in both chemical biology and drug discovery. When the structure of the intended target is available, one approach is to use molecular docking programs to assess the chemical complementarity of small molecules with the target; such calculations provide a qualitative measure of affinity that can be used in virtual screening (VS) to rank order a list of compounds according to their potential to be active. rDock is a molecular docking program developed at Vernalis for high-throughput VS (HTVS) applications. Evolved from RiboDock, the program can be used against proteins and nucleic acids, is designed to be computationally very efficient and allows the user to incorporate additional constraints and information as a bias to guide docking. This article provides an overview of the program structure and features and compares rDock to two reference programs, AutoDock Vina (open source) and Schrodinger's Glide (commercial). In terms of computational speed for VS, rDock is faster than Vina and comparable to Glide. For binding mode prediction, rDock and Vina are superior to Glide. The VS performance of rDock is significantly better than Vina, but inferior to Glide for most systems unless pharmacophore constraints are used; in that case rDock and Glide are of equal performance. The program is released under the Lesser General Public License and is freely available for download, together with the manuals, example files and the complete test sets, at http://rdock.sourceforge.net/

Web and education, a successful open entanglement

E-learning, understood as the intensive use of Information and Communication Technologies in mainly but not only) distance education, has radically changed the meaning of the latter. E-learning is an overused term which has been applied to any use of technology in education. Today, the most widely accepted meaning ofe-learning coincides with the fourth generation described by Taylor (1999), where there is an asynchronousprocess that allows students and teachers to interact in an educational process expressly designed in accordance with these principles. We prefer to speak of Internet-Based Learning or, better still, Web-Based Learning, for example, to explain the fact that distance education is carried out using the Internet, with the appearance of the virtual learning environment concept, a web space where the teaching and learning process is generated and supported (Sangrà, 2002). This entails overcoming the barriers of space and time of brickand mortar education (although we prefer the term face-to-face) or of classical distance education using broadcasting and adopting a completely asynchronous model that allows access to education by many more users, at any level (including secondary education, but primarily higher education and lifelong learning).

The practical application of e-Portfolio at the Open University of Catalonia : assessment of competence based learning

The paper presents the results of the piloting or pilot test in a virtual classroom. This e-portfolio was carried out in the 2005-2006 academic year, with students of the Doctorate in Information Society, at the Open University of Catalonia. The electronic portfolio is a strategy for competence based assessment. This experience shows the types of e-portfolios, where students show their work without interactions, and apply the competence-based learning theories in an interactive portfolio system. The real process of learning is developed in the competency based system, the portfolio not only is a basic bio document, has become a real space for learning with competence model. The paper brings out new ideas and possibilities: the competence-based learning promotes closer relationships between universities and companies and redesigns the pedagogic act.

Features extraction based on the Discrete Hartley Transform for closed contour

In this paper the authors propose a new closed contour descriptor that could be seen as a Feature Extractor of closed contours based on the Discrete Hartley Transform (DHT), its main characteristic is that uses only half of the coefficients required by Elliptical Fourier Descriptors (EFD) to obtain a contour approximation with similar error measure. The proposed closed contour descriptor provides an excellent capability of information compression useful for a great number of AI applications. Moreover it can provide scale, position and rotation invariance, and last but not least it has the advantage that both the parameterization and the reconstructed shape from the compressed set can be computed very efficiently by the fast Discrete Hartley Transform (DHT) algorithm. This Feature Extractor could be useful when the application claims for reversible features and when the user needs and easy measure of the quality for a given level of compression, scalable from low to very high quality.

eLab, a Personal Learning Environment for the Green Open Innovation Platform

Open Innovation is a relatively new concept which involves a change of paradigm in the R+D+i processes of companies whose aim is to create new technologies or new processes. If to this change, we add the need for innovation in the new green and sustainability economy, and we set out to create a collaborative platform with a learning space where this can happen, we will be facing an overwhelming challenge which requires the application of intelligent programming technologies and languages at the service of education.The aim of the Green IDI (Green Open Innovation) ¿ Economic development and job creation vector in SMEs, based on the environment and sustainability project is to create a platform where companies and individual researchers can perform open innovation processes in the field of sustainability and the environment.The Green IDI (Green Open Innovation) project is funded under the program INNPACTO by the Ministry of Science and Innovation of Spain and is being developed through a consortium formed by the following institutions: GRUPO ICA; COMPARTIA; GRUPO INTERCOM; CETAQUA and the Instituto de Investigación en Inteligencia Artificial (IIIA) from Consejo Superior de Investigaciones Científicas (CSIC). Also the consortium include FUNDACIÓ PRIVADA BARCELONA DIGITAL; PIMEC and UNIVERSITAT OBERTA DE CATALUNYA (UOC).Sustainability and positive action for the environment are considered the principle vector of economic development for companies. As Nicolás Scoli says (2007) ¿in short, preventing unnecessary consumption and the efficient consumption of resources means producing greater wealth with less. Both effects lead to reduced pollution linked to production and consumption¿.The Spanish Sustainable Development Strategy (EEDS) plan defends consumption and sustainable production linked to social and economic development by adhering to the commitment not to endanger ecosystems and abolishing the idea that economic growth is directly proportional to the deterioration of the environment.Uniting the Open Innovation and New Green Economy concepts leads to the "Green Open Innovation¿ Platform creation project.This article analyses the concept of open innovation and defines the importance of the new green and sustainable economy. Lastly, it proposes the creation of eLab. The eLab is defined as an Open Green Innovation Platform personal and collaborative education space which is fed by the interactions of users and which enables innovation processes based on new green economy concepts to be carried out.The creation of a personal learning environment such as eLab on the Green Open Innovation Platform meets the need to offer a collaborative space where platform users can improve their skills regarding the environment and sustainability based on collaborative synergies through Information and Communication Technologies.

Implementació d'un ERP open source amb programació a mida

This work presents, from the perspective of a freelancer professional, a case study of a practical and real implementation of an Open Source ERP software suite to a very small company, including the development of a custom software module to adapt the suite to the particular needs of the company.

MONALISA 2.0 and the sea traffic management - a concept creating the need for new maritime information standards and software solutions

Postprint (published version)

Brain dynamics sustaining rapid rule extraction from speech

Language acquisition is a complex process that requires the synergic involvement of different cognitive functions, which include extracting and storing the words of the language and their embedded rules for progressive acquisition of grammatical information. As has been shown in other fields that study learning processes, synchronization mechanisms between neuronal assemblies might have a key role during language learning. In particular, studying these dynamics may help uncover whether different oscillatory patterns sustain more item-based learning of words and rule-based learning from speech input. Therefore, we tracked the modulation of oscillatory neural activity during the initial exposure to an artificial language, which contained embedded rules. We analyzed both spectral power variations, as a measure of local neuronal ensemble synchronization, as well as phase coherence patterns, as an index of the long-range coordination of these local groups of neurons. Synchronized activity in the gamma band (2040 Hz), previously reported to be related to the engagement of selective attention, showed a clear dissociation of local power and phase coherence between distant regions. In this frequency range, local synchrony characterized the subjects who were focused on word identification and was accompanied by increased coherence in the theta band (48 Hz). Only those subjects who were able to learn the embedded rules showed increased gamma band phase coherence between frontal, temporal, and parietal regions.

Open Device Lab: movement to improve web and app experience

We present here the first part of the literature review regarding our study object, the Open Device Labs. The research on ODLs emerges from the observation of worldwide non-profit movement, which, through mutual collaboration, information and devices sharing, proposes a final improvement on user’s experience with the web and app.

Future vision of information networks according to EU 7th framework

The purpose of this thesis is to investigate projects funded in European 7th framework Information and Communication Technology- work programme. The research has been limited to issue ”Pervasive and trusted network and service infrastructure” and the aim is to find out which are the most important topics into which research will concentrate in the future. The thesis will provide important information for the Department of Information Technology in Lappeenranta University of Technology. First in this thesis will be investigated what are the requirements for the projects which were funded in “Pervasive and trusted network and service infrastructure” – programme 2007. Second the projects funded according to “Pervasive and trusted network and service infrastructure”-programme will be listed in to tables and the most important keywords will be gathered. Finally according to the keyword appearances the vision of the most important future topics will be defined. According to keyword-analysis the wireless networks are in important role in the future and core networks will be implemented with fiber technology to ensure fast data transfer. Software development favors Service Oriented Architecture (SOA) and open source solutions. The interoperability and ensuring the privacy are in key role in the future. 3D in all forms and content delivery are important topics as well. When all the projects were compared, the most important issue was discovered to be SOA which leads the way to cloud computing.

UCL Discovery: raising the Open Access profile at the institution

Presentation at the "Tutkimus vapaaksi verkkoon!" seminar in Helsinki, January 25, 2011

Non-Markovian dynamics and quantum information probes

This Thesis discusses the phenomenology of the dynamics of open quantum systems marked by non-Markovian memory effects. Non-Markovian open quantum systems are the focal point of a flurry of recent research aiming to answer, e.g., the following questions: What is the characteristic trait of non-Markovian dynamical processes that discriminates it from forgetful Markovian dynamics? What is the microscopic origin of memory in quantum dynamics, and how can it be controlled? Does the existence of memory effects open new avenues and enable accomplishments that cannot be achieved with Markovian processes? These questions are addressed in the publications forming the core of this Thesis with case studies of both prototypical and more exotic models of open quantum systems. In the first part of the Thesis several ways of characterizing and quantifying non-Markovian phenomena are introduced. Their differences are then explored using a driven, dissipative qubit model. The second part of the Thesis focuses on the dynamics of a purely dephasing qubit model, which is used to unveil the origin of non-Markovianity for a wide class of dynamical models. The emergence of memory is shown to be strongly intertwined with the structure of the spectral density function, as further demonstrated in a physical realization of the dephasing model using ultracold quantum gases. Finally, as an application of memory effects, it is shown that non- Markovian dynamical processes facilitate a novel phenomenon of timeinvariant discord, where the total quantum correlations of a system are frozen to their initial value. Non-Markovianity can also be exploited in the detection of phase transitions using quantum information probes, as shown using the physically interesting models of the Ising chain in a transverse field and a Coulomb chain undergoing a structural phase transition.

Memory Effects in the Dynamics of Open Quantum Systems

In this Thesis various aspects of memory effects in the dynamics of open quantum systems are studied. We develop a general theoretical framework for open quantum systems beyond the Markov approximation which allows us to investigate different sources of memory effects and to develop methods for harnessing them in order to realise controllable open quantum systems. In the first part of the Thesis a characterisation of non-Markovian dynamics in terms of information flow is developed and applied to study different sources of memory effects. Namely, we study nonlocal memory effects which arise due to initial correlations between two local environments and further the memory effects induced by initial correlations between the open system and the environment. The last part focuses on describing two all-optical experiment in which through selective preparation of the initial environment states the information flow between the system and the environment can be controlled. In the first experiment the system is driven from the Markovian to the non- Markovian regime and the degree of non-Markovianity is determined. In the second experiment we observe the nonlocal nature of the memory effects and provide a novel method to experimentally quantify frequency correlations in photonic environments via polarisation measurements.