Machine learning tools for protein annotation: the cases of transmembrane β-barrel and myristoylated proteins

Biology is now a “Big Data Science” thanks to technological advancements allowing the characterization of the whole macromolecular content of a cell or a collection of cells. This opens interesting perspectives, but only a small portion of this data may be experimentally characterized. From this derives the demand of accurate and efficient computational tools for automatic annotation of biological molecules. This is even more true when dealing with membrane proteins, on which my research project is focused leading to the development of two machine learning-based methods: BetAware-Deep and SVMyr. BetAware-Deep is a tool for the detection and topology prediction of transmembrane beta-barrel proteins found in Gram-negative bacteria. These proteins are involved in many biological processes and primary candidates as drug targets. BetAware-Deep exploits the combination of a deep learning framework (bidirectional long short-term memory) and a probabilistic graphical model (grammatical-restrained hidden conditional random field). Moreover, it introduced a modified formulation of the hydrophobic moment, designed to include the evolutionary information. BetAware-Deep outperformed all the available methods in topology prediction and reported high scores in the detection task. Glycine myristoylation in Eukaryotes is the binding of a myristic acid on an N-terminal glycine. SVMyr is a fast method based on support vector machines designed to predict this modification in dataset of proteomic scale. It uses as input octapeptides and exploits computational scores derived from experimental examples and mean physicochemical features. SVMyr outperformed all the available methods for co-translational myristoylation prediction. In addition, it allows (as a unique feature) the prediction of post-translational myristoylation. Both the tools here described are designed having in mind best practices for the development of machine learning-based tools outlined by the bioinformatics community. Moreover, they are made available via user-friendly web servers. All this make them valuable tools for filling the gap between sequential and annotated data.

Impact of Commercial Search Engines and International Databases on Engineering Teaching and Research

For the last three decades, the engineering higher education and professional environments have been completely transformed by the "electronic/digital information revolution" that has included the introduction of personal computer, the development of email and world wide web, and broadband Internet connections at home. Herein the writer compares the performances of several digital tools with traditional library resources. While new specialised search engines and open access digital repositories may fill a gap between conventional search engines and traditional references, these should be not be confused with real libraries and international scientific databases that encompass textbooks and peer-reviewed scholarly works. An absence of listing in some Internet search listings, databases and repositories is not an indication of standing. Researchers, engineers and academics should remember these key differences in assessing the quality of bibliographic "research" based solely upon Internet searches.

Teaching in rural and remote schools: a literature review

In this paper. the authors examine a wide range of recent research into the preparation and support for teachers working in rural and remote schools. The paper reviews many preservice and inservice initiatives which highlight issues affecting:teaching and learning in schools outside the major metropolitan centres. The work is reviewed from an Australian perspective but evaluates research from throughout the world. The paper concludes that despite a large body of research (Gibson, 1994), that has identified the need for specialised pre-service preparation which accommodates the social and professional differences associated with work in rural and remote areas, the implementation of such programs by teacher training institutions has been sparse, lacking in cohesion and in many cases non-existent. (C) 1998 Elsevier Science Ltd. All rights reserved.

Learning to manage in knowledge based organizations: the role of portfolios

Paper presented at the 8th European Conference on Knowledge Management, Barcelona, 6-7 Sep. 2008 URL: http://www.academic-conferences.org/eckm/eckm2007/eckm07-home.htm

Improving the learning experience and learning environment of adults in Higher Education – Project LIHE: the Portuguese case

Project LIHE: the Portuguese Case. ESREA Fourth Access Network Conference – “Equity, Access and Participation: Research, Policy and Practice”. Edinburgh (Scotland), 11 – 13 December, 2003.

Teaching with Moodle in higher education

Nowadays, with the use of technology and the Internet, education is undergoing significant changes, contemplating new ways of teaching and learning. One of the widely methods of teaching used to promote knowledge, consists in the use of virtual environments available in various formats, taking as example the teaching-learning platforms, which are available online. The Internet access and use of Laptops have created the technological conditions for teachers and students can benefit from the diversity of online information, communication, collaboration and sharing with others. The integration of Internet services in the teaching practices can provide thematic, social and digital enrichment for the agents involved. In this paper we will talk about the advantages of LMS (Learning Management Systems) such as Moodle, to support the presential lectures in higher education. We also will analyse its implications for student support and online interaction, leading educational agents to a mixing of different learning environments, where they can combine face-to-face instruction with computer-mediated instruction, blended-learning, and increases the options for better quality and quantity of human interaction in a learning environment. We also will present some tools traditionally used in online assessment and that are part of the functionalities of Moodle. These tools can provide interesting alternatives to promote a more significant learning and contribute to the development of flexible and customized models of an evaluation which we want to be more efficient.

Moodle and multiple-choice tests

Multiple-Choice items are used in many different kinds of tests in several areas of knowledge. They can be considered an interesting tool to the self-assessing or as an alternative or complementary instrument to the traditional methods for assessing knowledge. The objectivity and accuracy of the multiple-choice tests is an important reason to think about. They are especially useful when the number of students to evaluate is too large. Moodle (Modular Object-Oriented Dynamic Learning Environment) is an Open Source course management system centered around learners' needs and designed to support collaborative approaches to teaching and learning. Moodle offers to the users a rich interface, context-specific help buttons, and a wide variety of tools such as discussion forums, wikis, chat, surveys, quizzes, glossaries, journals, grade books and more, that allow them to learn and collaborate in a truly interactive space. Come together the interactivity of the Moodle platform and the objectivity of this kind of tests one can easily build manifold random tests. The proposal of this paper is to relate our journey in the construction of these tests and share our experience in the use of the Moodle platform to create, take advantage and improve the multiple-choices tests in the Mathematic area.

Effective teaching and optimal experiences: possible link

ISME, Thessaloniki, 2012

Using the learning tools interoperability framework for LMS integration in service oriented architectures

The LMS plays an indisputable role in the majority of the eLearning environments. This eLearning system type is often used for presenting, solving and grading simple exercises. However, exercises from complex domains, such as computer programming, require heterogeneous systems such as evaluation engines, learning objects repositories and exercise resolution environments. The coordination of networks of such disparate systems is rather complex. This work presents a standard approach for the coordination of a network of eLearning systems supporting the resolution of exercises. The proposed approach use a pivot component embedded in the LMS with two roles: provide an exercise resolution environment and coordinate the communication between the LMS and other systems exposing their functions as web services. The integration of the pivot component with the LMS relies on the Learning Tools Interoperability. The validation of this approach is made through the integration of the component with LMSs from two vendors.

Learning to manage in knowledge-based organizations: the role of learning logs or portfolios

Paper presented at the 8th European Conference on Knowledge Management, Barcelona, 6-7 Sep. 2008 URL: http://www.academic-conferences.org/eckm/eckm2007/eckm07-home.htm

Interoperability frameworks for competencies and learning outcomes: databases vs ontologies

The changes introduced into the European Higher Education Area (EHEA) by the Bologna Process, together with renewed pedagogical and methodological practices, have created a new teaching-learning paradigm: Student-Centred Learning. In addition, the last few years have been characterized by the application of Information Technologies, especially the Semantic Web, not only to the teaching-learning process, but also to administrative processes within learning institutions. On one hand, the aim of this study was to present a model for identifying and classifying Competencies and Learning Outcomes and, on the other hand, the computer applications of the information management model were developed, namely a relational Database and an Ontology.

Challenges in the creation and development of a mathematics MOOC

The fast development of distance learning tools such as Open Educational Resources (OER) and Massive Open Online Courses (MOOC or MOOCs) are indicators of a shift in the way in which digital teaching and learning are understood. MOOC are a new style of online classes that allow any person with web access, anywhere, usually free of charge, to participate through video lectures, computer graded tests and discussion forums. They have been capturing the attention of many higher education institutions around the world. This paper will give us an overview of the “Introduction to Differential Calculus” a MOOC Project, created by an engaged volunteer team of Mathematics lecturers from four schools of the Polytechnic Institute of Oporto (IPP). The MOOC theories and their popularity are presented and complemented by a discussion of some MOOC definitions and their inherent advantages and disadvantages. It will also explore what MOOC mean for Mathematics education. The Project development is revealed by focusing on used MOOC structure, as well as the quite a lot of types of course materials produced. It ends with a presentation of a short discussion about problems and challenges met throughout the development of the project. It is also our goal to contribute for a change in the way teaching and learning Mathematics is seen and practiced nowadays, trying to make education more accessible to as many people as possible and increase our institution (IPP) recognition.

Design a computer programming learning environment for Massive Open Online Courses

Teaching and learning computer programming is as challenging as difficult. Assessing the work of students and providing individualised feedback to all is time-consuming and error prone for teachers and frequently involves a time delay. The existent tools and specifications prove to be insufficient in complex evaluation domains where there is a greater need to practice. At the same time Massive Open Online Courses (MOOC) are appearing revealing a new way of learning, more dynamic and more accessible. However this new paradigm raises serious questions regarding the monitoring of student progress and its timely feedback. This paper provides a conceptual design model for a computer programming learning environment. This environment uses the portal interface design model gathering information from a network of services such as repositories and program evaluators. The design model includes also the integration with learning management systems, a central piece in the MOOC realm, endowing the model with characteristics such as scalability, collaboration and interoperability. This model is not limited to the domain of computer programming and can be adapted to any complex area that requires systematic evaluation with immediate feedback.

The development and implementation of math projects in a HEI: expectations, objectives, experiences and analysis

An overwhelming problem in Math Curriculums in Higher Education Institutions (HEI), we are daily facing in the last decade, is the substantial differences in Math background of our students. When you try to transmit, engage and teach subjects/contents that your “audience” is unable to respond to and/or even understand what we are trying to convey, it is somehow frustrating. In this sense, the Math projects and other didactic strategies, developed through Learning Management System Moodle, which include an array of activities that combine higher order thinking skills with math subjects and technology, for students of HE, appear as remedial but important, proactive and innovative measures in order to face and try to overcome these considerable problems. In this paper we will present some of these strategies, developed in some organic units of the Polytechnic Institute of Porto (IPP). But, how “fruitful” are the endless number of hours teachers spent in developing and implementing these platforms? Do students react to them as we would expect? Do they embrace this opportunity to overcome their difficulties? How do they use/interact individually with LMS platforms? Can this environment that provides the teacher with many interesting tools to improve the teaching – learning process, encourages students to reinforce their abilities and knowledge? In what way do they use each available material – videos, interactive tasks, texts, among others? What is the best way to assess student’s performance in these online learning environments? Learning Analytics tools provides us a huge amount of data, but how can we extract “good” and helpful information from them? These and many other questions still remain unanswered but we look forward to get some help in, at least, “get some drafts” for them because we feel that this “learning analysis”, that tackles the path from the objectives to the actual results, is perhaps the only way we have to move forward in the “best” learning and teaching direction.

Learning networks and moodle use in online courses: a social network analysis study

Dissertação para obtenção do Grau de Doutor em Ciências da Educação Especialidade em Tecnologias, Redes e Multimédia na Educação e Formação