The Comprehensive Microbial Resource

One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals. The bacterial information has been placed on the Web at http://www.tigr.org/CMR for retrieval using standard web browsing technology. Retrievals can be based on protein properties such as molecular weight or hydrophobicity, GC-content, functional role assignments and taxonomy. The CMR also has special web-based tools to allow data mining using pre-run homology searches, whole genome dot-plots, batch downloading and traversal across genomes using a variety of datatypes.

Majestic Gamification:a case study in the adoption of a service innovation

Purpose: A case study is presented concerning a gamified awards system designed to encourage software users to explore a suite of tools, and to share their expertise level in profile pages. Majestic is a high-tech business based in the West Midlands (UK) w hich offers a Link Intelligence database using a Software as a Service (SaaS) business model. Customers leverage the database for tasks including Search Engine Optimisation (SEO) by using a suite of web-based tools. Getting to know all the tools and how they can be deployed to good effect represents a considerable learning challenge, and Majestic were aware that. Design/methodology/approach: We present the development of Majestic Awards as a case study highlighting the most important design decisions. Then we reflect on the development process as an example of innovation adoption, thereby identifying resources and cu ltura l factors which were critical in ensuring the success of the project. Findings: The gamified awards system makes learning the tools an enjoyable, explorative experience. Success factors included identifying a clear business goal, the process/ project f it, senior management buy in, and identifying the knowledge and resources to resolve t echnical issues. Originality/value: Prior to gamification of the system, only the most expert users regu larly utilized all the tools. The user base is now more knowl edgable about the system and some users choose to use the system to publicize their expertise.

Surface Ocean CO2 Atlas (SOCAT) V1.4

A well-documented, publicly available, global data set of surface ocean carbon dioxide (CO2) parameters has been called for by international groups for nearly two decades. The Surface Ocean CO2 Atlas (SOCAT) project was initiated by the international marine carbon science community in 2007 with the aim of providing a comprehensive, publicly available, regularly updated, global data set of marine surface CO2, which had been subject to quality control (QC). Many additional CO2 data, not yet made public via the Carbon Dioxide Information Analysis Center (CDIAC), were retrieved from data originators, public websites and other data centres. All data were put in a uniform format following a strict protocol. Quality control was carried out according to clearly defined criteria. Regional specialists performed the quality control, using state-of-the-art web-based tools, specially developed for accomplishing this global team effort. SOCAT version 1.5 was made public in September 2011 and holds 6.3 million quality controlled surface CO2 data points from the global oceans and coastal seas, spanning four decades (1968-2007). Three types of data products are available: individual cruise files, a merged complete data set and gridded products. With the rapid expansion of marine CO2 data collection and the importance of quantifying net global oceanic CO2 uptake and its changes, sustained data synthesis and data access are priorities.

AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis

Affiliation: Département de biochimie, Faculté de médecine, Université de Montréal

The use of computer-based learning tools for teaching and clinical purposes: Interactive computing strategy for Iraq

Medical universities and teaching hospitals in Iraq are facing a lack of professional staff due to the ongoing violence that forces them to flee the country. The professionals are now distributed outside the country which reduces the chances for the staff and students to be physically in one place to continue the teaching and limits the efficiency of the consultations in hospitals. A survey was done among students and professional staff in Iraq to find the problems in the learning and clinical systems and how Information and Communication Technology could improve it. The survey has shown that 86% of the participants use the Internet as a learning resource and 25% for clinical purposes while less than 11% of them uses it for collaboration between different institutions. A web-based collaborative tool is proposed to improve the teaching and clinical system. The tool helps the users to collaborate remotely to increase the quality of the learning system as well as it can be used for remote medical consultation in hospitals.

Web GIS to support irrigation management: a prototype for SAGRA network, Alentejo Portugal

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

População e Enriquecimento de Ontologias através de Web Scraping

O surgir da World Wide Web providenciou aos utilizadores uma série de oportunidades no que diz respeito ao acesso a dados e informação. Este acesso tornou-se um ato banal para qualquer utilizador da Web, tanto pelo utilizador comum como por outros mais experientes, tanto para obter informações básicas, como outras informações mais complexas. Todo este avanço tecnológico permitiu que os utilizadores tivessem acesso a uma vasta quantidade de informação, dispersa pelo globo, não tendo, na maior parte das vezes, a informação qualquer tipo de ligação entre si. A necessidade de se obter informação de interesse relativamente a determinado tema, mas tendo que recorrer a diversas fontes para obter toda a informação que pretende obter e comparar, torna-se um processo moroso para o utilizador. Pretende-se que este processo de recolha de informação de páginas web seja o mais automatizado possível, dando ao utilizador a possibilidade de utilizar algoritmos e ferramentas de análise e processamento automáticas, reduzindo desta forma o tempo e esforço de realização de tarefas sobre páginas web. Este processo é denominado Web Scraping. Neste trabalho é descrita uma arquitetura de sistema de web scraping automático e configurável baseado em tecnologias existentes, nomeadamente no contexto da web semântica. Para tal o trabalho desenvolvido analisa os efeitos da aplicação do Web Scraping percorrendo os seguintes pontos: • Identificação e análise de diversas ferramentas de web scraping; • Identificação do processo desenvolvido pelo ser humano complementar às atuais ferramentas de web scraping; • Design duma arquitetura complementar às ferramentas de web scraping que dê apoio ao processo de web scraping do utilizador; • Desenvolvimento dum protótipo baseado em ferramentas e tecnologias existentes; • Realização de experiências no domínio de aplicação de páginas de super-mercados portugueses; • Analisar resultados obtidos a partir destas.

"I'll look it up on the Web first": barriers and overcoming barriers to consult for sexual dysfunction among young men.

QUESTIONS UNDER STUDY: Our aim was to identify the barriers young men face to consult a health professional when they encounter sexual dysfunctions and where they turn to, if so, for answers. METHODS: We conducted an exploratory qualitative research including 12 young men aged 16-20 years old seen in two focus groups. Discussions were triggered through vignettes about sexual dysfunction. RESULTS: Young men preferred not to talk about sexual dysfunction problems with anyone and to solve them alone as it is considered an intimate and embarrassing subject which can negatively impact their masculinity. Confidentiality appeared to be the most important criterion in disclosing an intimate subject to a health professional. Participants raised the problem of males' accessibility to services and lack of reason to consult. Two criteria to address the problem were if it was long-lasting or considered as physical. The Internet was unanimously considered as an initial solution to solve a problem, which could guide them to a face-to-face consultation if necessary. CONCLUSIONS: Results suggest that Internet-based tools should be developed to become an easy access door to sexual health services for young men. Wherever they consult and for whatever problem, sexual health must be on the agenda.

Open video tools to support the production of online collaborative audiovisual projects : how to promote collective creation in e-learning

This paper analyses the use of open video editing tools to support the creation and production of online collaborative audiovisual projects for higher education. It focuses on the possibilities offered by these tools to promote collective creation in virtual environments.

A Classification of Tools for Learning Logic

A table showing a comparison and classification of tools (intelligent tutoring systems) for e-learning of Logic at a college level.

A Classification of Tools for Learning Logic

A table showing a comparison and classification of tools (intelligent tutoring systems) for e-learning of Logic at a college level.

REGSTATTOOLS: freeware statistical tools for the analysis of disease population databases used in health and social studies

Background: The repertoire of statistical methods dealing with the descriptive analysis of the burden of a disease has been expanded and implemented in statistical software packages during the last years. The purpose of this paper is to present a web-based tool, REGSTATTOOLS http://regstattools.net intended to provide analysis for the burden of cancer, or other group of disease registry data. Three software applications are included in REGSTATTOOLS: SART (analysis of disease"s rates and its time trends), RiskDiff (analysis of percent changes in the rates due to demographic factors and risk of developing or dying from a disease) and WAERS (relative survival analysis). Results: We show a real-data application through the assessment of the burden of tobacco-related cancer incidence in two Spanish regions in the period 1995-2004. Making use of SART we show that lung cancer is the most common cancer among those cancers, with rising trends in incidence among women. We compared 2000-2004 data with that of 1995-1999 to assess percent changes in the number of cases as well as relative survival using RiskDiff and WAERS, respectively. We show that the net change increase in lung cancer cases among women was mainly attributable to an increased risk of developing lung cancer, whereas in men it is attributable to the increase in population size. Among men, lung cancer relative survival was higher in 2000-2004 than in 1995-1999, whereas it was similar among women when these time periods were compared. Conclusions: Unlike other similar applications, REGSTATTOOLS does not require local software installation and it is simple to use, fast and easy to interpret. It is a set of web-based statistical tools intended for automated calculation of population indicators that any professional in health or social sciences may require.

Intra-organizational use of communication tools in value nets - Cases from the ICT industry

Tutkimuksen tavoitteena oli selvittää sisäisen kommunikoinnin tilannetta case-yrityksissä. Yritykset kuuluvat kahteen case-arvoverkostoon, jotka toimivat informaatio- ja kommunikaatioteknologian alalla. Sisäinen kommunikointi valittiin tutkimusalueeksi, koska se muodostaa perustan ulkoiselle, yritysten väliselle kommunikoinnille. Tutkimuksen painopiste oli web-pohjaisessa kommunikoinnissa ja webin ominaisuuksissa arvoverkoston näkökulmasta. Tutkimusprosessissa käytettiin sekä kvalitatiivisia että kvantitatiivisia menetelmiä. Tutkimuksen kvantitatiivinen osa toteutettiin web-kyselynä, jonka tulokset osoittivat, että case-yritysten sisäinen kommunikointi perustuu pääasiassa perinteisten kommunikointivälineiden käyttöön. Toisin sanoen, webin hyödyntäminen on vähäistä, mihin vaikuttavat monet eri tekijät. Webissä on kuitenkin useita ominaisuuksia, jotka parantavat kommunikointia arvoverkostossa ja siksi nämä web-pohjaiset välineet tulisi huomioida, kun suunnitellaan yleistä kommunikointijärjestelmää. Tutkimuksen teoreettisessa osassa määriteltiin vuorovaikutteisuus-ominaisuuteen perustuva kommunikointivälineiden luokittelu. Tämän lisäksi määriteltiin myös arvoverkoston käsite. Empiirinen osa koostui web-kyselyn toteutuksen ja tulosten raportoinnista, jonka jälkeen yhteenvetokappale koosti merkittävimmät havainnot sekä mahdolliset jatkotutkimusaiheet.

Biomolecular screening for inhibitors of butyrylcholinesterase : identification and characterization using in vitro and in silico tools

Drug discovery is a continuous process where researchers are constantly trying to find new and better drugs for the treatment of various conditions. Alzheimer’s disease, a neurodegenerative disease mostly affecting the elderly, has a complex etiology with several possible drug targets. Some of these targets have been known for years while other new targets and theories have emerged more recently. Cholinesterase inhibitors are the major class of drugs currently used for the symptomatic treatment of Alzheimer’s disease. In the Alzheimer’s disease brain there is a deficit of acetylcholine and an impairment in signal transmission. Acetylcholinesterase has therefore been the main target as this is the main enzyme hydrolysing acetylcholine and ending neurotransmission. It is believed that by inhibiting acetylcholinesterase the cholinergic signalling can be enhanced and the cognitive symptoms that arise in Alzheimer’s disease can be improved. Butyrylcholinesterase, the second enzyme of the cholinesterase family, has more recently attracted interest among researchers. Its function is still not fully known, but it is believed to play a role in several diseases, one of them being Alzheimer’s disease. In this contribution the aim has primarily been to identify butyrylcholinesterase inhibitors to be used as drug molecules or molecular probes in the future. Both synthetic and natural compounds in diverse and targeted screening libraries have been used for this purpose. The active compounds have been further characterized regarding their potencies, cytotoxicity, and furthermore, in two of the publications, the inhibitors ability to also inhibit Aβ aggregation in an attempt to discover bifunctional compounds. Further, in silico methods were used to evaluate the binding position of the active compounds with the enzyme targets. Mostly to differentiate between the selectivity towards acetylcholinesterase and butyrylcholinesterase, but also to assess the structural features required for enzyme inhibition. We also evaluated the compounds, active and non-active, in chemical space using the web-based tool ChemGPS-NP to try and determine the relevant chemical space occupied by cholinesterase inhibitors. In this study, we have succeeded in finding potent butyrylcholinesterase inhibitors with a diverse set of structures, nine chemical classes in total. In addition, some of the compounds are bifunctional as they also inhibit Aβ aggregation. The data gathered from all publications regarding the chemical space occupied by butyrylcholinesterase inhibitors we believe will give an insight into the chemically active space occupied by this type of inhibitors and will hopefully facilitate future screening and result in an even deeper knowledge of butyrylcholinesterase inhibitors.

Project Management Tools in Agile Embedded Systems Development

Agile methods have become increasingly popular in the field of software engineering. While agile methods are now generally considered applicable to software projects of many different kinds, they have not been widely adopted in embedded systems development. This is partly due to the natural constraints that are present in embedded systems development (e.g. hardware–software interdependencies) that challenge the utilization of agile values, principles and practices. The research in agile embedded systems development has been very limited, and this thesis tackles an even less researched theme related to it: the suitability of different project management tools in agile embedded systems development. The thesis covers the basic aspects of many different agile tool types from physical tools, such as task boards and cards, to web-based agile tools that offer all-round solutions for application lifecycle management. In addition to these two extremities, there is also a wide range of lighter agile tools that focus on the core agile practices, such as backlog management. Also other non-agile tools, such as bug trackers, can be used to support agile development, for instance, with plug-ins. To investigate the special tool requirements in agile embedded development, the author observed tool related issues and solutions in a case study involving three different companies operating in the field of embedded systems development. All three companies had a distinct situation in the beginning of the case and thus the tool solutions varied from a backlog spreadsheet built from scratch to plug-in development for an already existing agile software tool. Detailed reports are presented of all three tool cases. Based on the knowledge gathered from agile tools and the case study experiences, it is concluded that there are tool related issues in the pilot phase, such as backlog management and user motivation. These can be overcome in various ways epending on the type of a team in question. Finally, five principles are formed to give guidelines for tool selection and usage in agile embedded systems development.