Collaborative web applications

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia Informática

A peer-to-peer approach to content dissemination and search in collaborative networks

There are three key driving forces behind the development of Internet Content Management Systems (CMS) - a desire to manage the explosion of content, a desire to provide structure and meaning to content in order to make it accessible, and a desire to work collaboratively to manipulate content in some meaningful way. Yet the traditional CMS has been unable to meet the latter of these requirements, often failing to provide sufficient tools for collaboration in a distributed context. Peer-to-Peer (P2P) systems are networks in which every node is an equal participant (whether transmitting data, exchanging content, or invoking services) and there is an absence of any centralised administrative or coordinating authorities. P2P systems are inherently more scalable than equivalent client-server implementations as they tend to use resources at the edge of the network much more effectively. This paper details the rationale and design of a P2P middleware for collaborative content management.

Mobile collaborative cloudless computing

Although the computational power of mobile devices has been increasing, it is still not enough for some classes of applications. In the present, these applications delegate the computing power burden on servers located on the Internet. This model assumes an always-on Internet connectivity and implies a non-negligible latency. The thesis addresses the challenges and contributions posed to the application of a mobile collaborative computing environment concept to wireless networks. The goal is to define a reference architecture for high performance mobile applications. Current work is focused on efficient data dissemination on a highly transitive environment, suitable to many mobile applications and also to the reputation and incentive system available on this mobile collaborative computing environment. For this we are improving our already published reputation/incentive algorithm with knowledge from the usage pattern from the eduroam wireless network in the Lisbon area.

Collaborative environment to support a professional community

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Towards increased productivity and quality in software development using agile, lean and collaborative approaches

Dagens programvaruindustri står inför alltmer komplicerade utmaningar i en värld där programvara är nästan allstädes närvarande i våra dagliga liv. Konsumenten vill ha produkter som är pålitliga, innovativa och rika i funktionalitet, men samtidigt också förmånliga. Utmaningen för oss inom IT-industrin är att skapa mer komplexa, innovativa lösningar till en lägre kostnad. Detta är en av orsakerna till att processförbättring som forskningsområde inte har minskat i betydelse. IT-proffs ställer sig frågan: “Hur håller vi våra löften till våra kunder, samtidigt som vi minimerar vår risk och ökar vår kvalitet och produktivitet?” Inom processförbättringsområdet finns det olika tillvägagångssätt. Traditionella processförbättringsmetoder för programvara som CMMI och SPICE fokuserar på kvalitets- och riskaspekten hos förbättringsprocessen. Mer lättviktiga metoder som t.ex. lättrörliga metoder (agile methods) och Lean-metoder fokuserar på att hålla löften och förbättra produktiviteten genom att minimera slöseri inom utvecklingsprocessen. Forskningen som presenteras i denna avhandling utfördes med ett specifikt mål framför ögonen: att förbättra kostnadseffektiviteten i arbetsmetoderna utan att kompromissa med kvaliteten. Den utmaningen attackerades från tre olika vinklar. För det första förbättras arbetsmetoderna genom att man introducerar lättrörliga metoder. För det andra bibehålls kvaliteten genom att man använder mätmetoder på produktnivå. För det tredje förbättras kunskapsspridningen inom stora företag genom metoder som sätter samarbete i centrum. Rörelsen bakom lättrörliga arbetsmetoder växte fram under 90-talet som en reaktion på de orealistiska krav som den tidigare förhärskande vattenfallsmetoden ställde på IT-branschen. Programutveckling är en kreativ process och skiljer sig från annan industri i det att den största delen av det dagliga arbetet går ut på att skapa något nytt som inte har funnits tidigare. Varje programutvecklare måste vara expert på sitt område och använder en stor del av sin arbetsdag till att skapa lösningar på problem som hon aldrig tidigare har löst. Trots att detta har varit ett välkänt faktum redan i många decennier, styrs ändå många programvaruprojekt som om de vore produktionslinjer i fabriker. Ett av målen för rörelsen bakom lättrörliga metoder är att lyfta fram just denna diskrepans mellan programutvecklingens innersta natur och sättet på vilket programvaruprojekt styrs. Lättrörliga arbetsmetoder har visat sig fungera väl i de sammanhang de skapades för, dvs. små, samlokaliserade team som jobbar i nära samarbete med en engagerad kund. I andra sammanhang, och speciellt i stora, geografiskt utspridda företag, är det mera utmanande att införa lättrörliga metoder. Vi har nalkats utmaningen genom att införa lättrörliga metoder med hjälp av pilotprojekt. Detta har två klara fördelar. För det första kan man inkrementellt samla kunskap om metoderna och deras samverkan med sammanhanget i fråga. På så sätt kan man lättare utveckla och anpassa metoderna till de specifika krav som sammanhanget ställer. För det andra kan man lättare överbrygga motstånd mot förändring genom att introducera kulturella förändringar varsamt och genom att målgruppen får direkt förstahandskontakt med de nya metoderna. Relevanta mätmetoder för produkter kan hjälpa programvaruutvecklingsteam att förbättra sina arbetsmetoder. När det gäller team som jobbar med lättrörliga och Lean-metoder kan en bra uppsättning mätmetoder vara avgörande för beslutsfattandet när man prioriterar listan över uppgifter som ska göras. Vårt fokus har legat på att stöda lättrörliga och Lean-team med interna produktmätmetoder för beslutsstöd gällande så kallad omfaktorering, dvs. kontinuerlig kvalitetsförbättring av programmets kod och design. Det kan vara svårt att ta ett beslut att omfaktorera, speciellt för lättrörliga och Lean-team, eftersom de förväntas kunna rättfärdiga sina prioriteter i termer av affärsvärde. Vi föreslår ett sätt att mäta designkvaliteten hos system som har utvecklats med hjälp av det så kallade modelldrivna paradigmet. Vi konstruerar även ett sätt att integrera denna mätmetod i lättrörliga och Lean-arbetsmetoder. En viktig del av alla processförbättringsinitiativ är att sprida kunskap om den nya programvaruprocessen. Detta gäller oavsett hurdan process man försöker introducera – vare sig processen är plandriven eller lättrörlig. Vi föreslår att metoder som baserar sig på samarbete när processen skapas och vidareutvecklas är ett bra sätt att stöda kunskapsspridning på. Vi ger en översikt över författarverktyg för processer på marknaden med det förslaget i åtanke.

EGHEP-ISFG collaborative exercise on mixture profiles of autosomal STRs (GHEP-MIX01, GHEP-MIX02 and GHEP-MIX03): Results and evaluation

One of the main objectives of the Spanish and Portuguese-Speaking Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and dissemination of scientific knowledge in the area of forensic genetics. Due to this fact, GHEP-ISFG holds different working commissions that are set up to develop activities in scientific aspects of general interest. One of them, the Mixture Commission of GHEP-ISFG, has organized annually, since 2009, a collaborative exercise on analysis and interpretation of autosomal short tandem repeat (STR) mixture profiles. Until now, three exercises have been organized (GHEP-MIX01, GHEP-MIX02 and GHEP-MIX03), with 32, 24 and 17 participant laboratories respectively. The exercise aims to give a general vision by addressing, through the proposal of mock cases, aspects related to the edition of mixture profiles and the statistical treatment. The main conclusions obtained from these exercises may be summarized as follows. Firstly, the data show an increased tendency of the laboratories toward validation of DNA mixture profiles analysis following international recommendations (ISO/IEC 17025: 2005). Secondly, the majority of discrepancies are mainly encountered in stutters positions (53.4%, 96.0% and 74.9%, respectively for the three editions). On the other hand, the results submitted reveal the importance of performing duplicate analysis by using different kits in order to reduce errors as much as possible. Regarding the statistical aspect (GHEP-MIX02 and 03), all participants employed the likelihood ratio (LR) parameter to evaluate the statistical compatibility and the formulas employed were quite similar. When the hypotheses to evaluate the LR value were locked by the coordinators (GHEP-MIX02) the results revealed a minor number of discrepancies that were mainly due to clerical reasons. However, the GHEP-MIX03 exercise allowed the participants to freely come up with their own hypotheses to calculate the LR value. In this situation the laboratories reported several options to explain the mock cases proposed and therefore significant differences between the final LR values were obtained. Complete information concerning the background of the criminal case is a critical aspect in order to select the adequate hypotheses to calculate the LR value. Although this should be a task for the judicial court to decide, it is important for the expert to account for the different possibilities and scenarios, and also offer this expertise to the judge. In addition, continuing education in the analysis and interpretation of mixture DNA profiles may also be a priority for the vast majority of forensic laboratories. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

What Google Maps can do for Biomedical Data Dissemination: Examples and a Design Study

Background: Biologists often need to assess whether unfamiliar datasets warrant the time investment required for more detailed exploration. Basing such assessments on brief descriptions provided by data publishers is unwieldy for large datasets that contain insights dependent on specific scientific questions. Alternatively, using complex software systems for a preliminary analysis may be deemed as too time consuming in itself, especially for unfamiliar data types and formats. This may lead to wasted analysis time and discarding of potentially useful data. Results: We present an exploration of design opportunities that the Google Maps interface offers to biomedical data visualization. In particular, we focus on synergies between visualization techniques and Google Maps that facilitate the development of biological visualizations which have both low-overhead and sufficient expressivity to support the exploration of data at multiple scales. The methods we explore rely on displaying pre-rendered visualizations of biological data in browsers, with sparse yet powerful interactions, by using the Google Maps API. We structure our discussion around five visualizations: a gene co-regulation visualization, a heatmap viewer, a genome browser, a protein interaction network, and a planar visualization of white matter in the brain. Feedback from collaborative work with domain experts suggests that our Google Maps visualizations offer multiple, scale-dependent perspectives and can be particularly helpful for unfamiliar datasets due to their accessibility. We also find that users, particularly those less experienced with computer use, are attracted by the familiarity of the Google Maps API. Our five implementations introduce design elements that can benefit visualization developers. Conclusions: We describe a low-overhead approach that lets biologists access readily analyzed views of unfamiliar scientific datasets. We rely on pre-computed visualizations prepared by data experts, accompanied by sparse and intuitive interactions, and distributed via the familiar Google Maps framework. Our contributions are an evaluation demonstrating the validity and opportunities of this approach, a set of design guidelines benefiting those wanting to create such visualizations, and five concrete example visualizations.

Research-based spin-offs as agents of knowledge dissemination: evidence from the analysis of innovation networks

The paper addresses the role played by research-based spin-offs (RBSOs) as knowledge dissemination mechanisms, through their position in knowledge networks. For this purpose the paper analyses the formal networks established by the Portuguese RBSOs in the context of publicly funded research, technology and pre-commercial product development projects, and investigates their configuration along two levels. At organisational level, in order to understand whether RBSOs extend their reach beyond the academic sphere; and if they do, whether they relate with similar firms or connect to organisations located downstream in the knowledge value chain, and which is their position in networks involving both research organisations and other firms. At spatial level, in order to understand whether RBSOs extend their reach beyond the region where they are created, thus potentially acting as connectors between diverse regions. The analysis starts from the population of RBSOs created in Portugal until 2007 (387) and identifies those that have established formal technological relationships as part of projects funded by all the programmes launched in the period 1993-2012. As a result, the analysis encompasses 192 collaborative projects and involves 82 spin-offs and 281 partners, of which only 20% are research organisations, the remaining being other firms and a variety of other user organisations. The results, although still preliminary, provide some insights into the knowledge networking behaviour of the RBSOs. As expected, research organisations are a central actor in spin-offs’ networks, being the sole partner for some of them. But half of the RBSOs have moved beyond the academic sphere, being frequently a central element in tripartite technological relationships between research and other organisations and occupying an intermediation position in the network, thus potentially acting as facilitators in knowledge circulation and transformation. Also as expected, RBSOs are predominantly located in the main metropolitan areas and tend to relate with organisations similarly located. But while geographical proximity emerges as important in the choice of partners, in about half of the cases, RBSOs knowledge networks have extended beyond regional boundaries. Given their central position in the network this suggests a role as connectors across regions that will be explored in subsequent research.

Research-based spin-offs as agents of knowledge dissemination: evidence from the analysis of innovation networks

The paper addresses the role played by research-based spin-offs (RBSOs) as knowledge dissemination mechanisms, through their position in knowledge networks. For this purpose the paper analyses the formal networks established by Portuguese RBSOs, in the context of publicly funded research, technology and pre-commercial product development projects, and investigates their configuration across two levels. At organisational level, in order to understand whether RBSOs extend their reach beyond the academic sphere; and if they do, whether they connect to organisations located downstream in the knowledge value chain, and which is their position in networks involving both research organisations and other firms. At spatial level, in order to understand whether RBSOs extend their reach beyond the region where they are created, thus potentially acting as connectors between diverse regions. The analysis starts from the population of RBSOs created in Portugal until 2007 (327 firms) and identifies those that have established formal technological relationships, as part of projects funded by all the relevant programmes launched in the period 1993-2012. As a result, the analysis encompasses 192 collaborative projects and involves 82 spin-offs and 281 partners, of which only 20% are research organisations, the remaining being other firms and a variety of other downstream organisations. The results, although still preliminary, provide some insights into the knowledge networking behaviour of the RBSOs. As expected, research organisations are a central actor in spin-offs’ networks, being the sole partner for some of them. But half of the RBSOs have moved beyond the academic sphere, being frequently a central element in tripartite technological relationships between research and other organisations, and occupying an intermediation position in the network, thus potentially acting as facilitators in knowledge circulation and transformation. Also as expected, RBSOs are predominantly located in the main metropolitan areas and tend to relate with organisations similarly located. But while geographical proximity emerges as important in the choice of partners, in about half of the cases, RBSOs knowledge networks have extended beyond regional boundaries. Given their central position in the network, this suggests a role as connectors across regions that will be explored in subsequent research.

Stromal Myofibroblasts In Squamous Cell Carcinoma Of The Tongue In Young Patients - A Multicenter Collaborative Study.

The purpose of this study was to evaluate the presence of myofibroblasts, frequently associated with a more aggressive neoplastic behavior, in oral tongue squamous cell carcinoma (TSCC) of young patients and to compare with the distribution observed in older patients. Tumor samples from 29 patients younger than 40 years old affected by TSCC were retrieved and investigated for the presence of stromal myofibroblasts by immunohistochemical reactions against α smooth muscle actin, and the results obtained were compared to TSCC cases affecting older patients. No positive reaction could be found in the stromal areas devoid of neoplastic tissue, whereas myofibroblasts were present in 58.6% of the lesions in young patients and in 75.9% of the older ones. No significant difference was found when comparing the invasive front and the overall stroma of both groups, and no correlation could be obtained with stromal α smooth muscle actin expression, higher tumor grades or clinical stage (P > .05). There was no significant difference between the presence of stromal myofibroblasts of TSCC affecting young and old individuals.

A Dynamic Analysis of Tuberculosis Dissemination to Improve Control and Surveillance

Background: Detailed analysis of the dynamic interactions among biological, environmental, social, and economic factors that favour the spread of certain diseases is extremely useful for designing effective control strategies. Diseases like tuberculosis that kills somebody every 15 seconds in the world, require methods that take into account the disease dynamics to design truly efficient control and surveillance strategies. The usual and well established statistical approaches provide insights into the cause-effect relationships that favour disease transmission but they only estimate risk areas, spatial or temporal trends. Here we introduce a novel approach that allows figuring out the dynamical behaviour of the disease spreading. This information can subsequently be used to validate mathematical models of the dissemination process from which the underlying mechanisms that are responsible for this spreading could be inferred. Methodology/Principal Findings: The method presented here is based on the analysis of the spread of tuberculosis in a Brazilian endemic city during five consecutive years. The detailed analysis of the spatio-temporal correlation of the yearly geo-referenced data, using different characteristic times of the disease evolution, allowed us to trace the temporal path of the aetiological agent, to locate the sources of infection, and to characterize the dynamics of disease spreading. Consequently, the method also allowed for the identification of socio-economic factors that influence the process. Conclusions/Significance: The information obtained can contribute to more effective budget allocation, drug distribution and recruitment of human skilled resources, as well as guiding the design of vaccination programs. We propose that this novel strategy can also be applied to the evaluation of other diseases as well as other social processes.

Collaborative e-learning and Learning Objects

The Learning Object (OA) is any digital resource that can be reused to support learning with specific functions and objectives. The OA specifications are commonly offered in SCORM model without considering activities in groups. This deficiency was overcome by the solution presented in this paper. This work specified OA for e-learning activities in groups based on SCORM model. This solution allows the creation of dynamic objects which include content and software resources for the collaborative learning processes. That results in a generalization of the OA definition, and in a contribution with e-learning specifications.

Dissemination of bla(IMP-1)-carrying integron In86 among Klebsiella pneumoniae isolates harboring a new trimethoprim resistance gene dfr23

The genetic context of the bla(IMP-1) gene was evaluated in 9 Klebsiella pneumoniae isolates recovered from 2 hospitals in Sao Paulo, Brazil. All isolates harbored a copy of In86 carrying bla(Imp-1), aac(6`)-31, and aadAl. Eight strains from the same hospital also carried another class I integron harboring a new trimethoprim resistance gene (dfr23) that was chromosomally embedded. In86 was likely to be in a 30-kb nontransferable plasmid and was flanked upstream by a sequence identical to one identified in an IMP-1-producing Pseudomonas putida isolate. The bla(IMP-1)-carrying integron In86 was recently reported from nonfermentative bacilli isolated in Sao Paulo. These isolates appear to be the Source of this integron now acquired by K. pneumoniae strains from different hospitals in the same city. Metallo-beta-lactamase production is still rare among Enterobacteriaceae isolates in Brazil, but the acquisition of genetic structures carrying these mobile resistance determinants is worrisome and could lead to an increase in the prevalence of these phenotypes of resistance. (C) 2008 Elsevier Inc. All rights reserved.