White paper sobre Open Source, Open Access, open Standards e o futuro da catalogação

The discussions on the future of cataloging has received increased attention in the last ten years, mainly due to the impact of rapid development of information and communication technologies in the same period, which has provided access to the Web anytime, anywhere. These discussions revolve around the need for a new bibliographic framework to meet the demand of this new reality in the digital environment, ie how libraries can process, store, deliver, share and integrate their collections (physical, digital or scanned), in current post-PC era? Faced with this question, Open Access, Open Source and Open Standards are three concepts that need to receive greater attention in the field of Library and Information Science, as it is believed to be fundamental elements for the change of paradigm of descriptive representation, currently based conceptually on physical item rather than intellectual work. This paper aims to raise and discuss such issues and instigate information professionals, especially librarians, to think, discuss and propose initiatives for such problems, contributing and sharing ideas and possible solutions, in multidisciplinary teams. At the end is suggested the effective creation of multidisciplinary and inter-institutional study groups on the future of cataloging and its impact on national collections, in order to contribute to the area of descriptive representation in national and international level

AcMus: an Open, Integrated Platform for Room Acoustics Research

This article describes the design, implementation, and experiences with AcMus, an open and integrated software platform for room acoustics research, which comprises tools for measurement, analysis, and simulation of rooms for music listening and production. Through use of affordable hardware, such as laptops, consumer audio interfaces and microphones, the software allows evaluation of relevant acoustical parameters with stable and consistent results, thus providing valuable information in the diagnosis of acoustical problems, as well as the possibility of simulating modifications in the room through analytical models. The system is open-source and based on a flexible and extensible Java plug-in framework, allowing for cross-platform portability, accessibility and experimentation, thus fostering collaboration of users, developers and researchers in the field of room acoustics.

Low-Cost Ultra-Wide Genotyping Using Roche/454 Pyrosequencing for Surveillance of HIV Drug Resistance

Background: Great efforts have been made to increase accessibility of HIV antiretroviral therapy (ART) in low and middle-income countries. The threat of wide-scale emergence of drug resistance could severely hamper ART scale-up efforts. Population-based surveillance of transmitted HIV drug resistance ensures the use of appropriate first-line regimens to maximize efficacy of ART programs where drug options are limited. However, traditional HIV genotyping is extremely expensive, providing a cost barrier to wide-scale and frequent HIV drug resistance surveillance. Methods/Results: We have developed a low-cost laboratory-scale next-generation sequencing-based genotyping method to monitor drug resistance. We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. Using this approach, we characterized drug resistance from plasma in 81 HIV infected individuals collected in Sao Paulo, Brazil. We describe the complexities of analyzing next-generation sequencing data and present a simplified open-source workflow to analyze drug resistance data. From this data, we identified drug resistance mutations in 20% of treatment naive individuals in our cohort, which is similar to frequencies identified using traditional genotyping in Brazilian patient samples. Conclusion: The developed ultra-wide sequencing approach described here allows multiplexing of at least 48 patient samples per sequencing run, 4 times more than the current genotyping method. This method is also 4-fold more sensitive (5% minimal detection frequency vs. 20%) at a cost 3-5 x less than the traditional Sanger-based genotyping method. Lastly, by using a benchtop next-generation sequencer (Roche/454 GS Junior), this approach can be more easily implemented in low-resource settings. This data provides proof-of-concept that next-generation HIV drug resistance genotyping is a feasible and low-cost alternative to current genotyping methods and may be particularly beneficial for in-country surveillance of transmitted drug resistance.

Introduction to the Software-defined Radio Approach

Telecommunications have been in constant evolution during past decades. Among the technological innovations, the use of digital technologies is very relevant. Digital communication systems have proven their efficiency and brought a new element in the chain of signal transmitting and receiving, the digital processor. This device offers to new radio equipments the flexibility of a programmable system. Nowadays, the behavior of a communication system can be modified by simply changing its software. This gave rising to a new radio model called Software Defined Radio (or Software-Defined Radio - SDR). In this new model, one moves to the software the task to set radio behavior, leaving to hardware only the implementation of RF front-end. Thus, the radio is no longer static, defined by their circuits and becomes a dynamic element, which may change their operating characteristics, such as bandwidth, modulation, coding rate, even modified during runtime according to software configuration. This article aims to present the use of GNU Radio software, an open-source solution for SDR specific applications, as a tool for development configurable digital radio.

Cone Beam Computed Tomographic Imaging: Perspective, Challenges, and the Impact of Near-Trend Future Applications

Cone beam computed tomography (CBCT) can be considered as a valuable imaging modality for improving diagnosis and treatment planning to achieve true guidance for several craniofacial surgical interventions. A new concept and perspective in medical informatics is the highlight discussion about the new imaging interactive workflow. The aim of this article was to present, in a short literature review, the usefulness of CBCT technology as an important alternative imaging modality, highlighting current practices and near-term future applications in cutting-edge thought-provoking perspectives for craniofacial surgical assessment. This article explains the state of the art of CBCT improvements, medical workstation, and perspectives of the dedicated unique hardware and software, which can be used from the CBCT source. In conclusion, CBCT technology is developing rapidly, and many advances are on the horizon. Further progress in medical workstations, engineering capabilities, and improvement in independent software-some open source-should be attempted with this new imaging method. The perspectives, challenges, and pitfalls in CBCT will be delineated and evaluated along with the technological developments.

GEDI: a user-friendly toolbox for analysis of large-scale gene expression data

Abstract Background Several mathematical and statistical methods have been proposed in the last few years to analyze microarray data. Most of those methods involve complicated formulas, and software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties when they attempting to use those methods in their research. Here we present an user-friendly toolbox which allows large-scale gene expression analysis to be carried out by biomedical researchers with limited programming skills. Results Here, we introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source, and freely-available tool that we believe will be useful to a wide range of laboratories, and to researchers with no background in Mathematics and Computer Science, allowing them to analyze their own data by applying both classical and advanced approaches developed and recently published by Fujita et al. Conclusion GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us. It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations. Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.

Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite.

Intelligent tutoring system for distance education

This study aims to develop and implement a tool called intelligent tutoring system in an online course to help a formative evaluation in order to improve student learning. According to Bloom et al. (1971,117) formative evaluation is a systematic evaluation to improve the process of teaching and learning. The intelligent tutoring system may provide a timely and high quality feedback that not only informs the correctness of the solution to the problem, but also informs students about the accuracy of the response relative to their current knowledge about the solution. Constructive and supportive feedback should be given to students to reveal the right and wrong answers immediately after taking the test. Feedback about the right answers is a form to reinforce positive behaviors. Identifying possible errors and relating them to the instructional material may help student to strengthen the content under consideration. The remedial suggestion should be given in each answer with detaileddescription with regards the materials and instructional procedures before taking next step. The main idea is to inform students about what they have learned and what they still have to learn. The open-source LMS called Moodle was extended to accomplish the formative evaluation, high-quality feedback, and the communal knowledge presented here with a short online financial math course that is being offered at a large University in Brazil. The preliminary results shows that the intelligent tutoring system using high quality feedback helped students to improve their knowledge about the solution to the problems based on the errors of their past cohorts. The results and suggestion for future work are presented and discussed.