Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

Feeling the life: a look into the visual culture of life scientists

In order to deal with human biological problems, life scientists have started investigating artificial ways of generating tissues and growing cells ? leading to the evolution of tissue engineering. In this paper we explore visualization practices of life scientists working within the domain of tissue engineering. We carried out a small scale ethnographic exploration with 8 scientists and explored that the real value of scientists' experiments (and simulations), reasoning and collaborative processes go beyond their end results. We observed that these scientists' three-dimensional reasoning, corporeal knowledge and intimacy with biological objects and tools play a vital role in overall success

Rise and Demise of Bioinformatics? Promise and Progress

The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself

Kajian Kebutuhan Bahan Ajar Bioteknologi di Jurusan Biologi Universitas Negeri Malang

penelitian ini bertujuan untuk memperoleh mengenai kebutuhan bahan ajar bioteknologi di Jurusan Biologi UM. Metode penelitian menggunakan angket yang diisi oleh mahasiswa S1 Jurusan Biologi yang telah menempuh mata kuliah Bioteknologi. Analisis data secara kuantitatif deskriptif berupa persentase. Hasil penelitian menunjukkan sekitar 72% mahasiswa yang menempuh mata kuliah bioteknologi membutuhkan bahan ajar cetak dengan pendekatan bioinformatika yang disertai panduan untuk melakukan pembelajaran berbasis proyek. Kesimpulan penelitian ini perlu adanya pengembangan bahan ajar  S1 Jurusan Biologi UM untuk menunjang perkuliahan bioteknologi

Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care

Medical Informatics (MI) and Bioinformatics (BI) are two interdisciplinary areas located at the intersection between computer science and medicine and biology, respectively. Historically, they have been separated and only occasionally have researchers of both disciplines collaborated. The completion of the Human Genome Project has brought about in this post genomic era the need for a synergy of these two disciplines to further advance in the study of diseases by correlating essential genotypic information with expressed phenotypic information. Biomedical Informatics (BMI) is the emerging technology that aims to put these two worlds together in the new rising genomic medicine. In this regard, institutions such as the European Commission have recently launched several initiatives to support a new combined research agenda, based on the potential for synergism of both disciplines. In this paper we review the results the BIOINFOMED study one of these projects funded by the E

Sistema de recuperação automática de informação biomédica

Mestrado em Engenharia de Electrónica e de TelecomunicaçõesOs avanços mais recentes nas áreas da genómica e proteómica têm resultado num crescimento significativo em termos de informação disponibilizada ao público. Espera-se que tais quantidades de informação tragam grandes vantagens à prática clínica onde diagnósticos e tratamentos passarão a ser suportados ao nível molecular. Contudo, a navegação através das bases de dados bioinfomáticas e genéticas revela-se actualmente uma tarefa complexa e improdutiva para grande parte dos profissionais de saúde. Além disso, no contexto das doenças genéticas raras, verifica-se que o conhecimento sobre determinadas doenças se encontra confinado a um pequeno grupo de utilizadores experientes. Novas perspectivas serão introduzidas ao nível da compreensão de varias doenças raras com a criação de interfaces intuitivas que permitam a extracção, a manutenção e a partilha desta informação por um maior número de utilizadores. Nesta dissertação é apresentado um sistema de recuperação automática, disponibilizado através de um portal web, diseasecard.org, utilizado para reunir e integrar informação relativa a doenças raras, cobrindo conceitos que vão desde o fenótipo até ao genótipo. ABSTRACT: The recent advances on genomics and proteomics research bring up a significant grow on the information that is publicly available. This huge amount of data is expected to give rise to a new clinical practice, where diagnosis and treatments will be supported by information at the molecular level. However, navigating through genetic and bioinformatics databases can be a too complex and unproductive task for a primary care physician. Moreover, considering the rare genetic diseases field, we verify that the knowledge about a specific disease is commonly disseminated over a small group of experts. The capture, maintenance and sharing of this knowledge over user-friendly interfaces will introduce new insights in the understanding of some rare genetic diseases. In this thesis we present an information retrieval engine that is being used to gather and join information about rare diseases, from the phenotype to the genotype, in a public web portal – diseasecard.org

Uma rede telemática para a prestação regional de cuidados de saúde

Doutoramento em Engenharia InformáticaAs tecnologias de informação e comunicação na área da saúde não são só um instrumento para a boa gestão de informação, mas antes um fator estratégico para uma prestação de cuidados mais eficiente e segura. As tecnologias de informação são um pilar para que os sistemas de saúde evoluam em direção a um modelo centrado no cidadão, no qual um conjunto abrangente de informação do doente deve estar automaticamente disponível para as equipas que lhe prestam cuidados, independentemente de onde foi gerada (local geográfico ou sistema). Este tipo de utilização segura e agregada da informação clínica é posta em causa pela fragmentação generalizada das implementações de sistemas de informação em saúde. Várias aproximações têm sido propostas para colmatar as limitações decorrentes das chamadas “ilhas de informação” na saúde, desde a centralização total (um sistema único), à utilização de redes descentralizadas de troca de mensagens clínicas. Neste trabalho, propomos a utilização de uma camada de unificação baseada em serviços, através da federação de fontes de informação heterogéneas. Este agregador de informação clínica fornece a base necessária para desenvolver aplicações com uma lógica regional, que demostrámos com a implementação de um sistema de registo de saúde eletrónico virtual. Ao contrário dos métodos baseados em mensagens clínicas ponto-a-ponto, populares na integração de sistemas em saúde, desenvolvemos um middleware segundo os padrões de arquitetura J2EE, no qual a informação federada é expressa como um modelo de objetos, acessível através de interfaces de programação. A arquitetura proposta foi instanciada na Rede Telemática de Saúde, uma plataforma instalada na região de Aveiro que liga oito instituições parceiras (dois hospitais e seis centros de saúde), cobrindo ~350.000 cidadãos, utilizada por ~350 profissionais registados e que permite acesso a mais de 19.000.000 de episódios. Para além da plataforma colaborativa regional para a saúde (RTSys), introduzimos uma segunda linha de investigação, procurando fazer a ponte entre as redes para a prestação de cuidados e as redes para a computação científica. Neste segundo cenário, propomos a utilização dos modelos de computação Grid para viabilizar a utilização e integração massiva de informação biomédica. A arquitetura proposta (não implementada) permite o acesso a infraestruturas de e-Ciência existentes para criar repositórios de informação clínica para aplicações em saúde.Modern health information technology is not just a supporting instrument to good information management but a strategic requirement to provide more efficient and safer health care. Health information technology is a cornerstone to build the future patient-centric health care systems in which a comprehensive set of patient data will be available to the relevant care teams, in spite of where (system or service point) it was generated. Such secure and efficient use of clinical data is challenged by the existing fragmentation of health information systems implementation. Several approaches have been proposed to address the limitations of the so called “information silos” in healthcare, ranging from full centralization (a single system) to full-decentralized clinical message exchange networks. In this work we advocate the use of a service-based unification layer, by federating distributed heterogeneous information sources. This clinical information hub provides the basis to build regional-level applications, which we have demonstrated by implementing a virtual Electronic Health Record system. Unlike the message-driven, point-to-point approaches popular in health care systems integration, we developed a middleware layer, using J2EE architectural patterns, in which the common information is represented as an object model, accessible through programming interfaces. The proposed architecture was instantiated in the Rede Telemática da Saúde network, a platform deployed in the region of Aveiro connecting eight partner institutions (two hospitals and six primary care units), covering ~ 350,000 citizens, indexing information on more than 19,000,000 episodes of care and used by ~350 registered professionals. In addition to the regional health information collaborative platform (RTSys), we introduce a second line of research towards bridging the care networks and the science networks. In the later scenario, we propose the use of Grid computing to enable the massive use and integration of biomedical information. The proposed architecture (not implemented) enables to access existing e-Science infrastructures to create clinical information repositories for health applications

Aplicación de la secuenciación masiva paralela para el análisis de alta definición de regiones genómicas de interés en el ganado ovino y para el estudio de la microbiota de la leche de oveja = Appliction of massively parallel secuencing to the high-resolution analysis of relevant genomic regions in dairy sheep and the study the sheep milk microbiota

262 p.El objetivo general de esta Tesis Doctoral es el aprovechamiento y la utilización de las NGS (Next Generation Sequencing = tecnologías de secuenciación de segunda generación) para estudiar caracteres complejos y algunos fenotipos de importancia económica en el ganado ovino lechero. Todos los trabajos incluidos en esta Tesis Doctoral proporcionan una visión global de la gran utilidad del uso de las tecnologías de secuenciación para profundizar en distintos aspectos relacionados con la genómica animal