Author Archives: Rui Lebre

egas

Egas is a web-based platform for biomedical text mining and collaborative curation, supporting manual and automatic annotation of concepts and relations.

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Cloud Thinking

Funding entity: QREN MaisCentro
Period: Feb.2013 – Dec.2014
The projects’ ambition is the creation of a new set of solutions based in novel ICT technologies, developing a concept that encompasses the synergistic usage of cloud computing, with large database access and information retrieval, associated with advanced methods for reasoning and data mining (and with the basic scalable […]

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NeuroPath – New Strategies Applied to Neuropathological Disorders

Funding entity: QREN MaisCentro
Period: Feb.2013 – Jun.2015
Neurodegenerative disorders are a major health concern worldwide, Portugal being no exception. With this project the University of Aveiro proposes extend existing research in the field of neurodegenerative diseases through the creation of a consortium of 5 research units from UA (CBC, QOPNA, I3N, IEETA, CICECO). The projects main […]

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Best Poster award at BioLINK SIG 2013

David Campos won the F1000 Research Poster Prize at BioLINK SIG 2013.

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iOS Development Seminar (Rui Pedro Lopes)

A 6-hour iOS Development Seminar will be held by Rui Pedro Lopes, Professor at Polytechnic Institute of Brangança, on the 29th July 2013, at Department of Electronics, Telecommunications and Informatics (DETI), Aveiro.

This Seminar will cover the following main topics: Objective-C, Storyboards, Core Data, Master-Detail User Interface

Universidade de Aveiro, DETI, Room 102, 10h

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Variobox

Variobox is a desktop tool for the annotation, analysis and comparison of human genes. Variant annotation data are obtained from WAVe, protein metadata annotations are gathered from PDB and UniProt, and sequence metadata is obtained from Locus Reference Genomic (LRG) and RefSeq databases. By using an advanced sequence visualization interface, Variobox provides an agile navigation through the various genetic regions.

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becas

BeCAS is a web application, API and widget for biomedical concept identification. It helps researchers, healthcare professionals and developers in the identification of over 1,200,000 biomedical concepts in text and PubMed abstracts.

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Diseasecard

DISEASECARD is a public web portal that integrates real-time information from distributed and heterogeneous medical and genomic databases, presenting it in a familiar visual paradigm.

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nccd

NCCD is a method and package tool designed to compute the Normalized Conditional Compression Distance.

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EU-ADR Web Platform

The EU-ADR Web Platform helps experts in the study of adverse drug reactions (ADRs) through the use of computational services and scientific workflows, provided by several European partners. This system assists in the earlier detection of adverse drug reactions, improving drug safety and contributing to public health benefit.

Posted in Knowledge management, Software | 1 Comment

On Multicriteria Pairwise Sequence Alignment: Algorithms and Applications

Talk from Luís Paquete, Anf. IEETA
The multiobjective formulation of the pairwise sequence alignment problem is introduced, where a vector score function takes into account the substitution score and indels or gaps separately. Two solution methods are introduced: a multiobjective dynamic programming that extends classical algorithms for this problem and an epsilon-constraint algorithm that solves a […]

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EMIF – European Medical Information Framework

Funding entity: IMI-JU
Period: 2013-2018
In recent years, the development and use of Electronic Healthcare Records (EHRs) throughout Europe has grown exponentially resulting in large volumes of clinical data. At the same time, large collections of disease‐specific data are recorded – in local, regional and/or national settings. Researchers also follow specific cohorts over time, and focus on […]

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RD-CONNECT – An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research

Funding entity: FP7-HEALTH-2012-INNOVATION-1
Period: 2012-2018
Despite examples of excellent practice, rare disease (RD) research is still mainly fragmented by data and disease types. Individual efforts have little interoperability and almost no systematic connection between detailed clinical and genetic information, biomaterial availability or research/trial datasets. By developing robust mechanisms and standards for linking and exploiting these data, RD-Connect […]

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Neji

Neji is a innovative and powerfull framework for faster biomedical concept recognition. It is open source and built around four key characteristics: modularity, scalability, speed, and usability. Neji integrates modules of various state-of-the-art methods for biomedical natural language processing (e.g., sentence splitting, tokenization, lemmatization, part-of-speech tagging, chunking and dependency parsing) and concept recognition (e.g., dictionaries and machine learning). The most popular input and output formats, such as Pubmed XML, IeXML, CoNLL and A1, are also supported.

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Systems Biology seminars series start on the 28th of September

Dr. Kim Sneppen from the Niels Bohr Institute, Copenhagen-DK, will give the give the inaugural Lecture of our Systems Biology seminars series entitled Simplified Models of Biological Networks, on the 28th of September.

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PhD Defense (Pedro Lopes)

Pedro Lopes, “Service Composition in Biomedical Applications”
Universidade de Aveiro, DETI/IEETA

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Talk (Kim Sneppen)

Dr. Kim Sneppen from the Niels Bohr Institute, Copenhagen-DK, will give the give the inaugural Lecture of our Systems Biology seminars series entitled Simplified Models of Biological Networks, on the 28th of September.

Universidade de Aveiro, Anf. Ambiente, 14h

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mRNA Optimiser

The mRNA optimiser is a tool that redesigns a gene messenger RNA to optimise its secondary structure, without affecting the polypeptide sequence. The tool can either maximize or minimize the molecule minimum free energy (MFE), thus resulting in decreased or increased secondary structure strength.

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OralCard

OralCard is an online bioinformatic tool that comprises results from manually curated articles reflecting the oral molecular ecosystem (OralPhysiOme), by merging the experimental information available from the oral proteome both of human (OralOme) and microbial origin (MicroOralOme). OralCard is a key resource for understanding the molecular foundations implicated in biology and disease mechanisms of the oral cavity.

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PhD Defense (Nuno Rosa)

Nuno Rosa, “From the Salivar Proteome to Oralome”
Universidade Católica Portuguesa, Viseu

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