Author Archives: Rui Lebre

rebico

A survey on data compression methods for biological sequences.
Domains: protein sequences, genomic sequences (reference-free and reference-based) and specific formats (FASTA, FASTQ, SAM/BAM).

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Masters thesis defense (Ricardo Ribeiro)

Ricardo Filipe Gonçalves Ribeiro, “TASKA: A modular and easily extendable system for repeatable workflows”
23 Mai, 14.30 pm

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GeCo

Compress and analyze genomic sequences. As a compression tool, GeCo is able to provide additional compression gains over several top specific tools, while as an analysis tool, GeCo is able to determine absolute measures, namely for many distance computations, and local measures, such as the information content contained in each element, providing a way to quantify and locate specific genomic events. GeCo can afford individual compression and referential compression.

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PhD Defense (Luis Bastião)

Luis Bastião Silva, “A federated architecture for biomedical data integration”
Universidade de Aveiro, DETI/IEETA

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smash

Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For visualisation, Smash outputs a SVG image, with an ideogram output architecture, where the patterns are represented with several HSV values. It can perform both in small- and large-scale.

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PhD Defense (Carlos Ferreira)

Carlos Ferreira, “Handling Data Access Latency in Distributed Medical Imaging Environments”
Universidade de Aveiro, DETI/IEETA
Date: 2015.04.10, 10.00 AM
Anfiteatro, Reitoria, Universiade de Aveiro
 

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eagle

EAGLE is an alignment-free method and associated program to compute relative absent words (RAW) in genomic sequences using a reference sequence. Currently, EAGLE runs on a command line linux environment, building an image with patterns reporting the absent words regions (in SVG) as well as reporting the associated positions into a file. EAGLE hast got scripts to run on the current outbreak 99 ebola virus genomes (using the human as a reference), including the download, filtering and processing of the entire data.

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PhD Defense (Paulo Gaspar)

Rectory amphitheater (sala de atos), 15h00

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MENT

MENT is a set of tools for lossless compression of microarray images. These tools can also be used for other types of images such as medical, RNAi, etc. This set of tools are divided into two categories. One where a bitplane decomposition approach is used and the other one where a binary tree decomposition is used.

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XS

XS is a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity. It has several running modes, depending on the time and memory available, and is aimed at testing computing infrastructures, namely cloud computing of large-scale projects, and testing FASTQ compression algorithms. Moreover, XS offers the possibility of simulating the three main FASTQ components individually (headers, DNA sequences and quality-scores)

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SACO

SACO is a method to handle the DNA bases and gap symbols that can be found in MAF files. SACO is based on a mixture of finite-context models. Contrarily Hanus et al approach, it addresses both the DNA bases and gap symbols at once, better exploring the existing correlations. For comparison with previous methods, our algorithm was tested in the multiz28way dataset. On average, it attained 0.94 bits per symbol, approximately 7% better than the previous best, for a similar computational complexity.

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MAFCO

MAFCO is a lossless compression tool specifically designed to compress MAF (Multiple Alignment Format) files. Compared to gzip, the proposed tool attains a compression gain from ≈ 34% to ≈ 57%, depending on the data set. When compared to a recent dedicated method, which is not compatible with some data sets, the compression gain of MAFCO is about 9%.

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ACE’14 Workshop on “Designing Systems for Health and Entertainment: what are we missing?”

Systems that aggregate health and entertainment goals are proliferating, but little is known about the way to design and evaluate these systems and how to manage the different (if nor opposite) needs of these two main areas. This workshop will promote the discussion of issues surrounding these areas, enabling a better understanding of the how’s […]

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SMBM 2014

The 6th International Symposium on Semantic Mining in Biomedicine (SMBM)
6th-7th October, 2014 will be held at the University of Aveiro, Portugal.
SMBM aims to bring together researchers from text and data mining in biomedicine, medical, bio- and chemoinformatics, and researchers from biomedical ontology design and engineering. SMBM 2014 is the follow-up event to SMBM 2012 (University of Zürich, Switzerland) SMBM 2010 (EBI, […]

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PhD Defense (Luis Ribeiro)

Mathematics Dept. amphitheater, 14h30

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PhD Defense (David Campos)

Environment Dept. amphitheater, 10h00

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Sérgio Matos was awarded a FCT Investigator grant

FCT Investigator grant awarded to Sérgio Matos

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FALCON

Machine learning system to classify metagenomic samples.

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Dna-at-glance

DNAatGlance is a program for the detection of large-scale genomic regularities by visual inspection. Several discovery strategies are possible, including the standalone analysis of single sequences, the comparative analysis of sequences from individuals from the same species, and the comparative analysis of sequences from different organisms.

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MFCompress

MFCompress is a compression tool for FASTA and multi-FASTA files. In comparison to gzip and applied to multi-FASTA files, MFCompress can provide additional average compression gains of almost 50%, i.e., it potentially doubles the available storage, although at the cost of some more computation time. On highly redundant data sets, and in comparison with gzip, 8-fold size reductions have been obtained.

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