7,447 research outputs found
SAD_BaSe: a blood bank data analysis software
Publicado em "6th International Conference on Practical Applications of Computational Biology & Bioinformatics (ISBN : 978-3-642-28838-8)"The main goal of this project was to build a Web-based information system – SAD_BaSe – that monitors blood donations and the blood production chain in a user-friendly way. In particular, the system keeps track of several data indicators and supports their analysis, enabling the definition of collection and production strategies and, the measurement of quality indicators required by the Quality Management System of blood establishments. Data mining supports the analysis of donor eligibility criteria
A Rare Disease Patient Manager
ABSTRACT publicado: 6th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB. Salamanca, 28-30 Março 2012The personal health implications behind rare diseases are seldom considered
in widespread medical care. The low incidence rate and complex treatment
process makes rare disease research an underrated field in the life sciences. However,
it is in these particular conditions that the strongest relations between genotypes
and phenotypes are identified. The rare disease patient manager, detailed in
this manuscript, presents an innovative perspective for a patient-centric portal integrating
genetic and medical data. With this strategy, patient’s digital records are
transparently integrated and connected to wet-lab genetics research in a seamless
working environment. The resulting knowledge base offers multiple data views,
geared towards medical staff, with patient treatment and monitoring data; genetics
researchers, through a custom locus-specific database; and patients, who for once
play an active role in their treatment and rare diseases research
A systematic approach to the interrogation and sharing of standardised biofilm signatures
Publicado em "6th International Conference on Practical Applications of Computational Biology & Bioinformatics", ISBN 978-3-642-28838-8The study of microorganism consortia, also known as biofilms, is associated to a number of applications in biotechnology, ecotechnology and clinical domains. A public repository on existing biofilm studies would aid in the design of new studies as well as promote collaborative and incremental work. However, bioinformatics approaches are hampered by the limited access to existing data. Scientific publications summarise the studies whilst results are kept in researchers’ private ad hoc files.
Since the collection and ability to compare existing data is imperative to move forward in biofilm analysis, the present work has addressed the development of a systematic computer-amenable approach to biofilm data organisation and standardisation. A set of in-house studies involving pathogens and employing different state-of-the-art devices and methods of analysis was used to validate the approach. The approach is now supporting the activities of BiofOmics, a public repository on biofilm signatures (http://biofomics.org).The authors thank, among others, Rosario Oliveira, Maria Joao Vieira, Idalina Machado, Nuno Cerca, Mariana Henriques, Pilar Teixeira, Douglas Monteiro, Melissa Negri, Susana Lopes, Carina Almeida and Helder Lopes, for submitting their data. The financial support from IBB-CEB, Fundacao para a Ciencia e Tecnologia (FCT) and European Community fund FEDER (Program COMPETE), project PTDC/SAU-ESA/646091/2006/FCOMP-01-0124-FEDER-007480, are also gratefully acknowledged
Towards a lightweight generic computational grid framework for biological research
Background: An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations – a characteristic of the emerging field of systems biology. Results: In this paper we present a lightweight generic framework for combining disparate computational resources at multiple sites (ranging from local computers and clusters to established national Grid services). A detailed guide describing how to set up the framework is available from the following URL: http://igrid-ext.cryst.bbk.ac.uk/portal_guide/. Conclusion: This approach is particularly (but not exclusively) appropriate for large-scale biology projects with multiple collaborators working at different national or international sites. The framework is relatively easy to set up, hides the complexity of Grid middleware from the user, and provides access to resources through a single, uniform interface. It has been developed as part of the European ImmunoGrid project
RasBhari: optimizing spaced seeds for database searching, read mapping and alignment-free sequence comparison
Many algorithms for sequence analysis rely on word matching or word
statistics. Often, these approaches can be improved if binary patterns
representing match and don't-care positions are used as a filter, such that
only those positions of words are considered that correspond to the match
positions of the patterns. The performance of these approaches, however,
depends on the underlying patterns. Herein, we show that the overlap complexity
of a pattern set that was introduced by Ilie and Ilie is closely related to the
variance of the number of matches between two evolutionarily related sequences
with respect to this pattern set. We propose a modified hill-climbing algorithm
to optimize pattern sets for database searching, read mapping and
alignment-free sequence comparison of nucleic-acid sequences; our
implementation of this algorithm is called rasbhari. Depending on the
application at hand, rasbhari can either minimize the overlap complexity of
pattern sets, maximize their sensitivity in database searching or minimize the
variance of the number of pattern-based matches in alignment-free sequence
comparison. We show that, for database searching, rasbhari generates pattern
sets with slightly higher sensitivity than existing approaches. In our Spaced
Words approach to alignment-free sequence comparison, pattern sets calculated
with rasbhari led to more accurate estimates of phylogenetic distances than the
randomly generated pattern sets that we previously used. Finally, we used
rasbhari to generate patterns for short read classification with CLARK-S. Here
too, the sensitivity of the results could be improved, compared to the default
patterns of the program. We integrated rasbhari into Spaced Words; the source
code of rasbhari is freely available at http://rasbhari.gobics.de
Jeeva: Enterprise Grid-enabled Web Portal for Protein Secondary Structure Prediction
This paper presents a Grid portal for protein secondary structure prediction
developed by using services of Aneka, a .NET-based enterprise Grid technology.
The portal is used by research scientists to discover new prediction structures
in a parallel manner. An SVM (Support Vector Machine)-based prediction
algorithm is used with 64 sample protein sequences as a case study to
demonstrate the potential of enterprise Grids.Comment: 7 page
A conditional compression distance that unveils insights of the genomic evolution
We describe a compression-based distance for genomic sequences. Instead of
using the usual conjoint information content, as in the classical Normalized
Compression Distance (NCD), it uses the conditional information content. To
compute this Normalized Conditional Compression Distance (NCCD), we need a
normal conditional compressor, that we built using a mixture of static and
dynamic finite-context models. Using this approach, we measured chromosomal
distances between Hominidae primates and also between Muroidea (rat and mouse),
observing several insights of evolution that so far have not been reported in
the literature.Comment: Full version of DCC 2014 paper "A conditional compression distance
that unveils insights of the genomic evolution
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