Search results for "Databases"
showing 10 items of 937 documents
Textual data compression in computational biology: a synopsis.
2009
Abstract Motivation: Textual data compression, and the associated techniques coming from information theory, are often perceived as being of interest for data communication and storage. However, they are also deeply related to classification and data mining and analysis. In recent years, a substantial effort has been made for the application of textual data compression techniques to various computational biology tasks, ranging from storage and indexing of large datasets to comparison and reverse engineering of biological networks. Results: The main focus of this review is on a systematic presentation of the key areas of bioinformatics and computational biology where compression has been use…
A parallel and sensitive software tool for methylation analysis on multicore platforms.
2015
Abstract Motivation: DNA methylation analysis suffers from very long processing time, as the advent of Next-Generation Sequencers has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. As it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed. Results: We present a new software tool, called HPG-Methyl, which efficiently maps bis…
Global stability of protein folding from an empirical free energy function
2013
The principles governing protein folding stand as one of the biggest challenges of Biophysics. Modeling the global stability of proteins and predicting their tertiary structure are hard tasks, due in part to the variety and large number of forces involved and the difficulties to describe them with sufficient accuracy. We have developed a fast, physics-based empirical potential, intended to be used in global structure prediction methods. This model considers four main contributions: Two entropic factors, the hydrophobic effect and configurational entropy, and two terms resulting from a decomposition of close-packing interactions, namely the balance of the dispersive interactions of folded an…
Overlap and diversity in antimicrobial peptide databases: Compiling a non-redundant set of sequences
2015
Abstract Motivation: The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced. Results: A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are inc…
RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing
2012
Abstract Motivation: Next-generation sequencing technology enables an entirely new perspective for clinical research and will speed up personalized medicine. In contrast to microarray-based approaches, RNA-Seq analysis provides a much more comprehensive and unbiased view of gene expression. Although the perspective is clear and the long-term success of this new technology obvious, bioinformatics resources making these data easily available especially to the biomedical research community are still evolving. Results: We have generated RNA-Seq Atlas, a web-based repository of RNA-Seq gene expression profiles and query tools. The website offers open and easy access to RNA-Seq gene expression pr…
To Hit or Not to Hit, That Is the Question - Genome-wide Structure-Based Druggability Predictions for Pseudomonas aeruginosa Proteins.
2015
Pseudomonas aeruginosa is a Gram-negative bacterium known to cause opportunistic infections in immune-compromised or immunosuppressed individuals that often prove fatal. New drugs to combat this organism are therefore sought after. To this end, we subjected the gene products of predicted perturbative genes to structure-based druggability predictions using DrugPred. Making this approach suitable for large-scale predictions required the introduction of new methods for calculation of descriptors, development of a workflow to identify suitable pockets in homologous proteins and establishment of criteria to obtain valid druggability predictions based on homologs. We were able to identify 29 pert…
In praise of artifice reloaded: Caution with natural image databases in modeling vision
2019
Subjective image quality databases are a major source of raw data on how the visual system works in naturalistic environments. These databases describe the sensitivity of many observers to a wide range of distortions of different nature and intensity seen on top of a variety of natural images. Data of this kind seems to open a number of possibilities for the vision scientist to check the models in realistic scenarios. However, while these natural databases are great benchmarks for models developed in some other way (e.g., by using the well-controlled artificial stimuli of traditional psychophysics), they should be carefully used when trying to fit vision models. Given the high dimensionalit…
Microrefrigeration by NIS tunnel junctions
1996
By using a normal metal-insulator-superconductor (NIS) tunnel junction one can manipulate the Fermi-Dirac distribution of the electrons in the normal electrode. If the junction is biased close to the superconducting gap, Δ, only “hot electrons” above Fermi level can tunnel from the normal electrode to the superconductor. Thus, due to the decoupling of the conduction electrons from the lattice at low temperatures, there exists a possibility to decrease the electronic temperature by this method. Because of the symmetry with bias voltage, two NIS tunnel junctions in series can form an efficient microrefrigerator. Temperature can be measured with two additional junctions by considering the vari…
Predicted very large thermoelectric effect in ferromagnet-superconductor junctions in the presence of a spin-splitting magnetic field.
2014
We show that a huge thermoelectric effect can be observed by contacting a superconductor whose density of states is spin split by a Zeeman field with a ferromagnet with a nonzero polarization. The resulting thermopower exceeds kB/e by a large factor, and the thermoelectric figure of merit ZT can far exceed unity, leading to heat engine efficiencies close to the Carnot limit. We also show that spin-polarized currents can be generated in the superconductor by applying a temperature bias. © 2014 American Physical Society.
Fusing storage and computing for the domain of business intelligence and analytics: research opportunities
2015
With the growing importance of external and shared data, the set of requirements for Business Intelligence and Analytics (BIA) is shifting. Current solutions still come with shortcomings, esp. In multi-stakeholder environments where sensitive content is exchanged. We argue that a new level in the evolution of BIA can be unlocked by tearing down the barriers between storage and computing based on upcoming storage technologies. In particular, we propose a revitalization of ideas from object-oriented databases. We present results from a joint project that aimed at delineating design options for BIA solutions built upon this idea. The paper outlines the interplay of various architectural layers…