A hybrid and scalable error correction algorithm for indel and substitution errors of long reads.

BACKGROUND: Long-read sequencing has shown the promises to overcome the short length limitations of second-generation sequencing by providing more complete assembly. However, the computation of the long sequencing reads is challenged by their higher error rates (e.g., 13% vs. 1%) and higher cost ($0.3 vs. $0.03 per Mbp) compared to the short reads. METHODS: In this paper, we present a new hybrid error correction tool, called ParLECH (Parallel Long-read Error Correction using Hybrid methodology). The error correction algorithm of ParLECH is distributed in nature and efficiently utilizes the k-mer coverage information of high throughput Illumina short-read sequences to rectify the PacBio long-read sequences.ParLECH first constructs a de Bruijn graph from the short reads, and then replaces the indel error regions of the long reads with their corresponding widest path (or maximum min-coverage path) in the short read-based de Bruijn graph. ParLECH then utilizes the k-mer coverage information of the short reads to divide each long read into a sequence of low and high coverage regions, followed by a majority voting to rectify each substituted error base. RESULTS: ParLECH outperforms latest state-of-the-art hybrid error correction methods on real PacBio datasets. Our experimental evaluation results demonstrate that ParLECH can correct large-scale real-world datasets in an accurate and scalable manner. ParLECH can correct the indel errors of human genome PacBio long reads (312 GB) with Illumina short reads (452 GB) in less than 29 h using 128 compute nodes. ParLECH can align more than 92% bases of an E. coli PacBio dataset with the reference genome, proving its accuracy. CONCLUSION: ParLECH can scale to over terabytes of sequencing data using hundreds of computing nodes. The proposed hybrid error correction methodology is novel and rectifies both indel and substitution errors present in the original long reads or newly introduced by the short reads.

Phase-change like process through bond switching in distorted and resonantly bonded crystal.

Although some methods to improve phase-change memory efficiency have been proposed, an effective experimental approach to induce a phase-change like process without external heat energy has not yet been reported. Herein we have shown that GeTe is a prototype phase-change material, which can exhibit a non-thermal phase-change-like process under uniaxial stress. Due to its structural characteristics like directional structural instability and resonance bonding under 1% uniaxial stress, we observed that bond switching in the GeTe film between short and long bonds is possible. Due to this phase change, GeTe displays the same phase-change as crystal layer rotation. Crystal layer rotation has not been observed in the conventional phase change process using intermediate states, but it is related to the structural characteristics required for maintaining local coordination. Moreover, since the resonance bonding characteristics are effectively turned off upon applying uniaxial stress, the high-frequency dielectric constant can be significantly decreased. Our results also show that the most significant process in the non-thermal phase transition of phase-change materials is the modulation of the lattice relaxation process after the initial perturbation, rather than the method inducing the perturbation itself. Finally, these consequences suggest that a new type of phase-change memory is possible through changes in the optical properties under stress.

Geohealth: biology based mapping of vector borne disease in the Americas using NASA satellite data / Geosaúde: mapeamento da biologia das doenças vetoriais nas Américas utilizando dados de satélites da NASA

Implementation of a geospatial surveillance and response system data resource for vector borne disease in the Americas (GeoHealth) will be tested using NASA satellite data, geographic information systems and ecological niche modeling to characterize the environmental suitability and potential for spread of endemic and epizootic vector borne diseases. The initial focus is on developing prototype geospatial models for visceral leishmaniasis, an expanding endemic disease in Latin America, and geospatial models for dengue and other Aedes aegypti borne arboviruses (zika, chikungunya), emerging arboviruses with potential for epizootic spread from Latin America and the Caribbean and establishment in North America. Geospatial surveillance and response system open resource data bases and models will be made available, with training courses, to other investigators interested in mapping and modeling other vector borne diseases in the western hemisphere and contributing brokered data to an expanding GeoHealth data resource as part of the NASA AmeriGEOSS initiative.(AU)

A implementação de uma fonte de dados de vigilância e um sistema de resposta geoespacial para doenças transmitidas por vetores nas Américas (GeoHealth) será testada utilizando dados provenientes de satélites da NASA, sistemas de informações geográficas e modelagem do nicho ecológico, para caracterizar a suceptibilidade ambiental e o potencial de dispersão de doenças endêmicas e epizooticas transmitidas por vetores vetores. O foco inicial será o desenvolvimento de protótipos de modelos geoespaciais para a leishmaniose visceral, uma doença endêmica e em expansão na América Latina, e modelos geoespaciais para dengue e outros transmitidos pelo Aedes aegypti (zika, chikungunya), arbovírus emergentes com potencial para disseminação epizoótica pela América Latina e Caribe e estabelecimento na América do Norte. Sistemas de vigilância e resposta geoespacial e modelos de recursos em bases de dados abertas serão diponibilizados, com cursos de treinamento, para outros pesquisadores interessados em mapear e modelar outras doenças transmitidas por vetores no hemisfério ocidental e contribuir intermediando dados para uma fonte de dados GeoHealth em expansão, como parte da Iniciativa AmeriGEOSS, da NASA. (AU)

Geohealth: biology based mapping of vector borne disease in the Americas using NASA satellite data / Geosaúde: mapeamento da biologia das doenças vetoriais nas Américas utilizando dados de satélites da NASA

Implementation of a geospatial surveillance and response system data resource for vector borne disease in the Americas (GeoHealth) will be tested using NASA satellite data, geographic information systems and ecological niche modeling to characterize the environmental suitability and potential for spread of endemic and epizootic vector borne diseases. The initial focus is on developing prototype geospatial models for visceral leishmaniasis, an expanding endemic disease in Latin America, and geospatial models for dengue and other Aedes aegypti borne arboviruses (zika, chikungunya), emerging arboviruses with potential for epizootic spread from Latin America and the Caribbean and establishment in North America. Geospatial surveillance and response system open resource data bases and models will be made available, with training courses, to other investigators interested in mapping and modeling other vector borne diseases in the western hemisphere and contributing brokered data to an expanding GeoHealth data resource as part of the NASA AmeriGEOSS initiative.

A implementação de uma fonte de dados de vigilância e um sistema de resposta geoespacial para doenças transmitidas por vetores nas Américas (GeoHealth) será testada utilizando dados provenientes de satélites da NASA, sistemas de informações geográficas e modelagem do nicho ecológico, para caracterizar a suceptibilidade ambiental e o potencial de dispersão de doenças endêmicas e epizooticas transmitidas por vetores vetores. O foco inicial será o desenvolvimento de protótipos de modelos geoespaciais para a leishmaniose visceral, uma doença endêmica e em expansão na América Latina, e modelos geoespaciais para dengue e outros transmitidos pelo Aedes aegypti (zika, chikungunya), arbovírus emergentes com potencial para disseminação epizoótica pela América Latina e Caribe e estabelecimento na América do Norte. Sistemas de vigilância e resposta geoespacial e modelos de recursos em bases de dados abertas serão diponibilizados, com cursos de treinamento, para outros pesquisadores interessados em mapear e modelar outras doenças transmitidas por vetores no hemisfério ocidental e contribuir intermediando dados para uma fonte de dados GeoHealth em expansão, como parte da Iniciativa AmeriGEOSS, da NASA.

Large-scale parallel genome assembler over cloud computing environment.

The size of high throughput DNA sequencing data has already reached the terabyte scale. To manage this huge volume of data, many downstream sequencing applications started using locality-based computing over different cloud infrastructures to take advantage of elastic (pay as you go) resources at a lower cost. However, the locality-based programming model (e.g. MapReduce) is relatively new. Consequently, developing scalable data-intensive bioinformatics applications using this model and understanding the hardware environment that these applications require for good performance, both require further research. In this paper, we present a de Bruijn graph oriented Parallel Giraph-based Genome Assembler (GiGA), as well as the hardware platform required for its optimal performance. GiGA uses the power of Hadoop (MapReduce) and Giraph (large-scale graph analysis) to achieve high scalability over hundreds of compute nodes by collocating the computation and data. GiGA achieves significantly higher scalability with competitive assembly quality compared to contemporary parallel assemblers (e.g. ABySS and Contrail) over traditional HPC cluster. Moreover, we show that the performance of GiGA is significantly improved by using an SSD-based private cloud infrastructure over traditional HPC cluster. We observe that the performance of GiGA on 256 cores of this SSD-based cloud infrastructure closely matches that of 512 cores of traditional HPC cluster.

Investigating combinatorial approaches in virtual screening on human inducible 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB3): a case study for small molecule kinases.

Efforts toward improving the predictiveness in tier-based approaches to virtual screening (VS) have mainly focused on protein kinases. Despite their significance as drug targets, small molecule kinases have been rarely tested with these approaches. In this paper, we investigate the efficacy of a pharmacophore screening-combined structure-based docking approach on the human inducible 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, an emerging target for cancer chemotherapy. Six out of a total 1364 compounds from NCI's Diversity Set II were selected as true actives via throughput screening. Using a database constructed from these compounds, five programs were tested for structure-based docking (SBD) performance, the MOE of which showed the highest enrichments and second highest screening rates. Separately, using the same database, pharmacophore screening was performed, reducing 1364 compounds to 287 with no loss in true actives, yielding an enrichment of 4.75. When SBD was retested with the pharmacophore filtered database, 4 of the 5 SBD programs showed significant improvements to enrichment rates at only 2.5% of the database, with a 7-fold decrease in an average VS time. Our results altogether suggest that combinatorial approaches of VS technologies are easily applicable to small molecule kinases and, moreover, that such methods can decrease the variability associated with single-method SBD approaches.