CCGrid 2010 - 10th IEEE/ACM International Conference on Cluster, Cloud, and Grid Computing, 2010
Abstract Parallel computing is becoming essential for nowadays data analysis in several disciplin... more Abstract Parallel computing is becoming essential for nowadays data analysis in several disciplines. In order to profit from parallel processing of experimental data, specialized skills, software tools and suitable computing resources are required. Desktop grids and volunteer-based systems have proved themselves as powerful options where distributed idle resources from heterogeneous computers are aggregated to build powerful met computers. Software solutions are required to automate and assist the process of transformation and ...
We present an extensible software model for the genotype and phenotype community, XGAP. Readers c... more We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (http://www.xgap.org) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.
microRNAs (miRNAs) are important post-transcriptional regulators in eukaryotes that target mRNAs ... more microRNAs (miRNAs) are important post-transcriptional regulators in eukaryotes that target mRNAs repressing their expression. The uncertain process of pig domestication, with different origin focuses, and the selection process that commercial breeds suffered, have generated a wide spectrum of breeds with clear genetic and phenotypic variability. The aim of this work was to define the miRNAs expression profile in kidney of several porcine breeds. Small RNA libraries from kidney were elaborated and high-throughput sequenced with the 454 Genome Sequencer FLX (Roche). Pigs used were classified into three groups: the European origin group (Iberian breed and European Wild Boar ancestor), European commercial breeds (Landrace, Large White and Piétrain breeds) and breeds with Asian origin (Meishan and Vietnamese breeds). A total of 229 miRNAs were described in the pig kidney miRNA profile, including 110 miRNAs out of the 257 previously described pig miRNAs and 119 orthologous miRNAs. The most expressed miRNAs in pig kidney microRNAome were Hsa-miR-200b-3p, Ssc-miR-125b and Ssc-miR-23b. Moreover, 5 novel porcine miRNAs and 3 orthologous miRNAs could be validated through RT-qPCR. miRNA sequence variation was determined in 116 miRNAs, evidencing the presence of isomiRs. 125 miRNAs were differentially expressed between breed groups. The identification of breed-specific miRNAs, which could be potentially associated to certain phenotypes, is becoming a new tool for the study of the genetic variability underlying complex traits and furthermore, it adds a new layer of complexity to the interesting process of pig evolution.
Porcine production is a primary market in the world economy. Controlling swine diseases in the fa... more Porcine production is a primary market in the world economy. Controlling swine diseases in the farm is essential in order to achieve the sector necessities. Aujeszky's disease is a viral condition affecting pigs and is endemic in many countries of the world, causing important economic losses in the swine industry. microRNAs (miRNAs) are non-coding RNAs which modulates gene expression in animals, plants and viruses. With the aim of understanding miRNA roles during the Aujeszky's disease virus [ADV] (also known as suid herpesvirus type 1 [SuHV-1]) infection, the expression profiles of host and viral miRNAs were determined through deep sequencing in SuHV-1 infected porcine cell line (PK-15) and in an animal experimental SuHV-1 infection with virulent (NIA-3) and attenuated (Begonia) strains. In the in vivo approach miR-206, miR-133a, miR-133b and miR-378 presented differential expression between virus strains infection. In the in vitro approach, most miRNAs were down-regulated in infected groups. miR-92a and miR-92b-3p were up-regulated in Begonia infected samples. Functional analysis of all this over expressed miRNAs during the infection revealed their association in pathways related to viral infection processes and immune response. Furthermore, 8 viral miRNAs were detected by stem loop RT-qPCR in both in vitro and in vivo approaches, presenting a gene regulatory network affecting 59 viral genes. Most described viral miRNAs were related to Large Latency Transcript (LLT) and to viral transcription activators EP0 and IE180, and also to regulatory genes regarding their important roles in the host -pathogen interaction during viral infection.
Background: High-dimensional biomolecular profiling of genetically different individuals in one o... more Background: High-dimensional biomolecular profiling of genetically different individuals in one or more environmental conditions is an increasingly popular strategy for exploring the functioning of complex biological systems. The optimal design of such genetical genomics experiments in a costefficient and effective way is not trivial.
Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software take... more Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software takes averages over probes. Important information may be lost if polymorphisms in the mRNA affect the hybridization of individual probes. We present custom software to analyze genetical genomics experiments in human, mouse and other organisms: (i) an R package providing functions for QTL analysis at the individual probe level and (ii) Perl scripts providing custom tracks in the UCSC Genome Browser to check for sequence polymorphisms in probe regions. http://gbic.biol.rug.nl/supplementary.
Genetical genomics projects accumulate on a large scale (molecular) phenotype and marker data for... more Genetical genomics projects accumulate on a large scale (molecular) phenotype and marker data for hundreds of genetically different individuals from human, mouse and C. elegans. For example, Keurentjes et al [1,2] treated expression and metabolite data from 160 Arabidopsis plants as quantitative traits and used quantitative trait locus (QTL) mapping to identify regulators (eQTLs and mQTLs) and (re)-construct regulatory and metabolic networks . Similar data have been or will be collected for other experimental populations using the same or other biomolecular methods.
We here present ATLS, a self scheduling scheme designed for execution of parallel loops in dynami... more We here present ATLS, a self scheduling scheme designed for execution of parallel loops in dynamic environments of non-dedicated networked computers. Since grid and volunteer systems based on desktop computers are proving themselves as real and powerful alternatives for ...
We here present ATLS, a self scheduling scheme designed for execution of parallel loops in dynami... more We here present ATLS, a self scheduling scheme designed for execution of parallel loops in dynamic environments of non-dedicated networked computers. Since grid and volunteer systems based on desktop computers are proving themselves as real and powerful alternatives for parallel computing, new scheduling schemes, better suited for these environments, are required. Our proposal, by tracking several performance change ratios at runtime, is able to properly adjust the load distribution using no prior information of the loop features nor the involved processors. The results obtained during the experiments performed to validate ATLS show that it is possible to improve former contributions of well-known parallel loop scheduling schemes in dynamic environments. The implementation of the scheduler has been done for the R language but, as it is exposed, it can easily be adapted to any other language and parallel loop based application.
CCGrid 2010 - 10th IEEE/ACM International Conference on Cluster, Cloud, and Grid Computing, 2010
Abstract Parallel computing is becoming essential for nowadays data analysis in several disciplin... more Abstract Parallel computing is becoming essential for nowadays data analysis in several disciplines. In order to profit from parallel processing of experimental data, specialized skills, software tools and suitable computing resources are required. Desktop grids and volunteer-based systems have proved themselves as powerful options where distributed idle resources from heterogeneous computers are aggregated to build powerful met computers. Software solutions are required to automate and assist the process of transformation and ...
We present an extensible software model for the genotype and phenotype community, XGAP. Readers c... more We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (http://www.xgap.org) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.
microRNAs (miRNAs) are important post-transcriptional regulators in eukaryotes that target mRNAs ... more microRNAs (miRNAs) are important post-transcriptional regulators in eukaryotes that target mRNAs repressing their expression. The uncertain process of pig domestication, with different origin focuses, and the selection process that commercial breeds suffered, have generated a wide spectrum of breeds with clear genetic and phenotypic variability. The aim of this work was to define the miRNAs expression profile in kidney of several porcine breeds. Small RNA libraries from kidney were elaborated and high-throughput sequenced with the 454 Genome Sequencer FLX (Roche). Pigs used were classified into three groups: the European origin group (Iberian breed and European Wild Boar ancestor), European commercial breeds (Landrace, Large White and Piétrain breeds) and breeds with Asian origin (Meishan and Vietnamese breeds). A total of 229 miRNAs were described in the pig kidney miRNA profile, including 110 miRNAs out of the 257 previously described pig miRNAs and 119 orthologous miRNAs. The most expressed miRNAs in pig kidney microRNAome were Hsa-miR-200b-3p, Ssc-miR-125b and Ssc-miR-23b. Moreover, 5 novel porcine miRNAs and 3 orthologous miRNAs could be validated through RT-qPCR. miRNA sequence variation was determined in 116 miRNAs, evidencing the presence of isomiRs. 125 miRNAs were differentially expressed between breed groups. The identification of breed-specific miRNAs, which could be potentially associated to certain phenotypes, is becoming a new tool for the study of the genetic variability underlying complex traits and furthermore, it adds a new layer of complexity to the interesting process of pig evolution.
Porcine production is a primary market in the world economy. Controlling swine diseases in the fa... more Porcine production is a primary market in the world economy. Controlling swine diseases in the farm is essential in order to achieve the sector necessities. Aujeszky's disease is a viral condition affecting pigs and is endemic in many countries of the world, causing important economic losses in the swine industry. microRNAs (miRNAs) are non-coding RNAs which modulates gene expression in animals, plants and viruses. With the aim of understanding miRNA roles during the Aujeszky's disease virus [ADV] (also known as suid herpesvirus type 1 [SuHV-1]) infection, the expression profiles of host and viral miRNAs were determined through deep sequencing in SuHV-1 infected porcine cell line (PK-15) and in an animal experimental SuHV-1 infection with virulent (NIA-3) and attenuated (Begonia) strains. In the in vivo approach miR-206, miR-133a, miR-133b and miR-378 presented differential expression between virus strains infection. In the in vitro approach, most miRNAs were down-regulated in infected groups. miR-92a and miR-92b-3p were up-regulated in Begonia infected samples. Functional analysis of all this over expressed miRNAs during the infection revealed their association in pathways related to viral infection processes and immune response. Furthermore, 8 viral miRNAs were detected by stem loop RT-qPCR in both in vitro and in vivo approaches, presenting a gene regulatory network affecting 59 viral genes. Most described viral miRNAs were related to Large Latency Transcript (LLT) and to viral transcription activators EP0 and IE180, and also to regulatory genes regarding their important roles in the host -pathogen interaction during viral infection.
Background: High-dimensional biomolecular profiling of genetically different individuals in one o... more Background: High-dimensional biomolecular profiling of genetically different individuals in one or more environmental conditions is an increasingly popular strategy for exploring the functioning of complex biological systems. The optimal design of such genetical genomics experiments in a costefficient and effective way is not trivial.
Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software take... more Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software takes averages over probes. Important information may be lost if polymorphisms in the mRNA affect the hybridization of individual probes. We present custom software to analyze genetical genomics experiments in human, mouse and other organisms: (i) an R package providing functions for QTL analysis at the individual probe level and (ii) Perl scripts providing custom tracks in the UCSC Genome Browser to check for sequence polymorphisms in probe regions. http://gbic.biol.rug.nl/supplementary.
Genetical genomics projects accumulate on a large scale (molecular) phenotype and marker data for... more Genetical genomics projects accumulate on a large scale (molecular) phenotype and marker data for hundreds of genetically different individuals from human, mouse and C. elegans. For example, Keurentjes et al [1,2] treated expression and metabolite data from 160 Arabidopsis plants as quantitative traits and used quantitative trait locus (QTL) mapping to identify regulators (eQTLs and mQTLs) and (re)-construct regulatory and metabolic networks . Similar data have been or will be collected for other experimental populations using the same or other biomolecular methods.
We here present ATLS, a self scheduling scheme designed for execution of parallel loops in dynami... more We here present ATLS, a self scheduling scheme designed for execution of parallel loops in dynamic environments of non-dedicated networked computers. Since grid and volunteer systems based on desktop computers are proving themselves as real and powerful alternatives for ...
We here present ATLS, a self scheduling scheme designed for execution of parallel loops in dynami... more We here present ATLS, a self scheduling scheme designed for execution of parallel loops in dynamic environments of non-dedicated networked computers. Since grid and volunteer systems based on desktop computers are proving themselves as real and powerful alternatives for parallel computing, new scheduling schemes, better suited for these environments, are required. Our proposal, by tracking several performance change ratios at runtime, is able to properly adjust the load distribution using no prior information of the loop features nor the involved processors. The results obtained during the experiments performed to validate ATLS show that it is possible to improve former contributions of well-known parallel loop scheduling schemes in dynamic environments. The implementation of the scheduler has been done for the R language but, as it is exposed, it can easily be adapted to any other language and parallel loop based application.
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