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https://www.readbyqxmd.com/read/28540698/introduction-on-using-the-fastpcr-software-and-the-related-java-web-tools-for-pcr-and-oligonucleotide-assembly-and-analysis
#1
Ruslan Kalendar, Timofey V Tselykh, Bekbolat Khassenov, Erlan M Ramanculov
This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-distance, inverse, real-time, group-specific, unique, overlap extension PCR for multi-fragments assembling cloning and loop-mediated isothermal amplification (LAMP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540697/in-silico-pcr-tools-for-a-fast-primer-probe-and-advanced-searching
#2
Ruslan Kalendar, Alexandr Muterko, Malika Shamekova, Kabyl Zhambakin
The polymerase chain reaction (PCR) is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. The principle of this technique has been further used and applied in plenty of other simple or complex nucleic acid amplification technologies (NAAT). In parallel to laboratory "wet bench" experiments for nucleic acid amplification technologies, in silico or virtual (bioinformatics) approaches have been developed, among which in silico PCR analysis. In silico NAAT analysis is a useful and efficient complementary method to ensure the specificity of primers or probes for an extensive range of PCR applications from homology gene discovery, molecular diagnosis, DNA fingerprinting, and repeat searching...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28535294/hgva-the-human-genome-variation-archive
#3
Javier Lopez, Jacobo Coll, Matthias Haimel, Swaathi Kandasamy, Joaquin Tarraga, Pedro Furio-Tari, Wasim Bari, Marta Bleda, Antonio Rueda, Stefan Gräf, Augusto Rendon, Joaquin Dopazo, Ignacio Medina
High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion...
May 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28534871/development-of-a-gridded-meteorological-dataset-over-java-island-indonesia-1985-2014
#4
Yanto, Ben Livneh, Balaji Rajagopalan
We describe a gridded daily meteorology dataset consisting of precipitation, minimum and maximum temperature over Java Island, Indonesia at 0.125°×0.125° (~14 km) resolution spanning 30 years from 1985-2014. Importantly, this data set represents a marked improvement from existing gridded data sets over Java with higher spatial resolution, derived exclusively from ground-based observations unlike existing satellite or reanalysis-based products. Gap-infilling and gridding were performed via the Inverse Distance Weighting (IDW) interpolation method (radius, r, of 25 km and power of influence, α, of 3 as optimal parameters) restricted to only those stations including at least 3,650 days (~10 years) of valid data...
May 23, 2017: Scientific Data
https://www.readbyqxmd.com/read/28520890/vcf-filter-interactive-prioritization-of-disease-linked-genetic-variants-from-sequencing-data
#5
Heiko Müller, Raul Jimenez-Heredia, Ana Krolo, Tatjana Hirschmugl, Jasmin Dmytrus, Kaan Boztug, Christoph Bock
Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28508804/ehealth-networking-information-systems-the-new-quality-of-information-exchange
#6
Karin Messer-Misak, Christoph Reiter
BACKGROUND: The development and introduction of platforms that enable interdisciplinary exchange on current developments and projects in the area of eHealth have been stimulated by different authorities. OBJECTIVES: The aim of this project was to develop a repository of eHealth projects that will make the wealth of eHealth projects visible and enable mutual learning through the sharing of experiences and good practice. METHODS: The content of the database and search criteria as well as their categories were determined in close co-ordination and cooperation with stakeholders from the specialist areas...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28508782/the-use-of-restful-web-services-in-medical-informatics-and-clinical-research-and-its-implementation-in-europe
#7
Jozef Aerts
BACKGROUND: RESTful web services nowadays are state-of-the-art in business transactions over the internet. They are however not very much used in medical informatics and in clinical research, especially not in Europe. OBJECTIVES: To make an inventory of RESTful web services that can be used in medical informatics and clinical research, including those that can help in patient empowerment in the DACH region and in Europe, and to develop some new RESTful web services for use in clinical research and regulatory review...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28508774/arden-syntax-mlm-building-blocks-for-microbiological-concepts-and-their-application-in-infection-surveillance
#8
Jeroen S de Bruin, Walter Koller, Julia Zeckl, Alexander Blacky, Andrea Rappelsberger, Klaus-Peter Adlassnig
BACKGROUND: The diagnosis - and hence definitions - of healthcare-associated infections (HAIs) rely on microbiological laboratory test results in specific constellations. OBJECTIVES: To construct a library that provides interoperable building blocks for the analysis of microbiological laboratory test results. METHODS: We used Java for preprocessing raw microbiological laboratory test results and Arden Syntax for knowledge-based querying of data based on microbiology information elements used in European surveillance criteria for HAIs...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28507416/pathotypic-characterization-of-newcastle-disease-virus-isolated-from-vaccinated-chicken-in-west-java-indonesia
#9
Dwi Desmiyeni Putri, Ekowati Handharyani, Retno Damajanti Soejoedono, Agus Setiyono, Ni Luh Putu Ika Mayasari, Okti Nadia Poetri
AIM: This research was conducted to differentiate and characterize eight Newcastle disease virus (NDV) isolates collected from vaccinated chicken at commercial flocks in West Java, Indonesia, in 2011, 2014 and 2015 by pathotype specific primers. MATERIALS AND METHODS: A total of eight NDV isolates collected from clinical outbreaks among commercial vaccinated flocks in West Java, Indonesia, in 2011, 2014, and 2015 were used in this study. Reverse transcription-polymerase chain reaction was used to detect and differentiate virulence of NDV strains, using three sets of primers targeting their M and F gene...
April 2017: Veterinary World
https://www.readbyqxmd.com/read/28505226/omtools-a-software-package-for-visualizing-and-processing-optical-mapping-data
#10
Alden King-Yung Leung, Nana Jin, Kevin Y Yip, Ting-Fung Chan
Summary: Optical mapping is a molecular technique capturing specific patterns of fluorescent labels along DNA molecules. It has been widely applied in assisted-scaffolding in sequence assemblies, microbial strain typing, and detection of structural variations. Various computational methods have been developed to analyze optical mapping data. However, existing tools for processing and visualizing optical map data still have many shortcomings. Here we present OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles...
May 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28503667/neopeptide-analyser-a-software-tool-for-neopeptide-discovery-in-proteomics-data
#11
Mandy Peffers, Andrew R Jones, Antony McCabe, James Anderson
Experiments involving mass spectrometry (MS)-based proteomics are widely used for analyses of connective tissues. Common examples include the use of relative quantification to identify differentially expressed peptides and proteins in cartilage and tendon. We are working on characterising so-called 'neopeptides', i.e. peptides formed due to native cleavage of proteins, for example under pathological conditions. Unlike peptides typically quantified in MS workflows due to the in vitro use of an enzyme such as trypsin, a neopeptide has at least one terminus that was not due to the use of trypsin in the workflow...
April 7, 2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28502701/fastpcr-an-in-silico-tool-for-fast-primer-and-probe-design-and-advanced-sequence-analysis
#12
Ruslan Kalendar, Bekbolat Khassenov, Erlan Ramanculov, Olga Samuilova, Konstantin I Ivanov
Polymerase chain reaction (PCR) is one of the most important laboratory techniques used in molecular biology, genetics and molecular diagnostics. The success of a PCR-based method largely depends on the correct nucleic acid sequence analysis in silico prior to a wet-bench experiment. Here, we report the development of an online Java-based software for virtual PCR on linear or circular DNA templates and multiple primer or probe search from large or small databases. Primer or probe sensitivity and specificity are predicted by searching a database to find sequences with an optimal number of mismatches, similarity and stability...
May 11, 2017: Genomics
https://www.readbyqxmd.com/read/28490704/-establishement-for-regional-pelvic-trauma-database-in-hunan-province
#13
Liang Cheng, Yong Zhu, Haitao Long, Junxiao Yang, Buhua Sun, Kanghua Li
To establish a database for pelvic trauma in Hunan Province, and to start the work of multicenter pelvic trauma registry.
 Methods: To establish the database, literatures relevant to pelvic trauma were screened, the experiences from the established trauma database in China and abroad were learned, and the actual situations for pelvic trauma rescue in Hunan Province were considered. The database for pelvic trauma was established based on the PostgreSQL and the advanced programming language Java 1.6.
 Results: The complex procedure for pelvic trauma rescue was described structurally...
April 28, 2017: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/28475668/mardre-efficient-mapreduce-based-removal-of-duplicate-dna-reads-in-the-cloud
#14
Roberto R Expósito, Jorge Veiga, Jorge González-Domínguez, Juan Touriño
Summary: This paper presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single-end and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted MapReduce programming model to fully exploit Big Data technologies on cloud-based infrastructures. Written in Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for scalable Big Data processing...
May 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28472503/dssr-enhanced-visualization-of-nucleic-acid-structures-in-jmol
#15
Robert M Hanson, Xiang-Jun Lu
Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures...
May 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28469418/pisma-a-visual-representation-of-motif-distribution-in-dna-sequences
#16
Rogelio Alcántara-Silva, Moisés Alvarado-Hermida, Gibrán Díaz-Contreras, Martha Sánchez-Barrios, Samantha Carrera, Silvia Carolina Galván
BACKGROUND: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code-like, as a gene-map-like, and as a transcript scheme. RESULTS: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28466451/multiscale-assessment-of-progress-of-electrification-in-indonesia-based-on-brightness-level-derived-from-nighttime-satellite-imagery
#17
Fatwa Ramdani, Putri Setiani
Availability of electricity can be used as an indicator to proximate parameters related to human well-being. Overall, the electrification process in Indonesia has been accelerating in the past two decades. Unfortunately, monitoring the country's progress on its effort to provide wider access to electricity poses challenges due to inconsistency of data provided by each national bureau, and limited availability of information. This study attempts to provide a reliable measure by employing nighttime satellite imagery to observe and to map the progress of electrification within a duration of 20 years, from 1993 to 2013...
June 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/28464826/microtaboo-a-general-and-practical-solution-to-the-k-disjoint-problem
#18
Mohammed Al-Jaff, Eric Sandström, Manfred Grabherr
BACKGROUND: A common challenge in bioinformatics is to identify short sub-sequences that are unique in a set of genomes or reference sequences, which can efficiently be achieved by k-mer (k consecutive nucleotides) counting. However, there are several areas that would benefit from a more stringent definition of "unique", requiring that these sub-sequences of length W differ by more than k mismatches (i.e. a Hamming distance greater than k) from any other sub-sequence, which we term the k-disjoint problem...
May 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28453986/facilitating-smallholder-tree-farming-in-fragmented-tropical-landscapes-challenges-and-potentials-for-sustainable-land-management
#19
Syed Ajijur Rahman, Terry Sunderland, James M Roshetko, John Robert Healey
Under changing land use in tropical Asia, there is evidence of forest product diversification through implementation of tree-based farming by smallholders. This paper assesses in two locations, West Java, Indonesia and eastern Bangladesh, current land use conditions from the perspective of smallholder farmers, the factors that facilitate their adoption of tree farming, and the potential of landscape-scale approaches to foster sustainable land management. Data were collected through rapid rural appraisals, focus group discussions, field observations, semi-structured interviews of farm households and key informant interviews of state agricultural officers...
April 25, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28452236/mobile-access-to-virtual-randomization-for-investigator-initiated-trials
#20
Thomas M Deserno, András P Keszei
Background/aims Randomization is indispensable in clinical trials in order to provide unbiased treatment allocation and a valid statistical inference. Improper handling of allocation lists can be avoided using central systems, for example, human-based services. However, central systems are unaffordable for investigator-initiated trials and might be inaccessible from some places, where study subjects need allocations. We propose mobile access to virtual randomization, where the randomization lists are non-existent and the appropriate allocation is computed on demand...
April 1, 2017: Clinical Trials: Journal of the Society for Clinical Trials
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