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Biomedical research depends upon increasingly high throughput instruments and sophisticated data analytics. In spite of the significant overhead of handling research data, there is little support for researchers to manage and organize data for purposes of exploration, analysis, and ultimately publication. Shared file systems with metadata coded into directory hierarchies and spreadsheets are the common...
Shuang-Huang-Lian (SHL) is a famous modern formula prepared from three medicinal herbs including Flos Lonicerae, Radix Scutellariae and Fructus Forsythiae. Currently, SHL has been developed a variety of dosage forms due to its proved clinical efficacy. However, the in-depth research on targets and pharmacological mechanisms of SHL preparations was scarce. In the presented study, the bioinformatics...
As the model species for woody plants, the poplar has excellent experimental properties. The studies of functional genes make up the foundation of improving genetic traits and cultivating elite lines at the molecular level. Although studies of functional genes have been carried out for many years, plenty of experimental data are still scattered across documents and are not unified by a comprehensive...
Advanced Persistent Threat (APT) poses a serious threat to cyber security, and its unique high unpredictability, deep concealment and grave harmfulness make the traditional network monitoring technology facing unprecedented challenges in the background of massive and complicated network traffic. This paper aimed for the urgent demand of APT network monitoring. Relying on the rapid development of big...
Many methods have been published to prioritize genes using network theory. By using protein-protein interaction (PPI) data, it is possible to use mathematical features to rank and prioritize genes products in the network. Taking into account that genes related to the same diseases tend to connect, in the network structure, the prioritization methods search for candidate genes in the neighborhood of...
Protein sub network biomarkers for 144 diseases and pathways are analyzed in terms of protein-protein interaction (PPI) score available in STRING database. Most of the sub network biomarker (SNB) studies are to classify disease samples from the control. But no de novo algorithm is available to identify SNB from the whole genome PPI network without the knowledge of differentially expressed genes. Recently,...
Multiple biological sequences alignment like protein sequences or DNA/RNA in order to discover the functions, structures and evolutionary relationships among species and also discovering drugs is a fundamental study in bioinformatics. Unfortunately the multiple sequence alignment is a NP-complete problem and the reliability of the existing algorithms is not so high. The objective of our study was...
Recent advancement of technologies in the field of bioinformatics and pattern recognition provides the opportunities for researchers and scientists to explore in depth the thermal human face image signals and to convert information into a meaningful knowledge through computational-based models, for the task of identification and recognition. Despite successes in indoor access control applications,...
Biometric measurements are now often routinely adopted as a robust means of determining individual identity. Such an approach is clearly beneficial in a variety of scenarios, including those relating to medical environments. In the medical context, however, the use of biometric data can potentially offer other valuable opportunities for harnessing the power of biometrics which have a more direct bearing...
Latest medical diagnostics generate increasing amounts of big medical data. Specific software tools optimized for the use by healthcare experts and researchers as well as systematic processes for data processing and analysis in clinical and research environments are still missing. Our work focuses on the integration of high-throughput next-generation sequencing data and its systematic processing and...
Nowadays, a growing number of researchers devote themselves to re-excavation of existing biomedical knowledge discovery, focusing on how to establish associations between clinical and genomic data. However, quantitative analysis is still inadequate for a particular disease. Colorectal cancer is the one of malignant tumors whose molecular mechanism is relatively clear, making it a more appropriate...
Today, many high performance computing platforms use hybrid architectures combining multi-core processors and hardware accelerators like GPUs (Graphic Processing Units). This paper presents a new method for scheduling tasks for biological sequence comparison applications with CPUs and GPUs. This strategy is called SWDUAL and is based on a dual approximation scheme for determining which tasks are most...
The well-known Smith-Waterman (SW) algorithm is a high-sensitivity method for local alignments. However, SW is expensive in terms of both execution time and memory usage, which makes it impractical in many applications. Some heuristics are possible but at the expense of losing sensitivity. Fortunately, previous research have shown that new computing platforms such as GPUs and FPGAs are able to accelerate...
This paper deals with the similarity of fingerprints of family members. The paper is divided into two parts, the first part introduces biometrics, then the oldest methods of biometric identification, which are fingerprints. The second part describes the experiment, which compared the similarity of fingerprints of family members and subsequent evaluation of the results obtained during the experiment.
BLAST[1] (Basic Local Alignment Search Tool) is a suite of programs used to identify similarity between genetic sequences. It is one of the most widely used tools in Bioinformatics. In recent years, with the size of gene and protein sequence database increasing exponentially, BLAST has become both a data-intensive and a computation-intensive application. How to run BLAST rapidly with low cost has...
Mass data has accumulated with the development of DNA barcoding technology for purpose of rapid identification using biological material samples. This is prepared for construction of the big phylogenetic tree including numerous species, but also raises a difficult question how to locate in the tree quickly using sample sequence representing the specific species. This paper presents a solution based...
With the growing numbers of both parallel architectures and related programming models, the benchmarking tasks become very tricky since parallel programming requires architecture-dependent compilers and languages as well as high programming expertise. More than just comparing architectures with synthetic benchmarks, benchmarking is also more and more used to design specialized systems composed of...
Finding associated Single nucleotide polymorphism (SNP) for complex diseases has been the goal of many genetic studies. By screening candidate SNPs and by performing genome wide association studies (GWAS), we can get risk loci of specific diseases. Case-control study is a kind of important method in this field. However, most of case-control studies are suffering from the puzzle that sample is too...
The last decade has seen the development of a variety of so-called ‘next-generation’ sequencing (NGS) technologies, that have revolutionized the field of genomics and post-genomics. In cancer research area, as NGS permeates the cancer biomarker realm and cost of NGS declines, hospitals and clinics will deploy deep sequencing as a means to personalize cancer diagnostics and therapeutics. Here we provide...
In this paper we present grid services for the biomolecular community offered by the Polish National Grid (Polish NGI). This work is motivated by the fact that in many application areas including life sciences there is increasing demand for disk space and computer power to store and process data. Emerging technologies such as Next Generation Sequencing (NGS) put additional stress on this demand. The...
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