A low-dose CT simulation technique is presented which might allow for a virtual ultra-low-dose trial in CT colonography without requiring raw sinogram data. A virtual sinogram is generated by performing the line integ...
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We demonstrated Ag/SiO2 metallic disk structure can be applied as an efficient narrow stop band filter in the IR region. The absorption spectra of such structure are investigated both theoretically and experimentally....
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作者：
Seong Yoon LimJunhyoung AhnJoon Seok LeeMin-Gon KimChan Beum ParkDepartment of Materials Science and Engineering
Korea Advanced Institute of Science and Technology (KAIST) 335 Science Road Daejeon 305-701 Korea Biomonitoring Research Center
Korea Research Institute of Bioscience and Biotechnology (KRIBB) 125 Science Road Daejeon 305-806 Korea Advanced Photonics Research Institute
Graduate Program of Photonics and Applied Physics Gwangju Institute of Science and Technology Gwangju 500-712 Korea Chan Beum Park
Department of Materials Science and Engineering Korea Advanced Institute of Science and Technology (KAIST) 335 Science Road Daejeon 305-701 Korea. Min-Gon Kim
Advanced Photonics Research Institute Graduate Program of Photonics and Applied Physics Gwangju Institute of Science and Technology Gwangju 500-712 Korea
Identifying transcription factor binding sites (TFBSs) is crucial for understanding the mechanism of transcriptional regulation. It is known that transcription factors (TFs) often cooperate to regulate genes. While tr...
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Background: In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. H...
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Background: In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions: Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability
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