Dataset Information

OpenTrack simulation model files and output dataset for a copenhagen suburban railway.

ABSTRACT: This data article offers two reference simulation models for the evaluation of performance and delays of a suburban railway line. Further, a sample output dataset is provided for validation of the model, and the sample output dataset could be used independently if the reader desires. The simulation is programmed in the OpenTrack railway simulation software Nash et al., 2004 ([2]). The models are provided as a reference and tool for other researchers to validate and extend their studies in railway operations. These models were originally created for the research article "A Closed Form Railway Line Delay Propagation Model" Harrod et al., 2019 [1]. That article proposes an analytical estimation of railway delay, and these models were used to validate the findings.

SUBMITTER: Harrod S

PROVIDER: S-EPMC6562172 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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OpenTrack simulation model files and output dataset for a copenhagen suburban railway.

Harrod Steven S Cerreto Fabrizio F Nielsen Otto Anker OA

Data in brief 20190428

This data article offers two reference simulation models for the evaluation of performance and delays of a suburban railway line. Further, a sample output dataset is provided for validation of the model, and the sample output dataset could be used independently if the reader desires. The simulation is programmed in the OpenTrack railway simulation software Nash et al., 2004 ([2]). The models are provided as a reference and tool for other researchers to validate and extend their studies in railwa ...[more]

PMID: 31211202

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Project description:Background Of the different bioinformatic methods used to recover transposable elements (TEs) in genome sequences, one of the most commonly used procedures is the homology-based method proposed by the RepeatMasker program. RepeatMasker generates several output files, including the .out file, which provides annotations for all detected repeats in a query sequence. However, a remaining challenge consists of identifying the different copies of TEs that correspond to the identified hits. This step is essential for any evolutionary/comparative analysis of the different copies within a family. Different possibilities can lead to multiple hits corresponding to a unique copy of an element, such as the presence of large deletions/insertions or undetermined bases, and distinct consensus corresponding to a single full-length sequence (like for long terminal repeat (LTR)-retrotransposons). These possibilities must be taken into account to determine the exact number of TE copies. Results We have developed a perl tool that parses the RepeatMasker .out file to better determine the number and positions of TE copies in the query sequence, in addition to computing quantitative information for the different families. To determine the accuracy of the program, we tested it on several RepeatMasker .out files corresponding to two organisms (Drosophila melanogaster and Homo sapiens) for which the TE content has already been largely described and which present great differences in genome size, TE content, and TE families. Conclusions Our tool provides access to detailed information concerning the TE content in a genome at the family level from the .out file of RepeatMasker. This information includes the exact position and orientation of each copy, its proportion in the query sequence, and its quality compared to the reference element. In addition, our tool allows a user to directly retrieve the sequence of each copy and obtain the same detailed information at the family level when a local library with incomplete TE class/subclass information was used with RepeatMasker. We hope that this tool will be helpful for people working on the distribution and evolution of TEs within genomes.

Dataset Information

OpenTrack simulation model files and output dataset for a copenhagen suburban railway.

Publications

OpenTrack simulation model files and output dataset for a copenhagen suburban railway.

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