- A Simple GUI-based Sequencing Format Conversion Tool for the Three NGS Platforms
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Rhie A, Yang S, Lee KE, Thong CT, Park HS
- KMID: 2166486
- Genomics Inform.
- 2010 Jun;8(2):97-99.
To allow for a quick conversion of the proprietary sequence data from various sequencing platforms, sequence format conversion toolkits are required that can be easily integrated into workflow systems. In... -
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- J2dpathway: A Global Metabolic Pathway Viewer with Node-Abstracting Features
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Song EH, Ham SI, Yang SD, Rhie A, Park HS, Lee SH
- KMID: 2166341
- Genomics Inform.
- 2008 Jun;6(2):68-71.
The static approach of representing metabolic pathway diagrams offers no flexibility. Thus, many systems adopt automatic graph layout techniques to visualize the topological architecture of pathways. There are weaknesses, however,... -
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- Java DOM Parsers to Convert KGML into SBML and BioPAX Common Exchange Formats
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Lee KE, Jang MH, Rhie A, Thong CT, Yang S, Park HS
- KMID: 2166485
- Genomics Inform.
- 2010 Jun;8(2):94-96.
Integrating various pathway data collections to create new biological knowledge is a challenge, for which novel computational tools play a key role. For this purpose, we developed the Java-based conversion... -
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- Refactoring the Code for Visualizing Protein Database Information in a 3D Viewer for Software Reusability
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Chun YJ, Ham SI, Yang SD, Rhie A, Park HS
- KMID: 2166322
- Genomics Inform.
- 2008 Mar;6(1):50-53.
We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier... -
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- J2.5dPathway: A 2.5D Visualization Tool to Display Selected Nodes in Biological Pathways, in Parallel Planes
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Ham SI, Song EH, Yang SD, Thong CT, Rhie A, Galbadrakh B, Lee KE, Park HS, Lee SH
- KMID: 1469578
- Genomics Inform.
- 2009 Sep;7(3):171-174.
The characteristics of metabolic pathways make them particularly amenable to layered graph drawing methods. This paper presents a visual Java-based tool for drawing and annotating biological pathways in twoand- a-half... -
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