{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:43:49Z","timestamp":1760708629333},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux, demands an efficient way for better visualization and interpretation beyond the conventional, two-dimensional visualization tools.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We developed a 3D Cytoscape Client\/Server (3DScapeCS) plugin, which adopted Cytoscape in interpreting different types of data, and UbiGraph for three-dimensional visualization. The extra dimension is useful in accommodating, visualizing, and distinguishing large-scale networks with multiple crossed connections in five case studies.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Evaluation on several experimental data using 3DScapeCS and its special features, including multilevel graph layout, time-course data animation, and parallel visualization has proven its usefulness in visualizing complex data and help to make insightful conclusions.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-14-322","type":"journal-article","created":{"date-parts":[[2013,11,14]],"date-time":"2013-11-14T04:02:07Z","timestamp":1384401727000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["3DScapeCS: application of three dimensional, parallel, dynamic network visualization in Cytoscape"],"prefix":"10.1186","volume":"14","author":[{"given":"Qi","family":"Wang","sequence":"first","affiliation":[]},{"given":"Biao","family":"Tang","sequence":"additional","affiliation":[]},{"given":"Lifu","family":"Song","sequence":"additional","affiliation":[]},{"given":"Biao","family":"Ren","sequence":"additional","affiliation":[]},{"given":"Qun","family":"Liang","sequence":"additional","affiliation":[]},{"given":"Feng","family":"Xie","sequence":"additional","affiliation":[]},{"given":"Ying","family":"Zhuo","sequence":"additional","affiliation":[]},{"given":"Xueting","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Lixin","family":"Zhang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,11,14]]},"reference":[{"issue":"11","key":"6858_CR1","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. 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