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YANAsquare comes as an easy-to-setup program package in Java. It is fully compatible and integrates the programs YANA (translation of gene expression values into flux distributions, metabolite network dissection) and Metatool (elementary mode calculation). As application examples we set-up and model the phospholipid network in the phagosome and genome-scale metabolic maps of <jats:italic>S.aureus<\/jats:italic>, <jats:italic>S.epidermidis<\/jats:italic> and <jats:italic>S.saprophyticus<\/jats:italic> as well as test their robustness against enzyme impairment.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>YANAsquare is an application software for rapid setup, visualization and analysis of small, larger and genome-scale metabolic networks.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-8-313","type":"journal-article","created":{"date-parts":[[2007,8,28]],"date-time":"2007-08-28T18:12:25Z","timestamp":1188324745000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":57,"title":["Integrated network reconstruction, visualization and analysis using YANAsquare"],"prefix":"10.1186","volume":"8","author":[{"given":"Roland","family":"Schwarz","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunguang","family":"Liang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christoph","family":"Kaleta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"K\u00fchnel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eik","family":"Hoffmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sergei","family":"Kuznetsov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Hecker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gareth","family":"Griffiths","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefan","family":"Schuster","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Dandekar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,8,28]]},"reference":[{"issue":"3","key":"1685_CR1","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1021\/bp990048k","volume":"15","author":"CH Schilling","year":"1999","unstructured":"Schilling CH, Schuster S, Palsson BO, Heinrich R: Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. 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