{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,1]],"date-time":"2022-04-01T21:19:48Z","timestamp":1648847988843},"reference-count":31,"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":[[2006,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Microarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, efficient production and appropriate array design are key determinants of experimental success. Inefficient production can make larger-scale studies prohibitively expensive, whereas poor array design makes normalisation and data analysis problematic.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and estimates the print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; the microtitre plate format; the printing pin configuration, and the achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>SimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. SimArray is an open-source program and is available from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.flychip.org.uk\/SimArray\/\" ext-link-type=\"uri\">http:\/\/www.flychip.org.uk\/SimArray\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-7-102","type":"journal-article","created":{"date-parts":[[2006,3,10]],"date-time":"2006-03-10T19:14:43Z","timestamp":1142018083000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["SimArray: a user-friendly and user-configurable microarray design tool"],"prefix":"10.1186","volume":"7","author":[{"given":"Richard P","family":"Auburn","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roslin R","family":"Russell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bettina","family":"Fischer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lisa A","family":"Meadows","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Santiago","family":"Sevillano Matilla","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven","family":"Russell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2006,3,1]]},"reference":[{"key":"841_CR1","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1126\/science.270.5235.467","volume":"270","author":"M Schena","year":"1995","unstructured":"Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270: 467\u2013470.","journal-title":"Science"},{"key":"841_CR2","doi-asserted-by":"publisher","first-page":"10614","DOI":"10.1073\/pnas.93.20.10614","volume":"93","author":"M Schena","year":"1996","unstructured":"Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW: Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci U S A 1996, 93: 10614\u201310619. 10.1073\/pnas.93.20.10614","journal-title":"Proc Natl Acad Sci U S A"},{"key":"841_CR3","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1046\/j.1365-2958.2000.01730.x","volume":"35","author":"RE Hayward","year":"2000","unstructured":"Hayward RE, Derisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK: Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Mol Microbiol 2000, 35: 6\u201314. 10.1046\/j.1365-2958.2000.01730.x","journal-title":"Mol Microbiol"},{"key":"841_CR4","doi-asserted-by":"publisher","first-page":"1089","DOI":"10.1046\/j.1365-2958.2003.03497.x","volume":"48","author":"A Zaigler","year":"2003","unstructured":"Zaigler A, Schuster SC, Soppa J: Construction and usage of a onefold-coverage shotgun DNA microarray to characterize the metabolism of the archaeon Haloferax volcanii. Mol Microbiol 2003, 48: 1089\u20131105. 10.1046\/j.1365-2958.2003.03497.x","journal-title":"Mol Microbiol"},{"key":"841_CR5","doi-asserted-by":"publisher","first-page":"e51","DOI":"10.1093\/nar\/30.11.e51","volume":"30","author":"A Relogio","year":"2002","unstructured":"Relogio A, Schwager C, Richter A, Ansorge W, Valcarcel J: Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res 2002, 30: e51. 10.1093\/nar\/30.11.e51","journal-title":"Nucleic Acids Res"},{"key":"841_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ygeno.2004.10.005","volume":"85","author":"TC Mockler","year":"2005","unstructured":"Mockler TC, Ecker JR: Applications of DNA tiling arrays for whole-genome analysis. Genomics 2005, 85: 1\u201315. 10.1016\/j.ygeno.2004.10.005","journal-title":"Genomics"},{"key":"841_CR7","doi-asserted-by":"publisher","first-page":"2306","DOI":"10.1126\/science.290.5500.2306","volume":"290","author":"B Ren","year":"2000","unstructured":"Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA: Genome-wide location and function of DNA binding proteins. Science 2000, 290: 2306\u20132309. 10.1126\/science.290.5500.2306","journal-title":"Science"},{"key":"841_CR8","doi-asserted-by":"publisher","first-page":"1331","DOI":"10.1038\/ng1473","volume":"36","author":"S Mukherjee","year":"2004","unstructured":"Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML: Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet 2004, 36: 1331\u20131339. 10.1038\/ng1473","journal-title":"Nat Genet"},{"key":"841_CR9","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/2524","volume":"20","author":"D Pinkel","year":"1998","unstructured":"Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998, 20: 207\u2013211. 10.1038\/2524","journal-title":"Nat Genet"},{"key":"841_CR10","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1146\/annurev.genom.6.080604.162140","volume":"6","author":"D Pinkel","year":"2005","unstructured":"Pinkel D, Albertson DG: Comparative genomic hybridization. Annu Rev Genomics Hum Genet 2005, 6: 331\u2013354. 10.1146\/annurev.genom.6.080604.162140","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"841_CR11","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/S1359-6446(05)03449-5","volume":"10","author":"A Lueking","year":"2005","unstructured":"Lueking A, Cahill DJ, Mullner S: Protein biochips: A new and versatile platform technology for molecular medicine. Drug Discov Today 2005, 10: 789\u2013794. 10.1016\/S1359-6446(05)03449-5","journal-title":"Drug Discov Today"},{"key":"841_CR12","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1016\/j.tibtech.2005.03.011","volume":"23","author":"G Chiosis","year":"2005","unstructured":"Chiosis G, Brodsky JL: Small molecule microarrays: from proteins to mammalian cells - are we there yet? Trends Biotechnol 2005, 23: 271\u2013274. 10.1016\/j.tibtech.2005.03.011","journal-title":"Trends Biotechnol"},{"key":"841_CR13","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1038\/4439","volume":"21","author":"VG Cheung","year":"1999","unstructured":"Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G: Making and reading microarrays. Nat Genet 1999, 21: 15\u201319. 10.1038\/4439","journal-title":"Nat Genet"},{"key":"841_CR14","doi-asserted-by":"crossref","first-page":"548","DOI":"10.2144\/00293bi01","volume":"29","author":"P Hegde","year":"2000","unstructured":"Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J: A concise guide to cDNA microarray analysis. Biotechniques 2000, 29: 548\u201350, 552\u20134, 556 passim.","journal-title":"Biotechniques"},{"key":"841_CR15","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1093\/bfgp\/2.1.7","volume":"2","author":"NA Affara","year":"2003","unstructured":"Affara NA: Resource and hardware options for microarray-based experimentation. Brief Funct Genomic Proteomic 2003, 2: 7\u201320. 10.1093\/bfgp\/2.1.7","journal-title":"Brief Funct Genomic Proteomic"},{"key":"841_CR16","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1016\/j.tibtech.2005.04.002","volume":"23","author":"RP Auburn","year":"2005","unstructured":"Auburn RP, Kreil DP, Meadows LA, Fischer B, Matilla SS, Russell S: Robotic spotting of cDNA and oligonucleotide microarrays. Trends Biotechnol 2005, 23: 374\u2013379. 10.1016\/j.tibtech.2005.04.002","journal-title":"Trends Biotechnol"},{"key":"841_CR17","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1093\/bioinformatics\/19.1.53","volume":"19","author":"L Wernisch","year":"2003","unstructured":"Wernisch L, Kendall SL, Soneji S, Wietzorrek A, Parish T, Hinds J, Butcher PD, Stoker NG: Analysis of whole-genome microarray replicates using mixed models. Bioinformatics 2003, 19: 53\u201361. 10.1093\/bioinformatics\/19.1.53","journal-title":"Bioinformatics"},{"key":"841_CR18","doi-asserted-by":"crossref","first-page":"42","DOI":"10.2144\/03351bm03","volume":"35","author":"J Qian","year":"2003","unstructured":"Qian J, Kluger Y, Yu H, Gerstein M: Identification and correction of spurious spatial correlations in microarray data. Biotechniques 2003, 35: 42\u20134, 46, 48.","journal-title":"Biotechniques"},{"key":"841_CR19","doi-asserted-by":"crossref","first-page":"916","DOI":"10.2144\/02334mt05","volume":"33","author":"SE Spruill","year":"2002","unstructured":"Spruill SE, Lu J, Hardy S, Weir B: Assessing sources of variability in microarray gene expression data. Biotechniques 2002, 33: 916\u201320, 922\u20133.","journal-title":"Biotechniques"},{"key":"841_CR20","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1198\/106186002317375640","volume":"11","author":"YH Yang","year":"2002","unstructured":"Yang YH, Buckley MJ, Dudoit S, Speed TP: Comparison of methods for image analysis on cDNA microarray data. J Comp Graph Stat 2002, 11: 108\u2013136. 10.1198\/106186002317375640","journal-title":"J Comp Graph Stat"},{"key":"841_CR21","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/30.4.e15","volume":"30","author":"YH Yang","year":"2002","unstructured":"Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30: e15. 10.1093\/nar\/30.4.e15","journal-title":"Nucleic Acids Res"},{"key":"841_CR22","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1093\/bib\/6.1.86","volume":"6","author":"DP Kreil","year":"2005","unstructured":"Kreil DP, Russell RR: There is no silver bullet--a guide to low-level data transforms and normalisation methods for microarray data. Brief Bioinform 2005, 6: 86\u201397. 10.1093\/bib\/6.1.86","journal-title":"Brief Bioinform"},{"key":"841_CR23","doi-asserted-by":"publisher","first-page":"1724","DOI":"10.1093\/bioinformatics\/bti199","volume":"21","author":"ME Futschik","year":"2005","unstructured":"Futschik ME, Crompton T: OLIN: optimized normalization, visualization and quality testing of two-channel microarray data. Bioinformatics 2005, 21: 1724\u20131726. 10.1093\/bioinformatics\/bti199","journal-title":"Bioinformatics"},{"key":"841_CR24","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1017\/S0016672301005055","volume":"77","author":"MK Kerr","year":"2001","unstructured":"Kerr MK, Churchill GA: Statistical design and the analysis of gene expression microarray data. Genet Res 2001, 77: 123\u2013128. 10.1017\/S0016672301005055","journal-title":"Genet Res"},{"key":"841_CR25","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1038\/ng1031","volume":"32 Suppl","author":"GA Churchill","year":"2002","unstructured":"Churchill GA: Fundamentals of experimental design for cDNA microarrays. Nat Genet 2002, 32 Suppl: 490\u2013495. 10.1038\/ng1031","journal-title":"Nat Genet"},{"key":"841_CR26","doi-asserted-by":"publisher","first-page":"e46","DOI":"10.1093\/nar\/gnh043","volume":"32","author":"L Brodsky","year":"2004","unstructured":"Brodsky L, Leontovich A, Shtutman M, Feinstein E: Identification and handling of artifactual gene expression profiles emerging in microarray hybridization experiments. Nucleic Acids Res 2004, 32: e46. 10.1093\/nar\/gnh043","journal-title":"Nucleic Acids Res"},{"key":"841_CR27","doi-asserted-by":"publisher","first-page":"5349","DOI":"10.1093\/nar\/gkh870","volume":"32","author":"N Le Meur","year":"2004","unstructured":"Le Meur N, Lamirault G, Bihouee A, Steenman M, Bedrine-Ferran H, Teusan R, Ramstein G, Leger JJ: A dynamic, web-accessible resource to process raw microarray scan data into consolidated gene expression values: importance of replication. Nucleic Acids Res 2004, 32: 5349\u20135358. 10.1093\/nar\/gkh870","journal-title":"Nucleic Acids Res"},{"key":"841_CR28","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1038\/sj.embor.7400253","volume":"5","author":"H van Bakel","year":"2004","unstructured":"van Bakel H, Holstege FC: In control: systematic assessment of microarray performance. EMBO Rep 2004, 5: 964\u2013969. 10.1038\/sj.embor.7400253","journal-title":"EMBO Rep"},{"key":"841_CR29","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1038\/nmeth1005-731","volume":"2","author":"SC Baker","year":"2005","unstructured":"Baker SC, Bauer SR, Beyer RP, Brenton JD, Bromley B, Burrill J, Causton HC, Conley MP, Elespuru R, Fero M, Foy C, Fuscoe J, Gao X, Gerhold DL, Gilles P, Goodsaid F, Guo X, Hackett J, Hockett RD, Ikonomi P, Irizarry RA, Kawasaki ES, Kaysser-Kranich T, Kerr K, Kiser G, Koch WH, Lee KY, Liu C, Liu ZL, Lucas A, Manohar CF, Miyada G, Modrusan Z, Parkes H, Puri RK, Reid L, Ryder TB, Salit M, Samaha RR, Scherf U, Sendera TJ, Setterquist RA, Shi L, Shippy R, Soriano JV, Wagar EA, Warrington JA, Williams M, Wilmer F, Wilson M, Wolber PK, Wu X, Zadro R: The External RNA Controls Consortium: a progress report. Nat Methods 2005, 2: 731\u2013734. 10.1038\/nmeth1005-731","journal-title":"Nat Methods"},{"key":"841_CR30","unstructured":"ActivePerl [ http:\/\/www.activestate.com\/ActivePerl\/]."},{"key":"841_CR31","unstructured":"SimArray [ http:\/\/www.flychip.org.uk\/SimArray ]."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-7-102.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T03:12:53Z","timestamp":1630465973000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-7-102"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,3,1]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["841"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-7-102","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,3,1]]},"assertion":[{"value":"11 October 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 March 2006","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 March 2006","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"102"}}