PIMS sequencing extension: A laboratory information management system for DNA sequencing facilities

BMC Research Notes

Volumn 4, Issue , 2011, Pages

  Troshin, Peter V ^a   Postis, Vincent Lg ^b   Ashworth, Denise ^b   Baldwin, Stephen A ^b   McPherson, Michael J ^b   Barton, Geoffrey J ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

^b UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79952324298     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-4-48     Document Type: Article

References (16)

1. Kaleidaseq: a Web-based tool to monitor data flow in a high throughput sequencing facility. NN Dedhia WR McCombie, Genome Res 1998 8 313 318 9521934 (Pubitemid 28177242)
2. VSQual: a visual system to assist DNA sequencing quality control. E Binneck JFV Silva N Neumaier JRB Farias AL Nepomuceno, Genet Mol Res 2004 3 474 482 15688314 (Pubitemid 40318042)
3. MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools. C Liang F Sun H Wang J Qu RM Freeman LH Pratt M Cordonnier-Pratt, BMC Bioinformatics 2006 7 115 10.1186/1471-2105-7-115 16522212
4. preAssemble: a tool for automatic sequencer trace data processing. AA Adzhubei JK Laerdahl AV Vlasova, BMC Bioinformatics 2006 7 22 10.1186/1471-2105-7-22 16417643
5. GARSA: genomic analysis resources for sequence annotation. AMR Dvila DM Lorenzini PN Mendes TS Satake GR Sousa LM Campos CJ Mazzoni G Wagner PF Pires EC Grisard MCR Cavalcanti MLM Campos, Bioinformatics 2005 21 4302 4303 16210424 (Pubitemid 41724311)
6. Research Article Gene projects: A genome Web tool for ongoing mining and annotation applied to. MF Carazzolle EF Formighieri LA Digiampietri MRR Araujo GGL Costa GAG Pereira
7. GENOTRACE: cDNA-based local GENOme assembly from TRACE archives. E Berezikov RH Plasterk E Cuppen, Bioinformatics 2002 18 1396 1397 10.1093/bioinformatics/18.10.1396 12376385 (Pubitemid 35244198)
8. ESTPiper - a web-based analysis pipeline for expressed sequence tags. Z Tang J Choi C Hemmerich A Sarangi J Colbourne Q Dong, BMC Genomics 2009 10 174 10.1186/1471-2164-10-174 19383159
9. EST-PAGE - managing and analyzing EST data. LK Matukumalli JJ Grefenstette TS Sonstegard CP Van Tassell, Bioinformatics 2004 20 286 288 10.1093/bioinformatics/btg411 14734326 (Pubitemid 38195692)
10. Hopper: software for automating data tracking and flow in DNA sequencing. TM Smith C Abajian L Hood, Comput Appl Biosci 1997 13 175 182 9146965 (Pubitemid 27190003)
11. Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping. B Jayashree PT Reddy Y Leeladevi JH Crouch V Mahalakshmi HK Buhariwalla KE Eshwar E Mace R Folksterma S Senthilvel RK Varshney K Seetha R Rajalakshmi VP Prasanth S Chandra L Swarupa P Srikalyani DA Hoisington, BMC Bioinformatics 2006 7 383 10.1186/1471-2105-7-383 16914063
12. Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design. HI Field SA Scollen C Luccarini C Baynes J Morrison AM Dunning DF Easton PDP Pharoah, BMC Bioinformatics 2009 10 180 10.1186/1471-2105-10-180 19523221
13. Protein Information Management System. http://www.pims-lims.org
14. Laboratory information management system for membrane protein structure initiative - from gene to crystal. PV Troshin C Morris SM Prince MZ Papiz, Mol Membr Biol 2008 25 639 652 10.1080/09687680802511766 18991141
15. BBSRC Data Sharing Policy. http://www.bbsrc.ac.uk/publications/policy/ data-sharing-policy.pdf
16. CCP4 academic software licence. ftp://ftp.ccp4.ac.uk/ccp4/academic- software-licence.pdf