Pathomx: An interactive workflow-based tool for the analysis of metabolomic data

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Fitzpatrick, Martin A ^a   McGrath, Catherine M ^a   Young, Stephen P ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

Analysis; Automation; Metabolomics; Nmr; Omics; Python; Visualisation; Workflow

Indexed keywords

AUTOMATION; COMPUTER PROGRAMMING; COMPUTER SOFTWARE REUSABILITY; MAMMALS; MATLAB; METABOLITES; MOBILE SECURITY; NUCLEAR MAGNETIC RESONANCE; VISUALIZATION;

ANALYSIS; METABOLOMICS; OMICS; PYTHON; WORKFLOW;

DATA HANDLING;

MAMMALIA;

BIOLOGY; CELL CULTURE; COMPUTER PROGRAM; CYTOLOGY; FACTUAL DATABASE; HUMAN; MACROPHAGE; METABOLISM; METABOLOMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROCEDURES; REPRODUCIBILITY; WORKFLOW;

CELLS, CULTURED; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; HUMANS; MACROPHAGES; MAGNETIC RESONANCE SPECTROSCOPY; METABOLIC NETWORKS AND PATHWAYS; METABOLOMICS; REPRODUCIBILITY OF RESULTS; SOFTWARE; WORKFLOW;

EID: 84924020376     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-014-0396-9     Document Type: Article

References (24)

1. Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB: Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol 2004, 22:245-252.
2. Armitage EG, Barbas C: Metabolomics in cancer biomarker discovery: Current trends and future perspectives. J Pharm. Biomed Anal 2013.
3. Fitzpatrick M, Young SP: Metabolomics - a novel window into inflammatory disease. Swiss Med Wkly 2013, 143:1-12.
4. Salek RM, Haug K, Conesa P, Hastings J, Williams M, Mahendraker T, Maguire E, González-Beltrán AN, Rocca-Serra P, Sansone S-A, Steinbeck C: The MetaboLights repository: curation challenges in metabolomics. Database (Oxford) 2013, 2013:bat029.
5. Ludwig C, Günther UL: MetaboLab-advanced NMR data processing and analysis for metabolomics. BMC Bioinformatics 2011, 12:366.
6. Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, Liu Y, Djoumbou Y, Mandal R, Aziat F, Dong E, Bouatra S, Sinelnikov I, Arndt D, Xia J, Liu P, Yallou F, Bjorndahl T, Perez-Pineiro R, Eisner R, Allen F, Neveu V, Greiner R, Scalbert A: HMDB 3.0-The Human Metabolome Database in 2013. Nucleic Acids Res 2013, 41:D801-D807.
7. Curcin V, Ghanem M: Scientific workflow systems - can one size fit all? Cairo Int Biomed Eng Conf 2008, 2008:1-9. 18-20 December.
8. Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P: Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004, 20:3045-3054.
9. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A: Galaxy: a platform for interactive large-scale genome analysis. Genome Res 2005, 15:1451-1455.
10. Xia J, Mandal R, Sinelnikov IV, Broadhurst D, Wishart DS: MetaboAnalyst 2.0-a comprehensive server for metabolomic data analysis. Nucleic Acids Res 2012, 40:W127-W133.
11. Hunter JD: Matplotlib: a 2D graphics environment. Comput Sci Eng 2007, 9:90-95.
12. Oliphant TE: Python for scientific computing. Comput Sci Eng 2007, 9:10-20.
13. Pedregosa F, Weiss R, Brucher M: Scikit-learn: machine learning in python. J Mach Learn Res 2011, 12:2825-2830.
14. Helmus JJ, Jaroniec CP: Nmrglue: an open source Python package for the analysis of multidimensional NMR data. J Biomol NMR 2013, 55:355-367.
15. Savorani F, Tomasi G, Engelsen SB: Icoshift: a versatile tool for the rapid alignment of 1D NMR spectra. J Magn Reson 2010, 202:190-202.
16. Gansner E, North SC: An open graph visualization system and its applications to software engineering. Softw - Pract Exp 1999, 00:1-5.
17. Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone S-A, Griffin JL, Steinbeck C: MetaboLights-an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res 2013, 41:D781-D786.
18. Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30:207-210.
19. Trupp M, Altman T, Fulcher CA, Caspi R, Krummenacker M, Paley S, Karp PD: Beyond the genome ( BTG ) is a ( PGDB ) pathway genome databasets. HumanCyc 2010, 11:2010.
20. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012, 40:D109-D114.
21. Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M: Reconciliation of metabolites and biochemical reactions for metabolic networks. Brief Bioinform 2014, 15:123-135.
22. Wu H, Southam AD, Hines A, Viant MR: High-throughput tissue extraction protocol for NMR- and MS-based metabolomics. Anal Biochem 2008, 372:204-212.
23. Ludwig C, Easton J, Lodi A, Tiziani S, Manzoor S, Southam A, Byrne J, Bishop L, He S, Arvanitis T, Günther U, Viant M: Birmingham Metabolite Library: a publicly accessible database of 1-D 1H and 2-D 1H J-resolved NMR spectra of authentic metabolite standards (BML-NMR). Metabolomics 2012, 8:8-18.
24. Tulpan D, Léger S, Belliveau L, Culf A, Čuperlović-Culf M: MetaboHunter: an automatic approach for identification of metabolites from 1H-NMR spectra of complex mixtures. BMC Bioinformatics 2011, 12:400.