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McGill University TMIC

Update History:

  • Added support for peak filtering based on QC samples for untargeted metabolomics (03/10/2017);
  • Added support for "flipping" PCA for cross-study comparison (02/09/2017);
  • Added support for network summary of enrichment analysis result (02/06/2017);
  • Fixed the bug in feature table display in Biomarker Tester module (01/05/2017);
  • Updated pathway result table to show all pathway compounds (with hits highlighted) (11/25/2016);
  • Improved Normalization and Data Editor for better user experience (11/15/2016);
  • Added support for sparse PLS-DA analysis (10/28/2016);
  • Minor bug fix and performance tuning (09/15/2016);
  • Fixed the issue for t-tests plotting (09/09/2016);
  • Added support for quantile normalization (08/29/2016);
  • Improved name mapping functions for common metabolite names (08/18/2016)
  • Joint-pathway analysis was back to work (08/01/2016)
  • Updated PCA to perform default data centering (07/28/2016)
  • Code refactoring to improve memory efficiency (07/20/2016)
  • More than 1 million jobs have been processed since 06/2015 (06/15/2016)
  • Updated Time Series module to support analysis of time-series only data (06/08/2016);
  • Added support for Orthogonal PLS-DA (05/16/2016);
  • Improved support for dealing with special characters and punctuations (05/11/2016);
  • Added support for batch effect correction for multiple data sets (Other Utilities module) (02/22/2016);
  • Upgraded the web framework for better performance (02/18/2016);
  • Updated the Google Cloud server for improved performance (10/30/2015);
  • Added support for detailed ROC curve analysis of individual biomakers (10/29/2015);
  • Several feature improvements and bug fixes based on user feedback (10/16/2015);
  • Added support for logistic regression in ROC Tester (08/12/2015);
  • Added support for computing compound ratios in biomarker analysis (08/03/2015);
  • Minor bug fixes and feature enhancements (data IO, PLS-DA, enrichment analysis) to deal with special cases in user inputs (07/20/2015);
  • Updated Multivariate Biomarker Analysis module with flexible interface and improved capacity for computing on large datasets (06/05/2015);
  • MetaboAnalyst now has its logo image (top right) (05/15/2015)
  • MetaboAnalyst 3.0 paper is now available on the 2015 NAR web server issue
  • Users can now specify symbols in the PCA/PLSDA scores plots (under Image options - previous Color picker) (04/20/2015)
  • The loading plots in PCA and PLS-DA are now clickable and zoomable (04/02/2015)
  • T-tests and ANOVA results, as well as volcano plot are now interactive and zoomable (03/31/2015)
  • Updated heatmaps to support both overview and high resolution details view (03/25/2015)
  • Users can now upload either tab delimited file (.txt) or csv file (03/20/2015)
  • Updated data filter to permit feature-specific normalization on low variance features (03/19/2015)
  • Updated dendrogram for better visualization and minor bug fixes (03/14/2015)
  • Bug fixes for feature-specific normalization and fold changes analysis (03/13/2015)
  • Minor bug fixes for two factor and time-series data analysis (03/04/2015)
  • Enhanced support on building biomarker models for predicting new samples under ROC Tester (02/06/2015);
  • Updated the confidence interval graphics for PCA, PLSDA and ROC curves; (01/06/2015)
  • Updated the Heatmaps function for better visualization of large data; (12/22/2014)
  • Added a new module for Integrated Pathway Analysis on genes and metabolites that have changed significantly under the same experimental conditions; (12/17/2014)
  • Added a new module for Biomarker Analysis; (12/12/2014)
  • Added sorting and filtering support in the feature details table; (11/12/2014)
  • Fixed a bug on broken functions after missing value imputation; (11/10/2014)
  • PCA and PLSDA 3D plots now are interactive; (10/31/2014)
  • A new module (Power Analysis) is added to support sample size and power analysis for pilot metabolomic studies; (10/30/2014)
  • Added Compound ID conversion support (under Other Utilities); (10/24/2014)
  • Added support for uploading custom metabolite sets and custom metabolome in Enrichment and Pathway analyses; (10/20/2014)
  • Fixed the dialog issue in compound name mapping; (10/17/2014)
  • Added support for labeling PCA/PLSDA loadings plot; (10/09/2014)
  • Added pathway analysis support for Schistosoma mansoni, Malaria, Trypanosoma brucei and Synechococcus elongatus; (09/30/2014)
  • Updated compound name mapping algorithm for improved performance; (09/29/2014)
  • Updated compound and pathway IDs based on the latest HMDB and SMPDB; (09/12/2014)
  • Users can now edit or re-order groups under Data Editor page; (08/26/2014)
  • Updated FAQs for recent changes; (08/08/2014)
  • Added a new tutorial on raw spectra processing using XCMS for MetaboAnalyst; (08/04/2014)
  • Completely upgraded the web application framework for better performance and user experience; (07/28/2014)
  • Fixed color reversing issue with PLS-DA VIP plot; (07/15/2014)
  • Updated two-way ANOVA for repeated measures; (06/05/2014)
  • Updated VIP plot for supporting black and white colors; (02/05/2014)
  • Added nonparametric version for t-tests and ANOVA, and minor bug fix; (02/22/2013)
  • Added support for heatmaps on grayscale; added link to download the underlying matrix for correlation heatmaps. (08/25/2012)
  • Presentation at the 8th Metabolomics Conference at Washington DC is available under Tutorial; (07/04/2012)
  • Updated Data Filtering and Data Normalization procedures; (07/03/2012)
  • Updated compound database; (06/22/2012)
  • Updated correlation heatmap analysis; (05/27/2012)
  • Pathway analysis now supports Mesorhizobium loti and Gallus gallus (chicken); (05/10/2012)
  • Minor bug fix and updates; (03/29/2012)
  • Pathway analysis now supports Gallus gallus (chicken); (03/18/2012)
  • Fixed missing link to high-resolution images generated for pathways. (03/03/2012)
  • Updated correlation heatmaps and some minor bug fixes. (02/16/2012)
  • Minor update and bug fix; (01/05/2012)
  • Added a new module for data quality check - available at QC and Other Utilities tab on the data upload page(01/02/2012);
  • All important images can be reproduced in high resolution (150/300/600 DPI) in PNG, TIFF, PostScript, SVG, or PDF format. Just click the above each image! (12/31/2011);
  • Updated Bioconductor to the latest version (2.9) and performed compatibility tests(12/17/2011);
  • Upgraded R to the latest version (2.14.0) and some visual enhancement (11/26/2011);
  • Added correlation heatmap visualization feature (under correlation node, 10/08/2011);
  • Enhanced support for univariate analysis and minor bug fixes (09/14/2011);
  • Minor bug fixes and some visual improvements (08/10/2011);
  • Updated graphical output for PLS-DA VIP plot (07/23/2011);
  • Minor bug fixes and some visual improvements (06/23/2011);
  • Added a new module for two-factor and time-series data analysis (05/12/2011);
  • MetaboAnalyst is featured on Nature Protocols (05/10/2011)
  • Enhanced support for Heatmap generation (03/03/2011);
  • Added two normalization methods - normalization to sample median and quantile normalization based on recent publications (02/26/2011);
  • Added an Outlier detection tab for data analysis using Random Forest (02/08/2011);
  • Added a Color picker (under Processing node) for setting colors for figures (02/07/2011);
  • Fixed several broken functions based on user feedback (02/06/2011);
  • Improved message output and minor bug fix due to some package updates (02/02/2011);
  • Added a Data filter function for large data with many noisy features (02/02/2011);
  • All significant features are now available as text files in the Download page (02/01/2011);
  • Fixed the issue with reading CSV files generated by Miscrosoft Excel (12/6/2010);
  • MetaboAnalyst server has been upgraded, let us know if you experience any problems (12/5/2010);
  • PLS-DA now calculates R2 and Q2 values in the Cross Validation section. (09/28/2010);
  • Upgraded unzip function to better support files created with WinZip (09/27/2010);
  • Fixed the image update issue associated with the new server (09/18/2010);
  • MetaboAnalyst is now hosted on a dedicated new, powerful server (09/12/2010);
  • Added support for applying a reference metabolome for enrichment analysis and pathway analysis. (09/08/2010);
  • Added Correlation Analysis to identify significant features with patterns of interests (09/05/2010);
  • MetaboAnalyst now supports metabolite set enrichment analysis and pathway analysis (09/01/2010);
  • Updated the error tracking system (07/18/2010);
  • High resolution (300 dpi) images are available for score or loadings plots from PCA and PLSDA analysis (07/17/2010);
  • PLSDA permutation test now supports multi-group data (07/14/2010);
  • Updated the pathway library to use SMPDB (07/13/2010);
  • Improved 3D visualization for PCA and PLSDA results (07/12/2010);
  • MetaboAnalyst was presented on the the Metabolomics Conference 2010 (Amsterdam, The Netherlands) (download slides)(07/09/2010);
  • Fixed the data upload problem encountered for transposed data (samples in columns, features in rows) and for paired comparison (07/07/2010) ;
  • Bug fix: Color inconsistencies b/w the confidence ellipses and sample class labels (used in PCA abd PLS-DA 2D plot)(06/17/2010) ;
  • Updated the interface for zip file upload to support multiple-group analysis of peak lists and spectra data (06/15/2010) ;
  • Introducing Data Editor to support samples/features exclusion (i.e. outliers) during analysis (06/14/2010) ;
  • Updated documentations and reports for multi-group analysis (06/11/2010) ;
  • Added a new function - Analysis of Variance (ANOVA) and associated post-hoc methods for multi-group analysis (06/10/2010) ;
  • Enhanced PLS-DA support for multi-group analysis (06/05/2010);
  • MetaboAnalyst now supports data analysis for more than two groups. (06/01/2010);
  • For data collected from human or other mammalian species, you may also want to visit our new web application MSEA (http://www.msea.ca) for more advanced data analysis. (05/11/2010);
  • Improved graphics for PCA and PLSDA result (03/21/2010);
  • MetaboAnalyst is now hosted on a new and powerful server (01/31/2010);
  • Fixed t-tests errors on constant values (01/31/2010);
  • Added functions to plot 2D confidence regions for PCA and PLS-DA scores plots (12/12/2009);
  • MetaboAnalyst tutorial presented on the Metabolomics Conference 2009 (Edmonton, Canada) (download slides)(09/12/2009);
  • MetaboAnalyst is now hosted on Tomcat (02/06/2009);
  • PLS-DA now provides p value based on permutations (20/05/2009);
  • Integrity check added for sample/feature names (28/05/2009);
  • High-resolution images for heatmap and dendrogram are available (15/05/2009);
  • Improved function for unzipping compressed data (.zip) (10/05/2009);