Genboree Microbiome Toolset - Release Notes / Bug Fixes

  • 2/13/12
    • RDP Pipeline
      • Fixed bug that mislabels grouped metadata columns for the metadata summary output and the stacked box plots for metadata columns that have 5 or more groups of samples.
      • Upgraded heatmap output to clean the metadata labels and properly re-size the heatmap so that the labels are not cut off by the plotting area.
  • 12/21/11
    • Machine Learning - Account for 'NA' values in metadata so that R does crash while running randomForest or Boruta
    • Merging metadata with different column headers
      • We have allowed users to provide metadata files that do not have matching metadata column headers, in which we can place a default "no value" value for attributes that are not shared and merge the metadata columns which share the same metadata column header name. This is especially helpful while using other samples as controls or outliers.
  • 8/9/11
    • New utility - Remove files and or folders (Located at: Data -> Files -> Remove File(s))
  • 8/8/11
    • New tutorial produced outlining how to utilize SampleSets and shows the newest features added to the Toolset.
  • 8/4/11
    • SampleSets deployed on production server. This allows for users to link and import samples in bulk, which dramatically decreases the amount of manual work necessary.
    • We have also provided the following utilities (Located at: Data -> Samples ):
      • Add sample set
      • Delete sample set
      • Add samples to sample set
      • Remove samples from sample set
  • 8/3/11
    • Fixed bug to correctly allow users to drag across multiple folders for analysis (i.e. multiple sequence import folders for input of QIIME or RDP pipelines)
  • 8/1/11
    • RDP Pipeline - A bug was identified and fixed that incorrectly pooled taxonomic depths.
  • 7/29/11
    • Machine Learning pipeline
      • Box plots are produced for confirmed features
      • Output summary produced in xls format for OOB estimated classification error
    • QIIME Pipeline - Concentric circular phylogenetic tree visualizations produced via iTOL API
    • Sequence Import Pipeline - Output comprehensive sequence metrics in xls format
    • RDP Pipeline - Output binned stacked bar charts in PNG format
  • 7/7/11
    • Fixed bug in Sample Import tool when using a compressed file.
  • 7/1/11
    • Update to the Sequence Import tool to allow users to drag over the 'Samples' folder instead of having to manually drag over each sample.
  • 6/30/11
    • Fixed the locking of large uploaded files.
  • 6/17/11
    • Chimera Slayer deployed within QIIME pipeline.
  • 6/3/11
    • Allow users to upload files in compressed formats (.gz/bz2/xz/tar/tar.gz/tar.bz2/tar.xz/zip) or compressed archives.
  • 5/26/11
    • Alpha Diversity pipeline updated to produce remove singletons from analysis, produce PNG output files (also visible via the Project pages), and remove labels from within the plots (that are almost always cut-off or hard to read).
    • Sequece Import pipeline updated to notify user of the samples that did not contain any sequences via email.
  • 5/12/11
    • Remove samples that do not contain any sequences from the meta data mapping file. This fixes a bug in the Alpha Diversity pipeline.
  • 5/10/11
    • Update to allow users to re-link samples to a different SFF/SRA file, which alleviates the need to create a whole new database as the result of a manual linking error.
  • 5/6/11
    • Removed the low-quality window option from the Sequence Import tool for further evaluation
  • 4/11/11
    • Improved speed of Sequence Import by obtaining copy of original sequence file once per sample group rather than once per sample.
  • 4/8/11
    • Update to allow the user to list 'V1V3' or 'V3V5' as the region and not have to specifically list the distal and proximal primer. If the user provides the distal and proximal primers, we will use those, otherwise if they are not listed we will obtain the stored primer sets for specified by the 'region' field (if they exist). Also, user can provide only the proximal primer if they do not wish to trim based on the distal primer. We will add more commonly used primer sets in the future.
  • 4/7/11
    • Update to allow for PC/UNIX/MAC file formats
  • 3/25/11
    • Update to allow a user to independently upload an OTU table for the machine learning pipeline
      • Machine Learning - Manual
  • 3/8/11
    • GMT deployed to production server
      • Transfer File
      • Import Samples
      • Sample - File Linker
      • Microbiome Sequence Import
      • RDP pipeline
      • QIIME pipeline
      • Alpha Diversity pipeline
      • Machine Learning pipeline
  • 2/10/11
    • Final planning stages of GMT

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