Table of Data Uploads
  Plot of Data Uploads
 
  Data Upload Methods
 
    DESCRIPTION of Methods
    Biofiles
    Data Upload Reporting
    ftp
 
  View Data, Information,
    and Analyses

 
    DESCRIPTION of Viewers
    VIMSS
      Biofiles
      data and analysis PIPELINE
      data upload REPORTS
      LIST uploaded data
      Microarray Database
      organism list
      SEARCH uploaded data
    LBNL
      LBNL Hazen Lab Data Center
      LBNL biomass production
      LBNL biomass QA/QC data
      LBNL phenotype microarray
 
  Custom Upload Interfaces
 
    LBNL Biolog
    LBNL Omnilog MT
    ORNL microarray
 
  Program/Project Links
 
    DOE Genomics:GTL
    MicrobesOnline
    VIMSS
 
  Organizations
 
    Arkin Lab
    LBNL
    UC Berkeley
  
  

VIMSS Repository for Experimental Data

The VIMSS Repository for Experimental Data consists primarily of data uploaded using the Biofiles Web interface, the Data Upload Reporting Web interface, or an ftp client, together with information about the laboratory analysis that generated the data, the data content, the data format, etc. These data upload methods are described in more detail in Description of Methods.

Several custom data upload Web interfaces also have been developed that include data processing and data display. Descriptions for these interfaces are not included, but links to the interfaces are listed in the links list to provide convenient access for current users.

A number of Web interfaces for listing, accessing, and viewing VIMSS experimental data and analysis results are available. Some of these pertain to data generated by a single lab (e.g., the Hazen Lab at LBNL) or to data analysis results for a single type of laboratory analysis (e.g., Microarray Database). Others cover the entire VIMSS project (e.g., Biofiles). The viewers listed in the links list are briefly described in Description of Viewers.

With one exception, all of the viewing and access interfaces were developed for data files uploaded through Biofiles, through the Data Upload Reporting interface, or through custom data upload interfaces developed at LBNL. Data files uploaded through other avenues are added to the VIMSS experimental data repository as time permits.Data generators are encouraged to contact the EDR team at <edr@tatooine.lbl.gov> with questions regarding uploading and providing information about data files.

N.B. Many of the links in the list are password protected. Send email to the EDR team at the address above to request access.

Summary of Experimental Data Uploaded to VIMSS ESPP Databases as of 12/31/2005
Data TypeNumber
of Uploads
Date of
Last Upload
 Lab Description/KeywordsLinks
 biomass production 83  12/13/2005  LBNL E66: DVH and JW707 on limited iron (5 µM Fe); log and stationary phases data
 electron microscopy 3  03/21/2005  LBNL SEM and TEM images: DVH, NaCl stress data
 FTIR 9  12/05/2005  LBNL FTIR spectra for biomass experiment E74 data
 growth curves 19  03/08/2005  LBNL Omnilog MT: DVH, salt (NaCl) stress, LS4D medium 
 metabolomics 11  12/03/2003  LBNL CE-MS analysis of organic acids: E. coli cell extract data
 phenotype 20  06/24/2005  LBNL Phenotype microarray for DVH mutant JW707 data
 proteomics 31  12/15/2005  Sandia Exogenous pulldown data for DvH and G20 data
 transcriptomics 30  12/12/2005  ORNL microarray: E74 biomass, DvH, oxygen stress with air and 1000 ppm oxygen analysis

Plot of Data Uploads


© 2006 The Arkin Lab | For more information about the Arkin Lab, contact Adam Arkin.
Comments/Questions | This site was last revised on May 20, 2005.