Release Notes

ImmPort Version 2.29
Released September 1, 2015
  • Updated Data submission, validator, and web service to
    • The subjectsHuman.txt template column 'Population(s)' has been modified to 'Ancestry Population(s)'
    • Accepting '.lmd' files as flow_cytometry result files.
    • Restricted the names of files uploaded must be 240 characters.
    • Removed Sample Type column in expSample.ELISA and ELISA_Result template
    • Removed experiment sample ID from flowTextFiles.txt
    • Replaced column header column name 'Detector Name' for templates reagents.flow_cytometry.txt and reagents.mass_cytometry.txt to 'Clone Name'.
    • A new treatment amount unit IU and units/mL
ImmPort Version 2.28
Released May 1, 2015
  • Data Submission
    • Development of an administrative application called ImmPort Sharing to help our team member with VPN access more efficiently share data from private workspace to public.
    • The ImmPort Curation tool is being updated to use new login framework.
    • Updated Data submission, validator, and web service to
      • added support for assessment and assessment components in the clinical data schema
      • provide consolidated templates to ease submission of summarized assay data
      • Improved automated de-identification of FCS result files
      • upgrade to Java 1.8
    • Data Validator
      • Modified the data validator to accept the new submission templates.
ImmPort Version 2.27
Released December 19, 2014
  • Data Submission
    • A column was added in the assay result tables to capture the preferred strain names provided by HIPC.
    • The Virus_Neutralization_Results and HAI_Results templates were modified to display the preferred values.
    • A flow text file for .fcs version 3.1 has been added.
    • Modified the system to disallow the string ?NaN? as a legitimate floating value, and reports a numeric error. All other forms of floating point values are successfully converted and storable in Oracle.
    • Updated code for extracting .fcs header files to accept missing keyword values, incorrect segment coordinates, avoiding loading the data and analysis segments.
    • Created a script that will make the file names in a directory structure unique and generate a report indicating what file have changed and how their names have changed.
    • Added additional values to the sample type table to allow for values to be accepted into the system.
    • Added new measurement technique values.
  • Data Validator
    • Modified the data validator to accept the new submission templates.
ImmPort Version 2.26
Released October 30, 2014
  • Data Submission
    • Enabled a list of HIPC preferred cell population names and gating definitions in flow and cytof derived data capture.
    • Created a lab test panel and lab test xml specified uploader templates and parser.
    • Added a comment column to the assay result.
    • Modified submission templates to remove empty rows.
  • Data Validator
    • Modified the data validator to accept the new submission templates.
  • Outreach
    • Added YouTube Videos.
    • Enhanced the News and Events.
ImmPort Version 2.25
Released September 3, 2014
  • Data Submission
    • Developed a non-ZIP based batch upload process for large file uploads.
    • Developed a process to associate a distinct age to each study for the subject.
    • Created an adverse events xml specified uploader template and parser.
    • Created a substance_merge xml specified uploader template and parser.
    • Created a cytof_derived_data.txt template.
    • Standardized file name columns to 250 bytes.
    • The Protocol Name column is now required within protocol.txt.
  • Data Validator
    • Modified the data validator to accept large files.
    • The new data validator will be a locally installed web application using embedded Tomcat and the latest Java and Spring.
    • Data Curation Tool
      • Enable sort by query parameter.
      • Enhanced the help topics.
      • Modified the curation tool to remove the description from Planned Visit Headings
ImmPort Version 2.24
Released June 13, 2014
  • Data Submission
    • Integrated Aspera software to optimize data transfers.
    • Rewrote the data upload code to upgrade the latest version of Java and Spring.
    • Modularized the template definition into an XML specification that can be used to generate documentation and templates themselves.
    • Modified Flow Cytometry templates per recommendations from HIPC consortium to better annotate markers.
    • Modified the templates to allow for references to other databases for data sharing (GEO, dbGAP, etc.)
    • Modified the bioSamples template to now require association of planned visit.
    • Improved error messages to be more meaningful to non-technical staff.
    • Rewrote Data Submission documentation to reflect changes.
  • Data Validator
    • Created a new validation tool to replace the existing Java application.
    • The new data validator will be a locally installed web application using embedded Tomcat and the latest Java and Spring.
    • Developed a RESTful API used by the data validator to authenticate user and retrieve previously submitted data from ImmPort to validate the local user data package.
    • The data validator syncs with the remote ImmPort server to ensure that latest version of validator is installed.
  • Data Curation Tool: Developed a query and reporting tool to help ImmPort scientists curate data.
ImmPort Version 2.23
Released February 15, 2014
  • Modifications to support the Data Release.
ImmPort Version 2.22
Released November 1, 2013
  • Removed Gene Pattern from ImmPort.
  • Added ImmPort Lab links to home page and navigation toolbar.
  • Updated the Data download pages to include .html formats.
  • Updated the homepage slide to include new studies.
ImmPort Version 2.21
Released September 30, 2013
  • Lengthen inactive session logout time.
  • Additional options are added in treatments template.
  • Added the BISC De-identification Process to the resources page.
  • Updated the Download Data page.
  • Added new study download pages.
  • Updated the homepage slide to include new studies.
ImmPort Version 2.20
Released August 16, 2013
  • Enhanced the study categorization options on the home page to include a keyword annotation of Studies.
  • Added new CV terms in search drop down box for file purpose and detail.
  • Improved the infrastructure for the validator and uploader.
  • Enabled the visibility of the study accession column in the study summary table.
  • Improved capturing the treatments for ImmPort uploads.
ImmPort Version 2.19
Released May 16, 2013
  • Home Page
    • Added Facebook, Twitter and RSS Feed to the home page.
    • Removed TagSNP from ImmPort.
    • Removed Genetic Analysis from ImmPort.
  • Data Submission
    • Removed the XML template loader, validator and XML template files.
    • Enhanced upload support for soluble protein measurement (plate based) MBAA Luminex and Meso Scale Discovery based on recommendations from the HIPC Standards Committee.
    • Updated the data validator to support the new soluble protein and treatment modifications.
    • Improved the capturing of treatments for ImmPort uploads.
  • AGI Interfaces: updated the query features based on input from NIAID
  • Provided new data download capabilities
    • Created MySQL DDL and load files for each study shared in ImmPort for download and re-use locally by ImmPort users.
    • Created tabbed text output compatible with R or Excel for each study shared in ImmPort for download and re-use locally by ImmPort users.
    • Created online documentation for the ImmPort data dictionary for the tables and columns in the new MySQL and tabbed text outputs.
    • Provided ERD diagrams for the tables and columns in the new MySQL outputs.
ImmPort Version 2.18
Released February 26, 2013
  • Home Page Refresh
    • Modified the post login
    • Added a feature block to highlight studies
    • Added Research Programs and studies to the home page
    • Added Keynote presenter block
    • Added Data Summary Totals
    • Certified ImmPort 2.18 on modern versions of Browsers
  • News and Events
    • Added a RSS Feed
  • Removed GBrowse from ImmPort
  • Updated Study Design Templates
    • Updated FLOCK guides to show the FLOCK - Centroid - Cross Sample work flow
  • Flow Cytometry
    • Enhanced flow cytometry experiment sample template to ensure capture of control and compensation files
    • Modified the file purpose and/or file detail to indicate the files are flow control or compensation files
    • Modified the file purpose and/or file detail for sample results files to indicate sample result
    • Added an Assay Group ID to capture which files were generated from a particular cytometry run
    • Modified control files
    • Extended EXP_ELISA_MBAA_RESULT.CAL_CON_UNIT from 20 to 100 characters
ImmPort Version 2.17
Released December 14, 2012
  • HLA Reference Data
    • Updated the IMGT HLA allele reference data
    • Updated the CWD reference data to come from a new data source
    • Updated the SFVT Reference data to reflect the new allele data
    • Updated the ANTT tool based on the new HLA allele reference data
  • Home Page Refresh to remove stale content
    • Removed features that are less utilized from the Home Page central tab
    • Removed the News and Events from the home page
    • Removed the Research Spotlight from the home
  • AGI Interface
    • Added more query and display features to the AGI interface
ImmPort Version 2.16
Released October 19, 2012
  • Home Page and Supporting Informational Pages
    • Created a Citing ImmPort Page
    • Updated the About ImmPort and Contacts to reflect the new Science Team
    • Updated NFS settings to speed backup
ImmPort Version 2.15
Released September 7, 2012
  • Data Submission
    • Developed data submission tools to support loading of study designs
    • Automated the loading of the basic_study_design.txt template that contains basic study metadata, arm and cohort definitions, study personnel, study periods, planned visits,and protocols
    • Updated the Data Validator to support the new basic_study_design.txt template and the associated business rules
ImmPort Version 2.14
Released June 30, 2012
  • Data Submission
    • Developed data submission tools to support KIR Typing results provided in either a newly developed ImmPort template or in EBI format/li>
    • Developed rules for allele interpretations based on loci and Present and Absent calls
    • Provide the ability to capture more detailed information about the KIR reagent and KIR Typing system
    • Created new experiment sample template for KIR specific results
  • Research Data
    • Created Advanced Search queries on KIR results based on gene name and population
    • Created new result Ext-JS tables for KIR results and included the table in Advanced Search, Experiment sample detail page and the Experiment Detail page
    • Modified the Experiment detail page to include additional experiment metadata, a subject table, biological sample table, and added derived results table for the appropriate experiment type (ELISA, ELISPOT, Flow Cytometry, HLA, KIR, HAI, Virus Neutralization, and qPCR)
  • Back to Top
  • ImmPort Version 2.13
    Released March 29, 2012
    • Research Data
      • Updated the capture and display of Subject demographics and biological sample information based on specifications from the Human Immunology Project Consortium (HIPC)
      • Modified data submission, subject update, and query screens to support the capture of age events, age units in subjects
      • Modified data submission for subject metadata to require arm definition, ethnicity, and race
      • Modified data submission, biological sample update, and query screens to support the capture of study time (instead of just day), study unit, study time zero event
      • Modified data submission to require study to be specified in biological sample
      • Created new experiment sample data submission templates, reagent templates, results templates, created new summary tables, and modified the experiment sample detail pages to support Hemagglutination Inhibition (HAI) and Virus Neutralization Assays
      • Pruned un-used columns from the subject table and template
    • Miscellaneous
      • Eliminated the requirement for excluding space characters from .zip file submission packages
      • Added links to outside sites for AGI data screen
    ImmPort Version 2.12
    Released July 21, 2011
    • Post-Login Homepage Redesign
      • Created a new homepage after login to highlight NIAID Programs submitting and sharing data to ImmPort
      • Created a new NIAID Programs in ImmPort page, displaying summary information about contracts or grants grouped by NIAID Research Program with a link to a Contract-Grant Detail page
      • Created a new Contract-Grant Detail page containing summary information about all projects and studies within projects for that contract
      • Created a new Shared Research Data Catalog, highlighting NIAID funded contract-grants that have shared research data available, grouped by NIAID research Program
      • Moved the existing My Workspace content to a new Browse data tab
      • Moved the Search, Visualize, and Analyze Data Tabs up higher on the page
    • Cell Detail Page
      • Created a Cell Detail page that is launched from the Cell Type Ontology viewer
      • Utilizes curation performed by UTSW staff to supplement Cell Type Ontology content
      • Displays information about Definitional Phenotype characteristics and expression related to Surface markers, Cytokines, Transcription Factors, and Gene Ontology with linkage to source repositories Protein Information Resource and GO
      • Displays information about Additional Phenotype characteristics and expression related to Surface markers, Cytokines, Transcription Factors, and Gene Ontology with linkage to source repositories Protein Information Resource and GO
    • Flow Cytometry Tools
      • Created a new 3D Viewer using Jmol for visualizing populations
      • 3D Viewer providers users the ability to hide and show identified populations and change marker axes on the viewer
      • 3D Viewer allows users to drag and rotate the presentation and to turn on continuous spinning of the 3-D image
      • 3D Viewer allows users to toggle on and off a view to display a representation of the Centroid
      • Modified binary fcs file converter to now support Accuri generated data
    • Research Data
      • Added Planned Visit to the Advanced Search query tree
      • Added Planned Visit to the Assessments and Lab Tests summary grids
      • Added templates for experiment sample for Illumina Gene Expression, Neutralizing Antibody Titer, and image histology
      • Updated Study Detail Treatment block to be named Study Interventions, and expanded data in the Substance merge to include all concommitant medications
      • Modified the Reagent Detail page to only show blocks with data
      • Modified Study Detail page to reference the source contract
    • HLA SFVT Analysis
      • Modified output files to improve readability and supply more information
      • Included alleles analyzed and number of subjects in case and control in analysis results page metadata header
      • Pull all information in analysis results page metadata header into the readme file
      • Generated SF_Anslysis_results as Excel instead of text
      • Added a HLA_Typing_for_SFVT_Analysis.xls for loading, to require inclusion of phenotype
      • Allow for analysis of all loci in one pass and display all loci download zips on one page, but removed existing individual download files
      • Added a multiple hypothesis correction value as an additional column in the SFVT Analysis results file
    • Admin
      • Modified the Program, Contract, and Project create and update screens to contain a new category field to allow filtering of which data to view on the new homepage
      • Provided Program Officers the ability to create a default project for the PI of a contract-grant
      • Modified registration to make it easier to associate users immediately to the project related to a contract
      • Added a required linkage between Contract-Grant and Project in all related interfaces
    ImmPort Version 2.11
    Released April 12, 2011
    • Flow Cytometry tools
      • Created a new interface for viewing populations based on user selection
      • Allows users to visualize individual or user-selected populations to overlay in the overview screen
      • Moved the population summary table, MFI, centroid and expression score to a single consolidated interface
      • Allows users to resize the screen to fill larger resolution monitors which then expands the thumbnails images
      • Expanded size of the images when a user moves their mouse over the population visualization thumbnails
    • Miscellaneous
      • Moved the ontology browsers outside of the login so they are available to the general public
    ImmPort Version 2.10
    Released March 14, 2011
    • Sequence Feature Variant Type Analysis
      • Implemented a chi-square analysis on Sequence Feature Variant type data outputs
      • Allows user to perform analysis for subjects characterized with two sets of values (such as case and control) and a sequence feature variant assignment for a set of sequence features for a given locus
      • For each sequence feature, a chi-square analysis across all the sequence feature variants for the sequence feature and provide results and provide the p-value after Bonferroni Correction
      • For each feature feature variant of a sequence feature a chi-square analysis where you consider all subjects with the variant and subject without the variant and provide results and provide the Odds Ratio and the Confidence Interval of Odds Ratio
    • Ontology Browser Improvements
      • Replaced the prior Ontology browser that utilized a Java applet with an improved version utilizing Ext-JS trees and AJAX calls
      • Improved performance on the ontology browser
      • Added the Cell Ontology data content to ImmPort in the ontology browser
      • Moved the Gene Ontology and the Diseases Ontology to the new ontology browser
      • Removed the Draft-GO Immunology and Taxonomy ontologies from the browser
      • Implemented an improved text search using Lucene that searches over all text fields in the ontology
    • Flow Cytometry tools
      • Provided more data management capabilities in the flow cytometry analysis by providing the ability to delete flow files, centroids, data sets, and analysis results
    • Research Data Improvements
      • Improved usability of research data management between the edit page and the detail page tabs for delete and update of all data types, subject, sample, experiment sample, experiment, and protocol
      • Modified the Collaborative workspace sharing feature to enable sharing of flow cytometry result .txt files to be available for flow analysis via the CW
      • Implemented saving of state via cookies for research data summary grids returned in simple and advanced research data queries, including the saving of the sort order, columns hidden and moved
    ImmPort Version 2.9.2
    Released December 17, 2010
    • Data Submission Improvements
      • Modified the experiment sample template for data submission to be multiple assay specific experiment sample templates to make the template more intuitive. A full list of changes can be found on the data submission home page
      • Modified the data validator to match the experiment sample template changes
      • Modified the data validator to make it easier to synch with modifications to the batch upload code
      • Created a new qPCR results submission template
    • Flow Cytometry tools
      • Added a new mouse-over zoom to result images
      • Added a marker display and search in the create data set pages
      • Added Visit as a searchable field in the create data set pages
    • Research Data Improvements
      • Added HLA typing results query parameters and as a return type in Advanced Search
      • Added qPCR results query parameters and as a return type in Advanced Search
      • Modified all displays for subject, experiment sample and biological sample so that user defined id is viewable for members of the private workspace and blanked out for others
      • Added a subject summary table to the Study detail page
      • Modified the display of the subject summary table to better display arm and study content
      • Cleaned up the Advanced Search tree text to be more consistent with summary tables and other pages
    ImmPort Version 2.9.1
    Released September 24, 2010
    • Flow Cytometry tools - new FLOCK version
      • Added the new FLOCK v2 algorithm as an additional option in the Flow analysis module
      • Compared with FLOCK v1, the v2 is able to generate results closer to manual gating (independent assessment of FLOCK v2 with other relevant methods will be released at FlowCAP: http://flowcap.flowsite.org) in a fully automated way, and therefore reduces the needs of user tuning of parameters and result adjustment. While we may plan to replace FLOCK v1 with v2 ultimately, we currently still make FLOCK v1 available to our users so that previous v1 users can still access it.
    • HLA Ambiguity Reduction Tool -- New!
      • Added a Novel (Beta release) Ambiguity reduction tool for HLA typing data.
      • Adds to the previous validation tool and now allows for allele and genotype ambiguity reduction, based on specifications by Dr. Steven J. Mack
    • Research Data
      • Modified the file download process to better accommodate large file sets; now if the data size requested is too large, the user is prompted to submit a request for a hardware shipment
      • Create a full Study Data Package page that will be available when the Casale study is released to the semi-public area
      • Modified the Uploaded Files summary pages to show more useful information related to the study, subject and sample that file relates to
      • PATCH deployed on 9/30/2010: per DAIT policy, removed user defined id and name for biological sample, experiment sample from summary table displays; enabled the detail pages to selectively display these fields based on private project access only
    ImmPort Version 2.9
    Released August 12, 2010
    • Flow Cytometry tools
      • Added the capability to remove columns for analysis that are translated from the fcs files, allowing removal of redundant or irrelevant markers
      • Added the display of markers used to multiple displays for single and cross sample analysis and the centroid detail screen
      • Provided a display to compare markers across multiple samples in cross sample preparation
      • Modified the fcs binary conversion script to version 1.1 to 1) Added data type checking on both FCS version 2; 2) Applied logicle conversion for all fluorescent channels.
      • Enabled FLOW analysis module input to access converted fcs results stored in the SPW
      • Improved performance of image generation in generating flock results by modifying how the data is stored in files
      • Modified the results page to include the number of populations identified
      • Modified the accompanying user documentation and tool tips to reflect these changes
    • HLA Reference and Research Data
      • Updated the HLA reference data area to support the new IMGT/HLA version 3.* format
      • Modified the MHC Query page to now accept both v2 and v3 names as query parameters
      • Modified the batch upload process to accept v2 or v3 names for HLA typing results and to accept a population name
      • Modified the HLA data set creation process to now allow data to be created in v2 or v3 format
      • Modified the HLA validation process to now convert v2 data as well as validate using the tool ANTT from http://www.igdawg.org/software/
    • Research Data
      • Modified the biosample update page to accommodate adding study references
      • Modified the study detail page and experiment detail page to better reflect experiments with subjects originating from multiple studies
      • Modified batch upload to accept study day for biosamples
    ImmPort Version 2.8
    Released April 30, 2010
    • New Gene Expression Analysis tool -- GenePattern
      • Integrated the best of breed open source gene expression analysis tool, GenePattern from the Broad Institute, into the ImmPort infrastructure
      • Included integration of the GenePattern web server, analysis server, analytical tools and the Sun Grid for task queuing and distribution
      • Worked to ensure that the usability of GenePattern matches the ImmPort look and feel
      • Integrated existing modules from GenePattern or implemented new ones from sources such as Bioconductor to support annotation, clustering, gene list selection, pathway, and prediction analysis
      • Created predefined pipelines utilizing combinations of modules for GO co-clustering analysis, Gene set enrichment analysis from CEl source files
      • Implemented a R+D multi-pipeline analysis comparison that can be run offline from tasks submitted through GenePattern
      • Developed user documentation to support the modules, pipelines, and overall workflow
    • Expanded support for clinical study data content
      • Modified the Subject detail page to include content related to assessments, adverse events, medications and lab tests
      • Modified the Biological Sample detail page to include laboratory tests
      • Modified the Subject, Biological Sample and Experiment Summary tables used in returning query results to include the Study and Arm information
      • Modified the Subject, Experiment, Experiment Sample, Biological Sample and Protocol detail pages to have a consistent look and feel and collapsible panes as in the reference data pages
    • Flow Cytometry Analysis
      • Developed a novel fcs binary to text file converter for analysis, eliminating the need for researchers to convert on their own
      • Integrated the binary to text converter to run automatically when flow data is uploaded into ImmPort
      • Added Advanced search capabilities when identifying flow files for analysis
      • Added sharing of results across research teams via projects
    • Sequence Feature Variant Type Visualization
      • Integrated the Jmol visualization tool for viewing Sequence Feature Variant type data for viewing PDB structures
      • Developed the ability to highlight selected sequence features on the source HLA molecule from PDB
      • Utilized several display options from Jmol (Ball and stick, Line, stick, space, etc) for visualizing the HLA molecule
      • Developed a panel for highlighting different features on the molecule
      • Developed a panel for displaying PDB information and color codes for the structure
      • Developed a panel for entering and highlighting the reference allele using IMGT/HLA coordinates onto the PDB structure
    • Data Submission
      • Modified the biological sample and experiment sample templates to better reflect clinical data and specific assays
      • Modified the exons interrogated CV terms to better meet the Silver Standard
    • Collaborative Workspace
      • Modified the Collaborative Workspace publishing interfaces to allow users to share studies explicitly or through reference to subjects and experiments
    ImmPort Version 2.7.1
    Released April 5, 2010
    • ImmPort Gene List content update
      • Modified the presentation of the ImmPort Gene area of ImmPort to be more intuitive
      • Modified the refresh time for the ImmPort Genes to be monthly
    ImmPort Version 2.7
    Released February 2, 2010
    • Support for clinical study data content
      • Expanded the ImmPort database to now capture detailed information about clinical studies
      • Can now support the collection of information about study metadata, study design, study documents, arms, subject assessments, lab tests, adverse events and medications
      • Created a study summary page to query on existing studies and to navigate to study details
      • Created a study detail page consisting of expandable panels of data, including study summary information, inclusion exclusion criteria, publications, mechanistic assay experiments, and summary statistics for demographics, assessments, lab tests, adverse events and medications
      • Created a study summary document available for download
      • Created a study schematic image to visually illustrate the study design, also containing links to the related row level data to assist navigation
      • Added study, arm, assessments, lab tests and substances/medications to advanced search to query, view and download row level results
    • Flow Cytometry Analysis
      • Provide the ability for users to batch upload data files for analysis in FLOCK
      • Created a new template for transformed fcs text results where users can bulk submit result files plus accompanying marker definition files
      • Created a new interface within the flow analysis module for this batch upload, and added the capability to include flow result file templates in standard batch upload in ImmPort data submission
    • Other
      • Added support for international phone numbers during registration
      • Modified the HLA QC Pipeline Ambiguity reduction process per user guidelines
      • Resolved issue with creating HLA data files for ambiguous genotyping results
    • Known Issues
      • In Safari 3, the disabling of invalid query attributes in the search tree is not working. This is working in Safari 4
    ImmPort Version 2.6.1
    Released December 17, 2009
    • Modified the My Workspace Page
      • Improved the display of the "Research Data", "Analysis Results" and Saved Lists displays to now show in tabs
      • Within Research data, created a click-able display of projects that can be expanded to view experiments
      • Modified the notifications display to match color schemes with the home page
      • Added the Research Spotlight to the My Workspace page including a View More/Hide button to save space
      • Removed panels of content from the right side of the page to the menu area
    • Other
      • Added support for IE8 and Safari 4 browsers
      • Did under the hood code cleanup of deprecated objects
      • Correct an issue with HLA data uploads when genotype ambiguity was present in the data file
      • Corrected prior known issues
    • Known Issues
      • In Safari 4, the Tools menu overlay with any table displayed is not showing properly opaque
    ImmPort Version 2.6
    Released October 23, 2009
    • Added a Flow Cytometry Analysis module including Cross Sample analysis and improved Data Management capabilities
      • Provided the ability to group data files into data sets using a drag and drop interface
      • Allowed users to edit their marker names for display online
      • Developed a batch analysis feature where data sets can be analyzed using FLOCK analysis instead of only individual files
      • Provide users the ability to save centroid files after adjustment and to annotate with meaningful metadata
      • Created a cross sample analysis function to allow users to identify population differences across data sets by applying saved centroids to full data sets and to visualize the results
      • Provided interfaces to view Population percentages across all samples and to visualize Populations for selected marker pairs across all samples side by side
      • Provide statistics for population assignment as well as all generated data from FLOCK for download
      • Created new user documentation to support the new Flow Cytometry Analysis Module
    • Continued to implement the ImmPort website redesign
      • Modified the ImmPort website to improve aesthetics, usability, and to better support multiple browsers
      • Eliminated the side bars that were present in prior ImmPort versions and migrated those links to a second horizontal drop down menu with a new look and feel
      • Created a new top menu design with fly-aways and new tabular drop-down displays to allow users to navigate across the website from the top menu
      • Modified the ImmPort web site to move to a fixed-width design to allow for greater consistency of look and feel, better cross browser support, and more page width for viewing content
      • Corrected previously known issues in displaying sidebars (by eliminating them) and the GDS Generation page in IE6
    • Research Data Search and details
      • Added a new search widget to assist with querying free text fields by providing a pop-up of all distinct values that can be selected and used as search attributes
      • Applied the new search widget to several query attributes in both Basic and Advanced Research Search pages
      • Added HLA Typing System Detail to Reagent Detail Page
    • Known Issues
      • On Internet Explorer 7 (only), there is a known bug in the browser that affects the selection of the Access Data button when moving from left to right
      • The Data Validator can incorrectly report non-unique user defined id's if being checked against project that data was deleted from
      • In Firefox 3 and IE7, in the Research Data Summary List, the Save Item and Save All buttons stay selected
      • The Haploview source throws an exception when spaces are used in Subject identifiers in PED files
    ImmPort Version
    Released October 6, 2009
    • Flow Cytometry Analysis: Note, this change would modify the results of a FLOCK run if the same data set is run again
      • We identified and replaced an outdated function in FLOCK; as a result of this change the user may see a slightly smaller number of populations if the same data set is run again. Most populations identified in the original results will still be identified in the updated results in the same way, while a few data regions that may have been over-partitioned in the original results will be merged and identified as a single population.

    • MHC SFVT Analysis
      • Fixed a display error when subjects are linked to more than one experiment sample in the subject summary table.

    • Save Lists
      • Resolved an issue where saved lists names were saved incorrectly with commas

    • Reference Data: Gene Detail Content
      • Fixed a browse pathway link in the ImmPort Gene Lists

    ImmPort Version 2.5.2
    Released August 2009
    • MHC SFVT Analysis
      • Created a new workflow where users can create and store data files in HLA typing or SFVT format from DAIT submitted research
      • Implemented a HLA QC Pipeline utilizing PyPop (www.pypop.org) for HLA typing data
      • Linked together the previous HLA typing upload and SFVT converter to the new workflows
    • Flow Cytometry Analysis: Note, this change would modify the results of a FLOCK run if the same data set is run again
      • Density threshold format: based on user feedback, the density threshold has been changed from a floating number to integer. The density threshold value is equal to the number of events in a hyper-bin. Increasing the density threshold value will generally result in fewer populations.
      • Parameter setting: to customize parameters, it is now possible to enter a value for either the number of bins or the density threshold; the parameter not defined by a custom value should be set to zero. FLOCK will select the optimal value for the zero-set parameter.
      • Rare population identification: the detecting capability of FLOCK for slight variations in data distribution has been increased. The intention of the improvement is to assist with the identification of rare populations. Should the number of populations generated under automated mode exceed expectations, please:
        a. Slightly increase the density threshold; an integer between 3 and 10 will meet your needs.
        b. Contact the helpdesk so we may assist you
      • Code change has been implemented to correct for the generation of empty populations.
    • List Management
      • Added the ability to union and intersect saved lists in the My Saved List Summary page
      • Modified the My Saved List Summary page to use the AJAX table format: this provides the ability to view details on multiple lists, save a new list, and sort on all columns
      • Modified the My Saved List Detail page to show multiple lists in tabs on one page
    • Advanced Search updates for derived results from assays
      • Added MBAA/ELISA Query attributes and summary table to Advanced Search
      • Added ELISPOT Query attributes and summary table to Advanced Search
      • Added FCM Query attributes and summary table to Advanced Search
    • Collaborative Workspace (CW) Improvements
      • Modified the CW Sharing workflow to automatically share protocols for a given entity when that entity is shared
      • Modified the process so Protocol sharing (when required) does not affect other entities
    • Reference Data: Gene Detail Content
      • Added content from the DIP, MINT, INTACT, BIND and BIOGRID databases to the Protein Interaction block of the Gene Detail page
    ImmPort Version
    Released June 2009
    • Fixed problem where the GO terms Excel output was showing extra erroneous terms for genes for the Human Immunologically Related Gene Lists
    ImmPort Version 2.5.1
    Released June 2009
    • Collaborative Workspace (CW) Improvements
      • Provided a new CW Publishing process where subsets of subjects, samples, reagents, experiment samples, and protocols can be shared for a given experiment
      • Modified the database to better store the relationship between entities and the Collaborative workspaces
      • Modified query pages and data set generation pages to use the new CW process
    • SFVT Data Converter
      • Modified the SFVT data process to allow for more file types plus addition descriptive columns for the subject phenotype input and output
    • Gene Expression Analysis: IMAC T-test and SAM results
      • Added a new AJAX based table display for T-test and SAM results
      • Added an option to save gene lists from T-Test and SAM results
    • Other
      • Made several aesthetic and functional feature enhancements to the AGI data pages
      • Automated the AGI load process
      • Corrected an issue where not all analysis tools activities were being audited
    • Known Issues
      • On Internet Explorer, the header on the MHC Allele Alignment display (ajax table), terminates at approximately 3600 characters, while the sequence continues to the the expected length. This has a impact only on long sequences such as MICB genomic.
      • The GDS Generation Experiment Sample selection page has known layout issues in IE6.0
      • The sidebar navigation has issues with length and positioning in IE6.0 for some pages
    ImmPort Version 2.5
    Released May 2009
    • New Website design and logo
      • Created a new website design with simplified menus, a new logo, and a refreshed home page
      • Added Research Spotlight section to the home page to highlight DAIT-funded research
      • Added a clearer What You Can Do section to highlight ImmPort functionality on the home page
      • Created a new Workspace page to provide a summary view of analysis tasks, research data, and useful links
    • Flow Cytometry Analysis - Result Adjustment System (RAS)
      • Created a new highly interactive RAS user interface to allow manual adjustment of FLOCK results
      • RAS allows users to move or split centroids of populations and delete populations through a drag and drop interface
      • Following centroid adjustment, RAS re-analyzes and adjusts existing populations based on the new centroids
      • Provided a Centroid summary table to view coordinates of the Population's centroids
      • Created an undo capability to reset all centroid adjustments performed
      • Created a Population color key legend that can persist through the adjustment process
      • Created a MFI table for each population
      • Provided download of the Results, Summary Table, Centroid table, and MFI table
      • Provided new user documentation for the RAS system
    • HLA Sequence Feature Variant Types Reference Content (SFVT)
      • Added novel content on SFVT data created by the DAIT Interoperability Science Committee HLA Subcommittee
      • Provided new query interfaces for the SFVT reference content to search by Allele or SFVT criteria
      • Created a new SFVT detail page to view locus information, allele alignment, allele grouping, and links to protein structure
    • SFVT Data Converter
      • Created a novel data converter, which takes HLA typing data as input and converts into a text-based SFVT file
      • The data converter also performs basic validation on the HLA typing data uploaded prior to conversion, and provides QC logs with the final file
    • Reference Data Updates
      • Updated the gene detail page to present the data content in a more aesthetically pleasing manner
      • Updated the gene detail page to include content on Protein interactions from Innate DB
      • Provided a comprehensive set of manually curated new gene lists and reports for Immunologically Important genes
      • Gene lists include genes related to Cytokines, Cytokine receptors, signalling pathways, antimicrobials, Natural Killer Cell Cytotoxicity, and Antigen Processing and Presentation
      • Gene lists also include statistically relevant genes from microarray analysis for B Cell Stimulation and B Cell Development
    • User Registration - New community for Life Scientist Researchers (LSR)
      • Created a new community of researchers to reflect non-DAIT scientists who want to use ImmPort
      • Created new registration pages specific to LSR users
      • Automatically created research project, contract, and program stubs for LSR users on registration
      • LSR users may now utilize the system as regular users with access to their own research content
    • Data Submission
      • Updated the XML templates to better support ELISA, ELISPOT, MBAA
    • Known Issues
      • On Internet Explorer, the header on the MHC Allele Alignment display (ajax table), terminates at approximately 3600 characters, while the sequence continues to the the expected length. This has a impact only on long sequences such as MICB genomic.
      • The GDS Generation Experiment Sample selection page has known layout issues in IE6.0
      • The sidebar navigation has issues with length and positioning in IE6.0 for some pages
    ImmPort Version 2.4.2
    Released February 2009
    • Genotyping Analysis: Added support for > 1 platform in PED generation in a BETA
      • Provided support for cross platform SNP genotyping results to be put into PED files
      • Validate the vendor annotation for the assay strands against dbSNP to ensure compatibility
      • Provide download of markers dropped due to incompatibility
      • Allow for the union or intersection of compatible markers to be used in final data file
    • Flow Cytometry Analysis (FLOCK Beta)
      • Added more stringent rules for manual definition of bin and density parameters
      • Added download of population result files
      • Added the parameters selected by auto-detection to the result pages
      • Added a summary of rating definitions to population summary page
    • Gene Expression Analysis: Improved the GDS data file definition UI
      • Added a UI that guides the user to projects with Gene expression data to select experiment samples
      • Added an option to specify experiment samples from previously saved lists
      • Added the parameters selected by auto-detection to the result pages
    • Data Submission
      • Added hints from the Children?s Hospital of Philadelphia staff to the main submission pages
    • Other
      • Updated Publications for the Immune Function and Biodefense in Children, Elderly, and Immunocompromised Populations Program
    ImmPort Version 2.4.1
    Released December 2008
    • Analysis: Redesigned the PED generation workflow to improve usability
      • Implemented a wizard-like interface to guide users on generating a PED and INFO data set
      • Added validation up-front to highlight subjects that have proper genotyping results and annotation
      • Allowed use of Subjects lists from other search areas (Advanced Search, Data Management) to be used as input
      • Implemented assignment of lists to case and control, instead of relying on the Database field
      • Linked any problem subjects identified back to detail pages and list details
      • Implemented the use of SNP Lists to filter down the SNPs present in the final data file
      • Updated the PED Generation user guide to reflect the new process
      • Optimized the PED generation process for larger data sets
    • Flow Cytometry Analysis
      • Implemented mouse-overs to better describe bins and parameters
      • Updated the User Guide to better explain bins and parameters
    • Other
      • Modified summary tables to better display PI and source project information for SPW content
      • Resolved a bug in the Ext-JS summary tables when multi-selecting across pages
    • Back to Top
    ImmPort Version 2.4
    Released November 2008
    • Flow Cytometry Analysis
      • Implemented a Beta release of FLOCK, a novel flow cytometry analysis tool.
      • FLOCK accepts .txt file output of FCS file content, and performs automatic population detection and visualization
      • The Beta implementation is optimized for > 6 markers and performs analysis for one a single data file
      • Developed a FLOCK User Guide and a FLOCK tutorial
    • Reference Data Search
      • Implemented an advanced search capability for returning reference data entities (genes, proteins, snps and MHC alleles) by utilizing a tree view to select query attributes and query criteria from any of the reference data entities
      • Implemented saving of lists from advanced search query results for selected or all rows
      • Implemented the usage of saved reference data entity lists within the Advanced Search query tree
      • Implemented an interactive AJAX table component when returning advanced search query results allowing sorting on multiple columns, re-ordering of columns, and hiding columns
      • Consolidated the MHC Allele Query page and the MHC Allele Alignment Query page into one query page with different result options
    • Saved Lists
      • Added AJAX summary tables to the display of all list details under My Saved Lists
      • Added My Saved List information for reference data content
    • Query Results in Summary Tables
      • Provided the ability to export any query results returned in an AJAX table to Excel or PDF, including Advanced Research Search, Advanced Research Search and Data management
      • Provided the ability to multi-select results by using SHIFT-CLICK within a summary table on single page
      • Provided the ability to multi-select results by using CTRL-SHIFT-CLICK across tables on multiple pages
    • Front Page Content
      • Added a catalog with details about DAIT-Funded research programs that will be submitting data into ImmPort.
      • Added a publication list that reflects the DAIT-Funded research programs within ImmPort.
    • Other
      • Upgraded the Ext-JS component
      • Updated the website to support latest Firefox, Internet Explorer, and Safari web browsers
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    ImmPort Version 2.3.2
    Released September 2008
    • Data Management and Research Data
      • Modified detail pages to be more experiment context-specific
      • Created an IGAT User Guide
      • Modified the Experiment Sample detail page result file description and download link
    • Advanced Search
      • Replaced the view details pop-up with a re-direct to the standard research data detail page
      • Added the saving of state when navigating away from Advanced Search, so when a user returns to their query their query parameters are still selected
    • Data Submission
      • Added support for ELISA, ELISPOT, MBAA results per the DAIT Minimum Information Guidelines
      • Modified the experiment samples and reagent templates for ELISA, ELISPOT, MBAA results
      • Created new results templates for ELISA, ELISPOT and MBAA results
      • Modified the user guide and tutorials to support ELISA, ELISPOT and MBAA results
    • Analysis
      • Modified Haploview results sorting to sort by p-value and chi-squared
      • Resolved an issue with descriptions of samples exceeding the defined size
      • Resolved an issue with Haploview where partial results sets were returned in certain circumstances
    • Other
      • Added prior Webinar slides to the front page
      • Added search tips on the page for Simple Search and to the user documentation
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    ImmPort Version 2.3.1
    Released August 2008
    • Analysis
      • Improved PED Generator to handle different Affy allele formats (Linkage proc)
      • Created an IGAT User Guide
      • Added figure legend to Haploview results page
      • Fixed a IMAC defect related to multple analysis servers and task initiation
      • Updated the TagSNP Tutorial
    • Data Management and Research Data
      • Added more Project information to the Data Management detail pages
      • Added a Pooled Sample indicator on BioSample Data Management detail page
      • Updated the Gene Expression and Flow Cytometry query tutorials
    • Reference Data
      • Increased the max character size to 1000 in the SNP query attribute
      • Updated the MHC Allele alignment tutorial
    • Data Submission
      • Modified the status for data submission from "Rejected" term to "Failed"
      • Fixed a defect with the new HLA Typing system and HLA allele templates
    • Other
      • Enabled the ImmPort icon to be a hyperlink to the main page
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    ImmPort Version 2.3
    Released August 2008
    • Research Data Search
      • Implemented an advanced search capability for returning research data entities (subjects, biological samples, experiments, experiment samples, reagents and protocols) by utilizing a tree view to select query attributes and query criteria from any of the research data entities
      • Implemented saving of lists from advanced search query results for selected or all rows
      • Implemented the usage of saved reserach data entity lists within the Advanced Search query tree
      • Implemented an interactive AJAX table component when returning advanced search query results allowing sorting on multiple columns, re-ordering of columns, and hiding columns
      • Enabled the querying and viewing of semi-publicly available research data within Advanced Search
      • Enabled those with the Program Officer role to view the Advanced Search interfaces
    • Data Management
      • Converted the existing query results tables to an interactive AJAX table component allowing sorting on multiple columns, re-ordering of columns, and hiding columns
      • Added the usage of saved research data entity lists within the Data Management filters
      • Modified the research data detail pages to load on demand to improve performance
      • Implemented a publish button for Primary Investigators (PI) to request to migrate research data into a semi-publicly available area
      • Enabled the querying and viewing of semi-publicly available research data within Data Management pages
      • Enabled those with the Program Officer role to view the Data Management interfaces
    • Reference Data
      • Supplemented the MHC Allele Query by adding allele frequencies to the summary and detail pages
      • Added support for MHC Allele aliases in the MHC Allele Query
      • Added the Common and Well Documented (CWD) allele information to the MHC Allele Query pages
    • Data Submission
      • Supplemented the HLA research data content to satisfy the HLA Silver Standard proposal
      • Modified the Experiment Sample, Biological Sample, Subject, and Experiment templates to require a protocol per the DAIT Minimum information standards
      • Created an example FCM data package
      • Added a responding variable field to the Experiment template
      • Synchronized the Data Validator code to match the data submission required fields
    • Adminstration
      • Added a shopping cart for adding users to projects
      • Added a My Saved List page for viewing list information for research data lists saved to research projects to which a user belongs
    • Other
      • Created a new Semi-public workspace (SPW) concept where any user with a valid ImmPort login can view published research data content
      • Created a publishing mechanism that moves data from private projects to the SPW *after* a PI requests their research data to be published into the SPW
      • Placed documentation related to the Data Submission Templates and User Guides, the DAIT Minimum Information Standards, the HLA Quality Control Pipeline, and the Proposal for HLA Data Validation on the ImmPort front page
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    ImmPort Version 2.2
    Released March 2008
    • Adminstration
      • Developed a Program Officer Data Submission Report for reviewing submission progress to date
    • Analysis:
      • Upgraded Haploview to Version 4.0
      • Modified Haploview result image navigation to utilize Google maps-styled mouse dragging
      • Modified IMAC result image navigation to utilize Google maps-styled mouse dragging
      • Implemented the CLASSIFI algorithm within IMAC single analysis
      • Improved the implementation of the CLASSIFI algorithm within Pipeline analysis by providing platform selection
    • Data Submission
      • Modified the data submission process to allow data submission greater than the prior limit of 100 MB (now 1 GB)
      • Shortened the wait time for data submission processes to be processed
      • Implemented parallel processing of data submission loads
      • Improved the under the hood status monitoring of data submission packages
      • Implemented an improved connection pooling mechanism to improve submission performance
      • Optimized the Illumina genotyping data loading process
      • Removed all references to FACS and changed to FCM
      • Implemented data submission package registration to generate a ticket number for labeling off-line data loads via external hard drives, FTP, etc
      • Implemented the first production version of the Data Validator, using a Graphical User Interface
      • Implemented column width checking in the Data Validator for all metadata fields
      • Improved the Data Validator installation and database synching processes
      • Developed the Data Validator to work on Windows, Linux, and Mac operating systems
      • Updated the Data Validator user guide
      • Added a version indicator to the Data Submission templates
    • Reference Data
      • Loaded IMGT HLA allele information into the ImmPort Reference schema
      • Developed a new MHC Allele query page
      • Developed a new MHC Allele alignment query page
      • Modified the gene detail page to link to MHC Alleles
    • Other
      • Implemented an off-line Data QC pipeline for HLA typing results
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    ImmPort Version 2.1.2
    Released December 2007
    • Analysis:
      • Made GBrowse queries available to the general public without login
      • Added support for HapMap Phase II data within TagSNP
      • Added tracks for HapMap Phase II populations for LDSelect tagSNP on ImmPort Genes
    • Reference Data
      • Made reference queries available to the general public without login
      • Added support for HapMap Phase II data in the SNP Query pages
      • Added support for HapMap Phase II data in the Gene Detail pages
      • Further tuned the SQL for the reference query result and reference query detail pages to improve performance
    • Other
      • Deployed the production ImmPort system on new hardware platform containing clustered and more modern application and web servers, new database servers, and BigIP load balancing to effectively handle larger numbers of concurrent users
      • Added the requirement to accept the data sharing agreement online before proceeding into ImmPort
      • Imposed a more stringent password requirement
      • Implemented a better mechanism for displaying to the user that a session has timed out due to inactivity
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    ImmPort Version 2.1.1
    Released November 2007
    • Analysis:
      • Added the ArrayGenius Support Vector Machines categorization algorithm to IMAC
      • Corrected a navigation bug in the IMAC UI where selecting certain methods scrolled to the bottom of the page
      • Added support for two human genome builds (hg17 and hg18) in TagSNP
      • Updated the TagSNP tutorial
      • Added Known Gene tracks to GBrowse for hg18
      • Added SNP tracks to GBrowse for hg18
    • Data Submission: Data Submission Validator Beta
      • Added the ability to synch with the ImmPort database in order to improve checking and verification of data packages
      • Developed verification checks against controlled vocabularies downloaded from the ImmPort database during synching
      • Developed verification checks against user metadata in the projects downloaded or synched from the website
      • Removed the requirement of the full JDK for running the Data Validator
      • Replaced the verification of data submission extracted files with verification against the actual zipped data package
      • Developed verification rules for the zip package integrity and naming
      • Wrote a Data Validator Tutorial
      • Wrote a Data Validator User Guide
    • Reference Data
      • Added support for multiple human genome builds (hg17 and hg18) to the summary pages and detail pages of the reference queries
      • Modified the reference query detail pages to significantly improve performance by loading on demand instead of loading the content of all tabs and blocks immediately
      • Further tuned the SQL for the reference query result and reference query detail pages to improve performance
    • Known Issues
      • For large numbers of rows returned for the SNP Query, performance navigation between between pages is not optimal and will be further tuned
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    ImmPort Version 2.1
    Released August 2007
    • Analysis: Implemented a new and improved ImmPort gene expression analysis tool (ImmPort Microarray Analysis Component, IMAC). This tool provides the ability to:
      • Retrieve gene expression data across experiments into a simple text format for download or use as an ImmPort analysis data set
      • Utilize stored ImmPort data as a data set as input into the Pipeline and single analysis processes
      • Create clustering and categorization pipelines allowing you to view and download intermediate results
      • Upload non-ImmPort expression data to create data sets for use in the single analysis or pipelines processes
      • Define user defined stages where the user may download intermediate results, run a task (i.e. feature selection) utilizing their own algorithm on their own PC, and upload those results back into ImmPort to continue the pipeline
      • Manage analysis pipelines by canceling, deleting or pausing pipelines
      • Utilize additional dataset extension, normalization, categorization, clustering and feature selection algorithms based on Biomind's ArrayGenius platform
      • Analyze data with a single constituent algorithm as a single analysis step
    • Data Management
      • Added the ability to update research metadata for subjects, experiments, biological samples, experiment samples, reagents and protocols
      • Implemented the ability to associate and dissociate research entities utilizing a more interactive AJAX table component
      • Implemented an audit trail on all research data modifications
    • Data Submission
      • Providing a means to upload and retrieve HLA Typing results data
      • Support for HLA Typing reagents
      • Improving the reagent templates for ELISPOT and ELISA
      • Provide a BETA, early access version of a downloadable, command line data submission validator to provide earlier notification (before upload to ImmPort) of potential data package inconsistencies
    • Other
      • Provide a more informative front page with Events, System alerts, conferences, publications, and links
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    ImmPort Version 2.0
    Released May 2007
    • Analysis
      • Implemented generation of Linkage Pedigree (pre MAKEPED) format (.ped and .info) files from uploaded genotype results
      • Enabled user defined selection of subjects and markers to include in .ped and .info files
      • Implemented editing of subject's affection status when generating files
    • Data Submission
      • Revised ImmPort Home Page to enhance visibility of "Submit Data" option
      • Simplified workflow
      • Added assay result format field to experimentSamples.xls template and eliminated need to designate experiment result format for all data submission
      • Enabled upload of any file within a .zip file and eliminated requirement that a metadata transfer file accompany all data submissions
      • Implemented association of multiple results files to an experiment sample
      • Enhanced comments in templates to clarify how data is to be formatted and linked
      • Eliminated need to rename .zip files with data submission ticket name
      • Revised data submission user guide and tutorials
      • Added data submission vignette to describe uploading genotype data that can be used to generate Linkage Pedigree (pre MAKEPED) format files
      • Added Affection Phenotype field to the Subjects templates
      • Enabled automatic redirection to Data Submission History when data submission package is sent to ImmPort
      • Added links to Data Management and Research Data Search from Submission History
      • Enabled upload of derived flow cytometry results
    • Data Management
      • Enabled seletion of multiple research projects in queries
      • Implemented deletion of research projects, data submission tickets, experiments, experiment samples, biological samples, reagents, protocols, subjects and results
      • Enabled direct access to experiment samples and result files from Data Management queries
    • Reference Data
      • Corrected an issue with the navigation between the Protein Network complex and interaction tabs
    • Research Data Search
      • Enabled queries on flow cytometry derived results to find data files
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    ImmPort Version 1.4.1
    Released December 2006
    • Data Management
      • Updated reagents detail page for flow cytometry unique reagents
      • Implemented shopping cart for selection of entities from summary pages for view of detail pages
      • Enabled display of parsed .fcs TEXT section on the experiment sample page within data management
    • Data Submission
      • Updated reagents metadata transfer files for flow cytometry unique reagents
      • Enabled use of data povider internal unique identifiers for upload
      • Implemented parse of flow cytometry .FCS file text content
    • Reference Data
      • Added MIPS data
    • Research Data Search
      • Enabled search and download of data files based on microarray results
      • Implemented new query against analyte data
      • Implemented new query against research data based on text index of primary entities
      • Updated tutorials for the Research Data Query
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    ImmPort Version 1.4
    Released October 2006
    • Adminstration
      • Enhanced sorting of ImmPort users
      • Added Program Manager role
      • Expanded DAIT Program Officer's data management tool suite
      • Implemented dissociation of experiments to collaborative projects
      • Removed requirement to specify a Contract-Grant when registering
    • Analysis
      • Created tutorials for TagSNP, Data Submission
      • Added evolutionary conservation scores to tagSNP output and SNP query
    • Data Management
      • Enabled download of result file(s)
      • Display links between biological samples derived from other biological samples or subjects
      • Enabled download of data submission report which reports user defined IDs, ImmPort accessions, etc
    • Data Submission
      • Implemented upload of spreadsheet based metadata transfer file templates for biological samples, experiments, experiment samples, protocols, reagents and subjects
    • Research Data Search
      • Enabled search and download of data files based on microarray results
      • Implement new query against analyte data
      • Implement new query against research data based on text index of primary entities
      • Updated tutorials for the Research Data Query
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    ImmPort Version 1.3.1
    Released June 2006
    • Advanced Search
      • Corrected sorting behavior
    • Reference Data
      • Updated BIND references in Protein Network results
      • Updated Mendelian Inheritance in Man using revised data source file format
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    ImmPort Version 1.3
    Released June 2006
    • Adminstration
      • Collaborative Project (workspace)
        • The new collaborative project (CP) feature allows a principal investigator to create a CP and to authorize user access to the CP, just as with a research project. In addition, any of those users can assign experiments from their home research project to the CP. This allows multiple research groups to selectively and securely share research data and to use that data with the analysis tools implemented within ImmPort.
    • Analysis
      • Enhanced display of LD Select tagSNP output
        • The LD Select native output is now converted into a tabular display that includes the SNP ID and the SNP function. SNPs can be selected from the tabular display for inclusion in a downloadable text file.
      • Use of only unrelated subjects in HapMap populations for tagSNP analysis
      • Genetic analysis toolset based on Haploview
        • The Haploview enterprise version implemented in ImmPort uses standard linkage format files (.ped and .info files) for association study genetic analysis.
      • Enhancements to the Gene Expression Microarray analysis toolset
        • Gene expression microarray experiment data stored in ImmPort can be analyzed using ImmPort's enterprise implementation of the TIGR TM4 suite of analysis tools
      • Enhanced documentation and instructions for use of Gene Expression Toolset and tagSNP tool
    • Experiment Data Upload
      • Batch submission of genotyping data from Illumina panels in two formats
      • Batch submission of experimental data that does not fit into any of the defined formats
    • Advanced search
      • Advanced search of experiment data loaded in ImmPort using the Unicorn semantic query tool integrated into ImmPort. The Unicorn semantic query tool uses an ImmPort Experiment Ontology to facilitate queries of experiment data in the user's secure workspace within the ImmPort system without requiring the user to understand how the data is organized.
    • Reference Data Refresh
      • All reference data sources used in ImmPort were refreshed
      • Downloadable ImmPort Gene List with documentation on the Resources link
    • Known Issues
      • The Advanced Search ontology browser currently works only with Internet Explorer
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    ImmPort Version 1.2.1
    Released May 2006
    • Enhanced Experiment Data Upload
      • ImmPort Experiment Data model implemented for collecting metadata and experiments results
      • XML based system for collecting descriptions of experiment results
      • Support for many more result formats
      • Documentation of Data Upload Process
    • Reference Data Refresh
      • All reference data sources used in ImmPort were refreshed
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    ImmPort Version 1.2
    Released April 2006
    • Analysis
      • tagSNP
        • LD Select enterprise version integrated into ImmPort for tagSNP selection. LD Select uses the HapMap genotyping data.
        • Added GBrowse tracks for tagSNPs determined using the LD Select algorithm with eachof the five HapMap population groups.
      • Integration of TM4 MeV gene expression tool set into ImmPort enterprise solution
        • Gene expression result sets can be selected from the user's secure workspace within ImmPort and submitted to the gene expression analysis tools * Reference Data Refresh
      • All reference data sources used in ImmPort were refreshed
    • Reference Data Refresh
      • All reference data sources used in ImmPort were refreshed
    • Ontology
      • Added immunology terms proposed for addition to the Gene Ontology to ontology browser data display options.
      • Added select terms from the NCBI taxonomy to ontology browser data display options.
    • Back to Top
    ImmPort Version 1.1
    Released January 2006
    • Data Submission
      • Added Affymetrix Genotyping MAS5 data format to Experiment Data Upload supported data formats.
      • Clarified text describing data upload requirements.
      • Expanded dropdown menu width to accommodate long titles.
      • State that only .GSM and Family record formats are supported for GEO SOFT files.
      • Add upload header file information to email status reports.
    • Search
      • Populating Gene Ontology column in query result summary.
      • Enhanced sort behavior in Protein and SNP query results.
      • Enhanced text searching option in queries to include exact, starts with, ends with.
      • Display both molecules in Protein Network query results.
      • Clarified that only SwissProt accessions are returned for protein records.
      • Indicate which SNP records have HapMap genotype data.
      • Display SNP build version.
      • Add Pubmed titles to references blocks of detail pages.
    • Analysis
      • Added track for Affymetrix Human Genotyping 100k mapping panel data to Gbrowse.
      • Added track for Affymetrix Human Genotyping 500k mapping panel data to Gbrowse.
      • Added track for Illumina Human Genotyping 100k mapping panel data to Gbrowse.
      • Added track for Illumina MHC exon-centric panel data to Gbrowse.
      • Added track for Illumina MHC mapping panel data to Gbrowse.
      • Added text to distinguish ImmPort Genes in Gbrowse RefSeq and Known Genes tracks.
    • Ontology
      • Added extensive Gene Ontology to ontology browser data display options.
    • Administration
      • Added sort capability to Update Grant/Contracts pages.
      • Added "Reset Password" button to "View User Detail" screen.
      • Email notification of new registration requests are sent to Principal Investigator and Project Officer as appropriate.
      • Email reminders sent to PIs for pending registration requests.
      • Display Contracts-Grants without an access end date.
      • Remove requirement to provide user ID in Forget password/user ID function.
    • Reference Data Refresh
      • All reference data sources used in ImmPort were refreshed.
    • Help
      • Data Refresh History dynamically populated from database.
      • Updated documentation
    • Back to Top
    ImmPort Version 1.0
    Released October 2005
    • Reference Data Standard Query Interfaces, Summary Results and Detailed Results for:
      • Genes
      • ImmPort Gene List
      • Proteins
      • SNPs
      • Protein Networks
      • Pathways
    • ImmPort Gene List
      • The ImmPort Gene List was generated using automatic searches for immunology-related keywords in the National Center for Biotechnology Information Entrez Gene database and the Gene Ontology (GO).
    • Link between SwissProt accessions and EntrezGene IDs
      • A PIR generated link between SwisspProt accessions and Entrez Gene ID is provided to enhance the integration and association of data from multiple sources.
    • Gbrowse
      • Graphic representation of genome based information for genes, transcripts, and SNPs
    • Ontology
      • Disease Ontology
      • Gene Ontology
      • Custom ontology browser to view ontologies
    • Experiment Data Upload
      • Affymetrix Gene expression as MAS5 output
      • Affymetrix Genotyping as MAS5 output
      • GEO GSM and family files
      • HAPMAP XML files
    • Biomind Array Genius
      • Array Genius is a suite of tools for gene expression analysis
    • Administration
      • Registration and secure access provided to ImmPort system for DAIT funded research community
    • Known Issues
      • Array Genius is currently not working
    • Back to Top

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