SysBioCube User Guide

SysBioCube: Mission & Purpose

SysBioCube is the US Army Medical Research and Materiel Command’s (USAMRMC) integrated biomedical research data access and analysis platform for studies of health optimization, trauma-related conditions, and diseases of military relevance. The goal of the SysBioCube is to serve as a central portal for biomedical research data integration, visualization, analysis, mining, and sharing among the US Army’s medical research community, including collaborators from academic and private institutions.

SysBioCube is being developed by the Advanced Biomedical Computational Sciences (ABCS) at the Frederick National Laboratory for Cancer Research (FNLCR) sponsored by the National Cancer Institute. The Systems Biology Collaboration Center (SBCC), an office hosted at the US Army Center for Environmental Health Research (USACEHR), oversees and coordinates the activities of the SysBioCube.

Additional programmatic guidance for the SysBioCube comes from the USAMRMC’s SysBioCube Governance Committee, which includes representation from active users. One of the most active users is USACEHR’s Integrative Systems Biology Research Program, which has been working with collaborators towards an improved understanding of the Coagulopathy of Trauma and Post-Traumatic Stress Disorder. Other US Army research centers contributing data and guidance include the US Army Medical Research Institute of Chemical Defense, the US Army Research Institute of Environmental Medicine, the US Army Institute of Surgical Research, and the Walter Reed Army Institute of Research. Moreover, USAMRMC researchers using the SysBioCube have collaborated with many academic and private institutions across the country, including Cornell University, Denver Health and Hospital Authority, Emory University, Harvard University, Icahn School of Medicine at Mount Sinai, Institute for Systems Biology, New York University, University of California at San Francisco, University of California at Santa Barbara, University of Vermont, and the Washington Hospital Center.

The SysBioCube allows collaborative study groups to share and analyze data through restricted-access web portals. Clinical, pathophysiological, psychological, molecular, and biochemical data from human study participants (de-identified data ONLY) and animal models generated by US Army study collaborators are uploaded into the SysBioCube repository. These datasets are made available to approved users through fine grained, role-based access and can also be publicly released when published. The approved users can access data through different SysBioCube features for browsing, querying, automated integration, and custom visualization in order to better understand military-relevant health issues.

Last Reviewed: 27 June, 2018

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Web Interface

SysBioCube is developed as a disease-agnostic and data-aware user interface. This means that once a feature is released into SysBioCube it automatically becomes available for any new project with similar data sets. The web pages are generated dynamically for each project based on available data.

The data in SysBioCube has restricted access and is available only to authorized users under specific collaborations. However, the current version includes sample cancer data sets from the National Cancer Institute’s TCGA project and published mRNA microarray data sets from the PTSD mouse project to demonstrate the features and functionalities in SysBioCube. These sample data sets are available to all without any access restrictions.

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Login

Authorized users can login to the interface using the username and password provided by SysBioCube. Users can also request to reset their password by clicking on the 'Forgot Password' button. Upon successful authentication, users will be able to access data available to them through authorization along with the public data sets.

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Explore Files

The Explore panel provides users with multiple options to browse through the available project-specific files and/or data sets in a selected project, as well as any publicly released project data sets. The documents and data are pulled dynamically through a database query allowing for custom interfaces for each user.

Tree View tab provides a comprehensive and dynamic branching schematic depicting project files organized by file metadata (e.g., Species, Strain, Group, Experiment, Data Type and Tissue).

Data Overview tab provides a tabular output of all available data by file counts and total size.

Data Files tab provides users with the option of a detailed file level browsing feature where metadata are displayed based on experimental categories. Users have the option to preview files which allows for visualization of the first 20 rows and all columns or the first page of a file, depending on the file type. Users can also download individual files by clicking on any of the file links.

The Manage Files tab is only available to registered users who uploaded files to the project or registered users who have been designated as managers of the files. It allows the user to manage their data through file archive and restoration features.

The PI Team Files tab is available only to the lead project principal investigator(s) (PI) and allows the PI to manage all files associated with their team/project(s).

Last Reviewed: 16 October, 2018

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Upload Data

Only authenticated users can upload files to their authorized projects. The upload form gathers minimal information on the file metadata, which allows the SysBioCube to categorize, organize and provide fine-grained access control on each of the uploaded files.

Note: File upload speed is directly related to the bandwidth on the user’s network.

Last Reviewed: 27 June, 2018

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Download Data

In addition to public data sets, authenticated SysBioCube users have access to private project data sets based on their role within a project. As with all other SysBioCube features, the user interface for download was designed in a data agnostic and modular fashion where the data matrix is built dynamically for each project and user. Overall, the dropdown project select boxes, table rows, column headers, and file counts in each of the cells are generated dynamically based on the access levels of the user and the current information for the project. Unlike the Data Files tab in the Explore panel, users are able to download sets of files, rather than single files; the files are zipped for ease of accessibility. Zipping the file(s) may take time when requesting a substantial number of files or a large amount of data, as such users are sent a link via email to access the zipped file when completed.

Note: File upload speed is directly related to the bandwidth on the user’s network.

Last Reviewed: 27 June, 2018

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Analysis Pipelines

Authenticated users can upload their own data sets and run automated analysis using any of the approved SysBioCube analysis algorithms. The feature uses the compute cluster available at the FNLCR and currently has analysis capabilities for transcriptomics, metabolomics and variant annotations.

This feature is restricted to registered users only.

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Integrated Analysis

The feature uses the biological identifier conversion application 'bioDBnet' and the functional clustering application 'DAVID' to integrate analyzed data sets from different omics experiments such as mRNA microarrays, methylation, metabolomics and proteomics. The feature can also be used to compare functional impact across different cohort groupings and species.

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Assay Tracker

Complex collaborations across multiple clinical, assay and analysis sites often necessitate the need to communicate and translate the information on samples and progress of the assays under the study. The dynamic and interactive Assay Tracker feature is designed to allow those communications happen in a seamless intuitive fashion so that the assays can be prioritized and time-lines established for different components of the collaboration to progress smoothly.

This feature is restricted to registered users only.

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Clinical Explorer

Generating clinical reports on patient cohorts is often a complicated manual process. The explorer is a data agnostic interactive visualization module that helps clinicians and researchers to dynamically filter, download and run analytics on the clinical data collected across multiple clinical sites. The feature also allows the users to do cohort comparisons using box plots and line charts.

Dashboards can be defined, saved and shared with other study members. This allows for collaborative discussions and sharing of findings.

This feature is restricted to registered users only.

Last Reviewed: 17 August, 2018

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Sample Tracker

The feature was developed for tracking sample aliquot collections at multiple clinical sites. The tool allows clinicians and researchers to track sample availability, for conducting planned assays, by patients, time points and biospecimen types. The interactive and custom features in Sample Tracker guide changes to the clinical collection or enrollment protocols by providing insights into the patient populations.

This feature is restricted to registered users only.

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User Guide

The User Guide provides an overview on the SysBioCube application and a short description on each feature, along with current access controls. The guide can be accessed using the navigation menu, or by clicking on the information icon ‘?’ in the upper right corner of any page to reference the specific section of the guide associated with the page.

Note: When the information icon is selected, the User Guide will be opened in a separate tab.

Last Reviewed: 15 June, 2018

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Publications

The Publications interface was created by integrating with the Tool for Text Mining (ToTeM) developed by the Advanced Biomedical Computational Sciences (ABCS) at the Frederick National Lab for Cancer Research (FNLCR). ToTeM provides a text mining interface to MEDLINE® abstracts that are automatically updated on a daily basis. The Publications interface aims to provide a convenient link to PubMed® publications related to projects within SysBioCube. The current configuration references abstracts authored by the systems biology collaborators in the PTSD and Coagulopathy of Trauma consortiums.

Last Reviewed: 15 June, 2018

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Documents

The Documents interface serves as a resource for sharing files that provide background information on policies, procedures and details related to SysBioCube.

Last Reviewed: 15 June, 2018

v2.5.14, April 24, 2019

This patch includes updated SOPs.

Tickets (Admin Notes Only)
Improvements
  • SBC-363 [General] : Update several SOPs

v2.5.13, April 17, 2019

This patch includes file management logging, Explore and Clinical Explorer improvements.

Tickets (Admin Notes Only)
Improvements
  • SBC-362 [Explorer] : Hide Explorer Preview Button if file size is greater then defined preview limit
  • SBC-361 [Clinical Explorer] : Hide Refresh Data tab after loading a dashboard
  • SBC-360 [Clinical Explorer] : Add keyboard stroke time delay on search field
  • SBC-359 [Administration] : Add system log for File Management
Fixes
  • SBC-350 [General] : Dashboard does not remember data provider settings
  • SBC-292 [General] : Change audit logs permissions

v2.5.12, April 3, 2019

This patch includes file management functionality, 508 compliance fixes and a new Explorer SOP.

Tickets (Admin Notes Only)
Improvements
  • SBC-356 [Administration] : Update File Administration
  • SBC-355 [General] : Add new Explore SOP
  • SBC-353 [General] : Fix 508 compliance issues
  • SBC-352 [Pipeline Analysis] : Implement Pipeline Analysis on the Slurm cluster
Fixes
  • SBC-358 [Clinical Explorer] : Prevent Dashboard update dialog from colliding with message dialog
  • SBC-357 [Clinical Explorer] : Restore FilterMode & FilterInput after opening dashboard
  • SBC-354 [General] : Change the word Disease to Study

v2.5.11, March 08, 2019

This patch includes file management functionality and bug fixes.

Infrastructure and Backend (Admin Notes Only)
Tickets (Admin Notes Only)
Improvements
  • SBC-349 [Clinical Explorer] : Add additional coagulopathy data elements (Burn.totalBodySurfaceArea and Outcome.Discharge.*)
  • SBC-348 [Assay Tracker] : Add TEG/Rotem assay grouping
  • SBC-347 [Administration] : Only allow certain logs to be shown via UI
  • SBC-345 [Pipeline Analysis] : Allow Pipeline Analysis to support multiple configurations
  • SBC-343 [Administration] : Add File Management
  • SBC-342 [General] : Update New User request document
  • SBC-77 [Pipeline Analysis] : Move the logs, uploads and outputs directories to shared space
Fixes
  • SBC-346 [Administration] : Attempting to display System Logs for missing months causes an error
  • SBC-341 [Explore] : File preview unable to show mp4 videos

v2.5.10, February 05, 2019

This patch includes study management functionality and audit enhancements.

Tickets (Admin Notes Only)
Improvements
  • SBC-339 [Administration] : Refactor the Exceptions audit to be viewable in Administration system logs
  • SBC-326 [Administration] : Add Study Management functionality
Fixes
  • SBC-340 [Explore] : File preview raising error

v2.5.9, January 24, 2019

This patch includes bug fixes and system log viewing.

Tickets (Admin Notes Only)
Improvements
  • SBC-338 [General] : Update SOP Getting Started: New Project
  • SBC-337 [Administration] : Refactor the FileUpload audit to be viewable in Administration system logs
  • SBC-336 [Administration] : Add predefined filters for system logs
  • SBC-335 [Administration] : Allow systems logs to be viewed by date range

v2.5.8, January 15, 2019

This patch includes bug fixes and role management functionality.

Tickets (Admin Notes Only)
Improvements
  • SBC-333 [Administration] : Improve audit log format/information
  • SBC-330 [Analysis Pipelines] : Centralize SOP documents
  • SBC-329 [Administration] : Role Administration improvements
  • SBC-328 [Administration] : User Administration improvements
Fixes
  • SBC-334 [General] : Explicitly set timezone in application
  • SBC-332 [Administration] : Add headers for audit logs
  • SBC-331 [General] : Assign correct permission (chmod) to audit files when created

v2.5.7, January 8, 2019

This patch includes bug fixes and role management functionality.

Tickets (Admin Notes Only)
Improvements
  • SBC-325 [Explore] : Show Upload time (HH24:MI) along with the date
  • SBC-324 [DB-Oracle] : Cleanup the Access_Role table
  • SBC-320 [Explore] : Order Explore Tree View alphabetically (case-insensitive)
  • SBC-319 [Administration] : Add Role Management functionality
Fixes
  • SBC-327 [Download] : Error downloading files with spaces in the path name
  • SBC-323 [Integrated Analysis] : Integrated Analysis convert SQL ListAgg call to wm_concat
  • SBC-322 [Integrated Analysis] : Integrated Analysis has incorrect file counts
  • SBC-321 [Explore] : Data Overview has incorrect file counts and file sizes
  • SBC-318 [Download] : Download Matrix has incorrect file counts
  • SBC-029 [Upload] : Change FileId type from number to identity

v2.5.6, December 11, 2018

This patch includes role improvements and user management functionality.

Tickets (Admin Notes Only)
Improvements
  • SBC-312 [Clinical Explorer] : Only show dashboards based on user role that they own or are shared
  • SBC-311 [General] : Add Project Access Request form
  • SBC-310 [Clinical Explorer] : Selecting '---' from a Pie Chart causes no records to be shown in datatable
  • SBC-306 [General] : Provide public role as implicit access
  • [Administration] : Add User Management functionality
Fixes
  • SBC-308 [Explore] : Order Projects alphabetically (case-insensitive)
  • SBC-307 [Clinical Explorer] : Attempting to delete a newly created dashboard fails

v2.5.5, October 31, 2018

This patch includes a new Assay Tracker report.

Tickets (Admin Notes Only)
Improvements
  • SBC-301 [Assay Tracker] : Full Details report.
Fixes
  • SBC-305 [Database] : Provide general database warnings to user
  • SBC-304 [General] : Update .htaccess
  • SBC-303 [Analysis Pipelines] : Relocate Pipelines SOP symbolic link
  • SBC-302 [General] : Resolve AppScan identified issues

v2.5.4, October 16, 2018

This patch includes Assay Tracker report updates and minor updates to the Clinical Explorer.

Tickets (Admin Notes Only)
Improvements
  • SBC-300 [User Guide] : Update User Guide --> Explore.
  • SBC-296 [General] : Use min.js and min.css where possible in the controllers.
Fixes
  • SBC-299 [Clinical Explorer] : ScatterPlot brush visualization issues.
  • SBC-298 [General] : Resolve AppScan identified issues.
  • SBC-297 [Clinical Explorer] : Patch slimscroll library for Firefox.
  • SBC-294 [General] : Update Composer install script.
  • SBC-293 [Assay Tracker] : Fix the Assay Tracker Assay/Clinical Details report.

v2.5.3, October 4, 2018

This patch includes Internet Explorer browser fixes, minor updates to the Clinical Explorer and upgrades several 3rd party libraries.

Infrastructure and Backend (Admin Notes Only)
Tickets (Admin Notes Only)
Improvements
  • SBC-290 [Clinical Explorer] : Add debounce to certain event handlers to improve performance.
  • SBC-288 [Clinical Explorer] : Implement RangeMin, RangeMax and RangePad preferences for LineCharts.
Fixes
  • SBC-287 [General] : Resolve AppScan identified issues.
  • SBC-284 [Clinical Explorer] : Combine Fields in DataTable can't be saved in Clinical Explorer Dashboard
  • SBC-283 [Explore] : IE Browser raising an error.

v2.5.2, September 19, 2018

This patch includes Internet Explorer browser fixes, minor updates to the Clinical Explorer and upgrades several 3rd party libraries.

Infrastructure and Backend (Admin Notes Only)
Tickets (Admin Notes Only)
Improvements
  • SBC-278 [Clinical Explorer] : The invalid chart path dialog should only be display on an initial dashboard load.
  • SBC-276 [Clinical Explorer] : Do not allow a dashboard to be saved with no charts.
  • SBC-275 [Clinical Explorer] : Allow saving of a dashboard while still in name field.
  • SBC-271 [Upload Data] : Virus scans are executing slow on development servers.
Fixes
  • SBC-279 [Explore] : IE Browser raising an error.
  • SBC-277 [Clinical Explorer] : Removing a chart using the quick link doesn't fully remove it.
  • SBC-274 [Integrated Analysis] : Perl library location change.

v2.5.1, September 11, 2018

This patch adds the ability to create and delete Clinical Explorer dashboards. Also included are several improvements to the various charts within the Clinical Explorer.

Tickets (Admin Notes Only)
Improvements
  • SBC-262 [Explore] : Explore preview for excel shows extra blank lines.
  • SBC-261 [Clinical Explorer] : Charts should allow range preferences from metadata.
  • SBC-260 [Clinical Explorer] : Box Plot chart precision is too small.
  • SBC-257 [Clinical Explorer] : Allow the user to create a new (empty) dashboard.
  • SBC-256 [Clinical Explorer] : Allow the user to view dashboard information after loading.
  • SBC-255 [Clinical Explorer] : Display the dashboard name currently loaded.
  • SBC-252 [Clinical Explorer] : Allow dashboards to be deleted.
Fixes
  • SBC-270 [Upload Data] : Large files timeout during virus scanning.
  • SBC-269 [Clinical Explorer] : Crossfilter dimensions are not being disposed properly.
  • SBC-268 [Clinical Explorer] : Charts redraw multiple times when filters applied after a dashboard load.
  • SBC-264 [Clinical Explorer] : If no data exists when determining statistics display "No Data".
  • SBC-259 [Clinical Explorer] : HTML legend color disappears on long test items.
  • SBC-258 [Clinical Explorer] : Allow Line Charts to be loaded from dashboard without and filter IDs.
  • SBC-254 [Clinical Explorer] : Ignore dashboards that are no longer associated with an active or missing dataset.
  • SBC-253 [Clinical Explorer] : Verify dashboard fields and alert user is not found in metadata.

v2.5, August 22, 2018

This release allows users to load and save Dashboards defined in the Clinical Explorer. Dashboards can be shared with other members of a study or kept private. Also included are several improvements to the various charts within the Clinical Explorer.

Tickets (Admin Notes Only)
Improvements
  • SBC-250 [Clinical Explorer] : Pie Chart should always display the missingLabel as the last element in the legend.
  • SBC-248 [Clinical Explorer] : Remove chart capture button until it can be enhanced.
  • SBC-244 [Clinical Explorer] : Remove Documents section for Cloud Computing.
  • SBC-243 [Clinical Explorer] : Allow dashboards to be saved and loaded.
  • SBC-242 [Clinical Explorer] : Line Chart is ignoring metadata format for X axis.
  • SBC-241 [Clinical Explorer] : Line Chart Y Axis is not dynamic.
  • SBC-238 [Clinical Explorer] : Increase the default color schema from 10 to 20 for Pie, Box and Line charts.
  • SBC-235 [Clinical Explorer] : Allow EHP role access to the Clinical Explorer.
Fixes
  • SBC-251 [Clinical Explorer] : Line Charts need to handle undefined/NaN values.
  • SBC-240 [Clinical Explorer] : Scatter Plot tool tip shows duplicate info when element is a collection key.
  • SBC-237 [Clinical Explorer] : Box Plots ignore metadata legend preference order.
  • SBC-236 [Clinical Explorer] : Scatter Plot statistics not including duplicate values for a unique ID in the active or filtered data.

v2.4.1, July 20, 2018

This patch fixes an issue when requesting a download larger than 9GB from the Download Data matrix.

Tickets (Admin Notes Only)
Fixes
  • SBC-233 [Clinical Explorer] : Cleanup sidebar jitters when expanding tree.
  • SBC-232 [Clinical Explorer] : Clear crossfilter dimensions before clearing the chart registry.
  • SBC-231 [Clinical Explorer] : Handle filtering of undefined values ('---') for PieCharts.
  • SBC-217 [Download Data] : Downloading large files (9GB+) fail via the Access Download Data.

v2.4, July 11, 2018

This release has added Line Charts to the Clinical Explorer for longitudinal data analysis. Also included are new/updated SOP documents and User Guide sections along with bug fixes.

Infrastructure and Backend (Admin Notes Only)
Tickets (Admin Notes Only)
Improvements
  • SBC-226 [Clinical Explorer] : Performance improvement when creating general charts.
  • SBC-223 [Clinical Explorer] : Assign yAxisLabel to last element of path if title is not defined in metadata.
  • SBC-221 [Clinical Explorer] : Assign default yAxisFormat if not defined by metadata.
  • SBC-219 [Clinical Explorer] : Added search icon to dropdown selector search text boxes.
  • SBC-213 [Documents] : Added New Project and New Account SOPs.
  • SBC-211 [Clinical Explorer] : Added Line Charts to analyze longitudinal data.
  • SBC-210 [User Guide] : Update User Guide --> Overview and Access sections.
Fixes
  • SBC-225 [Clinical Explorer] : Handle array metadata definitions that store the data as a string.
  • SBC-222 [Clinical Explorer] : Searching for Chart and DataTable fields in sidebar loses previous selections.
  • SBC-220 [Clinical Explorer] : Change unit attribute wrapping from [] to ().
  • SBC-218 [Clinical Explorer] : BoxPlot X-Axis dropdown caret not enabled.
  • SBC-212 [Upload Data] : Upload Data showing incorrect PI Location and institute.
  • SBC-208 [Download Data] : Error when attempting to view category with more than 1000 files.

v2.3.7, June 15, 2018

This patch includes a new feature in the Clinical Explorer to allow filtering on the Primary Key element. Plus additional bug fixes and improvements.

Infrastructure and Backend (Admin Notes Only)
Tickets (Admin Notes Only)
Improvements
  • SBC-202 [User Guide] : Update User Guide --> About sections.
  • SBC-201 [Clinical Explorer] : Allow filtering based on primary key.
  • SBC-200 [Infrastructure] : Upgrade to crossfilter 1.4.6.
Fixes
  • SBC-206 [Clinical Explorer] : DataTable empty after refreshing data with a scatterplot filtered.
  • SBC-205 [Clinical Explorer] : Update chart statistics after removing filter from a scatterplot chart.
  • SBC-204 [Pipeline Analysis] : Allow approved file extensions to be uploaded.

v2.3.6, May 30, 2018

This patch includes minor updates to the Clinical Explorer and Pipeline Analysis modules.

Infrastructure and Backend (Admin Notes Only)
Tickets (Admin Notes Only)
Improvements
  • SBC-195 [Clinical Explorer] : Add search box to BoxPlot field selection dropdowns.
  • SBC-194 [Assay Tracker] : Add new Study Summary report.
  • SBC-193 [Infrastructure] : Upgrade to jsPdf 1.4.0 and jsPdf AutoTable 2.3.4.
  • SBC-192 [Infrastructure] : Upgrade to dc.js 2.2.0 which includes the new BoxPlot enhancements.
  • SBC-191 [Assay Tracker] : Re-arrange chart groups and add 5 new assays to the Inflammatory Markers chart.
Fixes
  • SBC-199 [Clinical Explorer] : Add Reset button to BoxPlots panel.
  • SBC-198 [Pipeline Analysis] : Add SOP link to Microbiome Pipeline card.
  • SBC-197 [Pipeline Analysis] : Move close button from Pipeline cards to Pipeline tabs.
  • SBC-196 [Clinical Explorer] : Fix jsTree search to show no results when search string does not match any fields.
  • SBC-180 [Clinical Explorer] : DataTable needs to show collections tabs (if needed) on initial dataset load.

v2.3.5, May 10, 2018

Gene clusters, and functional overlap across the various omics analysis, derived from our Integrated Analysis feature can now be visualized using the Panoromics application.

Infrastructure and Backend (Admin Notes Only)
  • Upgraded jsTree library from 3.3.3 to 3.3.5
Tickets (Admin Notes Only)
Improvements
  • SBC-189 [Assay Tracker] : Add Injury Severity Score (ISS) chart for COAG to assist in determining priority list.
  • SBC-186 [Integrated Analysis] : DAVID Term Clusters, Gene Clusters and Integrated Analysis can be exported to be viewed in the Panoromics application.
  • SBC-181 [Clinical Explorer] : Allow preference for default xAxis for BoxPlot configuration.
  • SBC-179 [Clinical Explorer] : Allow preference for dropdown label (title, or path) for BoxPlot configuration.
Fixes
  • SBC-187 [Clinical Explorer] : Element tree All button will not show all elements after Selected button pressed.
  • SBC-185 [Clinical Explorer] : ResetAll link caused multiple statistic function calculations.
  • SBC-183 [Clinical Explorer] : ScatterPlot statistics being called twice during filtering.
  • SBC-182 [Clinical Explorer] : ScatterPlot disable standard tooltip.
  • SBC-178 [Clinical Explorer] : Chart statistics calculated incorrectly.

v2.3.3, Apr 23, 2018

Improvments
  • The User Guide is standardized and Help links are added across the site for easier access to documentation.
Tickets (Admin Notes Only)
Improvements
  • SBC-168 [User Guide] : Add Help icons to modules.
  • SBC-167 [User Guide] : Refactor User Guide module.
Fixes
  • SBC-177 [Clinical Explorer] : Unwinding chart data does not include pseudo index value in dataset.
  • SBC-176 [Clinical Explorer] : BoxPlot does not handle invalid numeric values.
  • SBC-175 [Clinical Explorer] : BoxPlot yAxis does not use prefYAxisFormat metadata.
  • SBC-174 [Clinical Explorer] : BoxPlot has blank x and y axis labels.
  • SBC-173 [Clinical Explorer] : Assigning Infinity to null values from Mongo causes interpretation issues in charts.
  • SBC-172 [Clinical Explorer] : ScatterPlot tooltip missing pseudo collectionkey.
  • SBC-171 [Clinical Explorer] : ScatterPlot tooltip missing collectionKey definition if values is 0.
  • SBC-170 [Clinical Explorer] : ScatterPlot tooltip title is blank if the elements title is not defined
  • SBC-169 [Clinical Explorer] : Collections will not display in a datatable tab if a subkey is not defined.
  • SBC-166 [Clinical Explorer] : Collections below 1st level can not be unwound for datatables.

v2.3.2, Mar 29, 2018 (Admin Notes Only)

This patch includes bug fixes to virus scanning and large file downloads.

Tickets
Fixes
  • SBC-163 [Download] : Enabled Apache module XSendFile to allow large file downloads (10GB+).
  • SBC-162 [Upload] : Fixed bug in our code whiched caused false positives during virus scans.

v2.3.1, Mar 14, 2018 (Admin Notes Only)

This patch includes enhancements to the Clinical Explorer.


v2.3, Mar 12, 2018

New
  • An initial release of the Clinical Explorer feature is available for our Coagulopathy collaborators. A public dataset is planned to be released in the near future.
Infrastructure and Backend (Admin Notes Only)
Tickets (Admin Notes Only)
Improvements
  • SBC-### [Upload] : Add virus alert email.
Fixes
  • SBC-### [Upload] : Upgrade phpMussel to fix false positives.
  • SBC-### [Database] : Change SQL LISTAGG call to wm_concat.

v2.2.1, Nov 9, 2017

New
  • Files can now be archived and restored by users who own the files and their principle investigators (PI) using the Explorer module.
Tickets (Admin Notes Only)
Improvements
  • SBC-154 [Explorer] : Allow users to archive/restore files they own
Fixes
  • SBC-161 [Explorer] : After resizing browser window table headers can become misaligned
  • SBC-160 [Upload] : Upload workspace directory does not sanitize variable used for directory name
  • SBC-159 [Upload] : Upload workspace directory not unset after use
  • SBC-158 [Upload] : Uploading a duplicate filename inserts a row in the database
  • SBC-157 [Explorer] : Email interface can not send to only SysBioCube email address
  • SBC-156 [Explorer] : File Actions are not properly disabled on Pages > 1
  • SBC-155 [Explorer] : Download causes blank tab to display temporarily

v2.2, Oct 26, 2017

New
  • The Integrated Analysis feature allowing functional integration of data sets across experiments and studies is now part of SysBioCube.
  • A pilot implementation of the Assay Tracker feature is available for our Coagulopathy collaborators.
Tickets (Admin Notes Only)
Improvements
  • SBC-152 [Assay Tracker] : Initial development of Assay Tracker

v2.1.7, September 29, 2017 (Admin Notes Only)

This patch includes SQL Injection HRV fix.

TICKETS
Fixes
  • SBC-152 : SQL Injection HRV (INC-3258315)

v2.1.6, August 21, 2017 (Admin Notes Only)

This patch includes Sample Tracker enhancements.

TICKETS
Improvements
  • SBC-148 [Release Notes] : Standardize release notes
  • SBC-146 [Sample Tracker] : Enhance sample tracker features

v2.1.5, July 13, 2017 (Admin Notes Only)

This patch includes a download fix and an enhancement to display file size information.

TICKETS
Fixes
  • SBC-123 [Oracle] : User account creation incorrectly assigning User_ID
  • SBC-121 [Download] : Disease and Species name missing from front-end of download file name
Improvements
  • SBC-135 [Oracle] : Populate the File_Size for all existing files in the FILE_INFO table
  • SBC-134 [Upload] : Update File_Size column when file is Uploaded
  • SBC-133 [Explorer] : Update column information for Explore | Data Overview
  • SBC-132 [Oracle] : Add Oracle function - Humanize_Filesize
  • SBC-131 [Oracle] : Add File_Size column to existing views
  • SBC-130 [Explorer] : Change default sort order for Explore | Data Overview to Strain & Tissue
  • SBC-129 [Explorer] : Change default sort order for Explore | Data Files to Upload Date descending
  • SBC-128 [Explorer] : Add column File_Size to the Explore | Data Files
  • SBC-127 [Oracle] : Add File_Size column to File_Info table

v2.1.4, July 6, 2017 (Admin Notes Only)

This patch includes browser compatibility fixes for Internet Explorer.

TICKETS
Fixes
  • SBC-117 [General] : Update carousel buttons & links to new routes
  • SBC-111 [Sample Tracker] : Internet Explorer bug related to javascript ES6
Improvements
  • SBC-120 [Integrated Analysis] : Remove Pipeline_User_File table
  • SBC-119 [Integrated Analysis] : Remove Integrated Analysis
  • SBC-118 [Analysis Pipeline] : Refactor Analysis Pipelines code into MVC format
  • SBC-116 [Explorer] : Prevent malicious URL manipulation file downloads
  • SBC-86 [Analysis Pipeline] : Upgrade to latest plUpload library

v2.1.3, June 19, 2017 (Admin Notes Only)

This patch includes bug fixes for Forgot Password, session timeout and infrastructure improvements.

TICKETS
Fixes
  • SBC-112 [Explorer] : Large files are causing explorer preview to raise an error
  • SBC-108 [General] : Assign Integrated Analysis to Admin role only
  • SBC-106 [Explore] : Remove .biom and .fasta extensions from preview
  • SBC-104 [General] : Forgot Password panel will not accept emails with incorrect case
  • SBC-103 [General] : Password with "$" symbol are not recognized during login
  • SBC-102 [Infrastructure] : Confusing message displayed after session timeout and subsequent login
  • SBC-097 [General] : Error during password reset process
Improvements
  • SBC-109 [Infrastructure] : Remove old Oracle DB Utilities and variables
  • SBC-107 [Upload] : Add .qual extension as a valid upload
  • SBC-100 [Download/Upload] : Refactor download and upload modules
  • SBC-099 [Explorer] : Refactor explorer modules

v2.1.2, May 25, 2017 (Admin Notes Only)

This patch includes bug fixes for data downloads.

TICKETS
Fixes
  • SBC-098 [Download] : Bug fix for data downloads

v2.1.1, May 22, 2017 (Admin Notes Only)

This patch includes bug fixes and infrastructure improvements, focused on the Explore | Data Files and Analysis Pipelines pages.

TICKETS
Fixes
  • SBC-095 [Oracle] : Cleanup file_info table extensions
  • SBC-093 [Oracle] : Filename discrepancies between the database and file repository
  • SBC-092 [Infrastructure] : phpmussel configuration incorrect after installation via composer
  • SBC-091 [Explore] : Can not preview xls file extensions
  • SBC-088 [Explore] : Handle all errors when trying to preview a file
  • SBC-087 [Explore] : Can not preview file with extension in all CAPS
  • SBC-080 [Analysis Pipeline] : Disable output file links until pipeline execution has completed
  • SBC-078 [Oracle] : Add update/insert privileges to user_view object
  • SBC-076 [Analysis Pipeline] : Empty directories (logs/outputs/uploads) need to be created during deployment
Improvements
  • SBC-094 [Infrastructure] : Remove old libraries from repository
  • SBC-090 [Explore] : Validate the upload data form fields on the fly
  • SBC-089 [Explore] : Convert m1v videos to mp4 so they can be previewed
  • SBC-084 [Analysis Pipeline] : Add Dashboard button to allow user to navigate back to the Pipeline Analysis Dashboard
  • SBC-081 [Analysis Pipeline] : Add Delete button to allow the user the delete an analysis output
  • SBC-075 [Analysis Pipeline] : Rerun all pipelines save as sample outputs
  • SBC-074 [Analysis Pipeline] : Add final report when pipeline execution has completed

v2.1, May 9, 2017

New
  • A Health and Human Services (HHS) warning banner is displayed before the user logs into SysBioCube.
  • Users can now preview most files from the Explorer Data Files tab before downloading the file locally.
  • A user that is logged into SysBioCube can submit a request to have their profile updated.
  • Microbiome pipeline has been add to Pipeline Analysis.
  • New extensions (.biom and .fasta) have been allowed for file uploads.
Improvements
  • Only files related to the selected pipeline are shown for selection.
Infrastructure and Backend
  • Upgraded Crossfilter library to 1.4.0-alpha.06
  • All uploaded files are scanned for viruses. If a virus is found the file will be quarantine and the user will be notified.
  • The user table has been redesigned to add several new features that allow for a more effective user management.
  • Additional details have been added to the audit logs for user access, file downloads and uploads.
  • Filename sanitation rules have been corrected during file uploads.
Tickets (Admin Notes Only)
  • SBC-001 [General] : Cross-site forgery
  • SBC-002 [General] : Standardize DB connection configurations
  • SBC-004 [General] : Audit file downloads
  • SBC-006 [General] : User profile updates
  • SBC-012 [Clinical Explorer] : Develop initial release of Clinical Explorer (Admin only)
  • SBC-039 [General] : Remove unused files and refactor current files
  • SBC-040 [Infrastructure] : Integrated Composer
  • SBC-041 [Infrastructure] : Integrated phpMailer library
  • SBC-043 [Infrastructure] : Began to use internal Gitea repository
  • SBC-044 [Upload] : Changed validator for upload group field
  • SBC-046 [Analysis Pipeline] : Only show related files based on selected pipeline
  • SBC-048 [Download/Upload] : Changed default Disease and Species to first item in the list
  • SBC-052 [Sample Tracker] : Update Assay Volume requirements
  • SBC-056 [Download] : Add modal preview to the Explorer download load file links
  • SBC-057 [DB - Oracle] : Enhance the Users table
  • SBC-058 [General] : Add warning banner requirement
  • SBC-060 [Clinical Explorer] : Dimension field should not be hardcoded
  • SBC-061 [Clinical Explorer] : Allow different fields to be displayed in charts and the datatable
  • SBC-062 [Infrastructure] : Upgrade Crossfilter library
  • SBC-063 [Upload] : Scan for viruses in uploaded files
  • SBC-066 [Upload] : Fix filename sanitation during file upload
  • SBC-067 [Upload] : Fix group field sanitation during file upload
  • SBC-068 [Analysis Pipeline] : Add Microbiome pipeline
  • SBC-071 [Upload] : Allow new extension for file uploads (.biom)
  • SBC-072 [Upload] : Allow new extension for file uploads (.fasta)

v2.0.2, February 21, 2017 (Admin Notes Only)

Fixes
  • SBC-023 [Upload/Download] : Update email headers sent from SysBioCube
  • SBC-031 [General] : Fix session expiration when user logs in from any csrf enabled page
  • SBC-033 [General] : Create Symbolic Link for Analysis Pipelines documents
  • SBC-034 [General] : Allow pages to define access permissions
Improvements
  • SBC-015 [Upload/Download] : Centralize upload and download configuration tokens
  • SBC-025 [Upload] : Handle uploads with duplicate names
  • SBC-028 [Upload] : Auto-focus associated input when Other is selected in dropdown
  • SBC-036 [Upload] : Validate upload drop-downs when Other is selected

v2.0.1, February 8, 2017 (Admin Notes Only)

Fixes
  • SBC-008 [Upload] : Modify filenames based on standards
  • SBC-011 [Upload] : File extension incorrectly determined
Improvements
  • SBC-007 [Upload] : Allow Group dropdown to select Other and define a new group
  • SBC-014 [Upload] : Standardize upload email template
  • SBC-019 [User Guide] : Dynamic Release Notes based on role
  • SBC-024 [Audit] : Breakout user login audits to a separate log
  • SBC-027 [Sample Tracker] : Legend/Note modifications for Scat and Citrate bar charts

v2.0, February 6, 2017

New
  • The Sample Tracker is a computational tool for tracking sample aliquot collections at multiple clinical sites and availability for conducting planned assays. The tool is initially developed for the Coagulopathy of Trauma collaborative systems biology research team.
  • The Publication Portal has been created by integrating with the Tool for Text Mining (ToTeM) developed by the Advanced Biomedical Computing Center (ABCC) at the Frederick National Lab. All PubMed publications authored by any of the systems biology collaborators in the PTSD and Coagulopathy of Trauma consortiums can be viewed on SysBioCube. The publications are automatically updated on a weekly basis.
Improvements
  • Embraced responsive web design by using Bootstrap front-end framework.
  • The SysBioCube Download interface has been completely redesigned to build the interface dynamically based on the project selected.
  • The SysBioCube Explore interface has been completely redesigned to build the interface dynamically based on the project selected.
Infrastructure