Release Notes



DEV-2803 Add run constraints JSON to results download ZIP file


  • Add global_constraints.json (input parameters) to the Consensus zipped results download


DEV-616 Add option to browse all public playlists.

ThermoSleuth_main, Consensus_main, PanelPlex_main

  • Update - allow users to page through all public playlists, with most popular listed first


DEV-2622 Change "Thermoblast" to "ThermoSleuth"

ThermoSleuth_main, Consensus_main, PanelPlex_main

  • Update log verbage


DEV-1082 Remove sentences about max nucleotides and sequences

Application Portal WebUI

  • Update - remove instructions regarding out-dated limits on FASTA file uploads


DEV-2617 Update CC regular plate "Run" button


  • Update CopyCount submit button


DEV-2843 Expose ThermoSleuth run/subrun config for minimum fraction bound parameter

Application Portal WebUI, ThermoSleuth_main, Consensus_main, PanelPlex_main

  • Makes the minimum fraction bound for ThermoSleuth configurable
  • Exposes versions of this parameter specific to the background and exclusivity runs


DEV-2849 Move session timeout to config

Application Portal WebUI

  • Move session timeout to config


DEV-2824 Add keep-alive timer to ThermoSleuth DB connection

ThermoSleuth_main, Consensus_main, PanelPlex_main

  • Adds keep-alive timer to ThermoSleuth
  • Adds code to save server log to catch statements


DEV-2850 Add user session logging

Application Portal WebUI

  • Update logging for user sessions, page requests
  • Update EULA and release notes



DEV-2731 Debug email not verified error in debugger

Application Portal WebUI

  • Error reports from the portal, cc the user
  • Manage email addresses as lower case


DEV-2740 Fix problem in CopyCount page

Application Portal WebUI

  • Add missing tag


DEV-2751 Exclude "Not Started" from BHM DB run_time calculation

Application Portal WebUI, PanelPlex_main, Consensus_main, Thermosleuth_main

  • Bug fix - Distinguish between project submission time and processing start time
  • Add submission time to run info
  • New feature - processor info


DEV-2749 Fix Playlist Download list with no accessions

Application Portal WebUI

  • Debug "Download List" for public and private playlists, remove extra blank lines
  • New feature - add accessions to "Download List"


DEV-2753 Remove dependencies to reduce AMI

Application Portal WebUI

  • Remove Datadog dependencies


DEV-2734 Improve performance of portal runs

Consensus_main, Application Portal WebUI

  • Improve performance of result file generation
  • Add additional playlist creation logging


DEV-2753 Remove dependencies to reduce AMI

Consensus_main, Application Portal WebUI

  • Restore metrics registry


DEV-2757 Fix Simulator data load and concurrency issues

PanelPlex_main, Consensus_main

  • Makes Simulator data load multithreaded
  • Fixes concurrency issue in Simulator data update


DEV-2759 Show TS run time during processing

Application Portal WebUI

  • Bug fix - display submitted ThermoSleuth projects


DEV-2754 Fix Design Dashboard duplicates when table sorted

Application Portal WebUI

  • Bug fix - disallow duplicate data in the Designs Dashboard - Oligo Details


DEV-2756 Restrict PP Variant MAF Threshold to variant package

Application Portal WebUI

  • Bug fix - MAF threshold for SNP allele frequency disabled without the variant license


DEV-2760 Update error report email message

Application Portal WebUI

  • Update error report message


DEV-2785 Update simulation results view check to allow same group access

Application Portal WebUI

  • New feature - allow users of the same institution to view results (ThermoSleuth, Consensus, PanelPlex)


DEV-2786 Update CC results view check to allow same group access

Application Portal WebUI

  • New feature - allow users of the same institution to view results (CopyCount)


DEV-605 Migrate playlist sharing selection to Playlist Edit page

Application Portal WebUI

  • New feature - allow users to share playlists up to the institution level from the Edit Playlist screen


DEV-2787 Create new tab for "Group Playlists"

Application Portal WebUI

  • New feature - allow users to use playlists shared by other users from their institution


DEV-2801 Make query hit limit consistent between product/playlist/component TS analyses

Application Portal WebUI, PanelPlex_main, Consensus_main

  • Move query hit limit calculation to single utility function, and add it to exclusivity and background


DEV-2808 Invalidate session on user logout

Application Portal WebUI

  • Bug fix - Session cleanup on logout and clean session on login


DEV-2800 Threading and logging cleanup

Application Portal WebUI

  • Remove unnecessary multithreading
  • Remove unnecessary file creation
  • Add check the prevent unnecessary null pointer exception


DEV-2810 Update EULA

Application Portal WebUI

  • Update EULA
  • Update release notes



DEV-2697 Increase Simulator efficiency and capacity

PanelPlex_main, Consensus_main

  • Add multithreading and chunking to Simulator calls


DEV-2700 Improve delay between ThermoSleuth and Simulator

PanelPlex_main, Consensus_main

  • Improve performance, add logging


DEV-2701 Improve performance of output file creation


  • Improve performance of file generation


DEV-2702 Prevent connection timeout in long-running jobs

PanelPlex_main, Consensus_main

  • Add safeguards against the database connection timing out during long-running jobs


DEV-2704 Update reset user password action

Application Portal WebUI, PanelPlex_main, Consensus_main

  • Update the API service call action
  • Remove unnecessary sort
  • Remove redundant calculations


DEV-2705 Fix file load crash in webserver

Application Portal WebUI, PanelPlex_main, Consensus_main

  • Breaks up results JSON into individual files for oligos and for hits for a given design


DEV-2706 Fix remaining issues and cleanup from JSON changes

Application Portal WebUI, PanelPlex_main, Consensus_main

  • Changes false amplicon Design objects to DesignHit objects
  • Fix coverage statistics


DEV-2708 Track features used or attempted

PanelPlex_main, ThermoSleuth_main

  • Track features used or attempted during project setup


DEV-2709 Remove custom number formats

Application Portal WebUI

  • Update - remove custom number format selection (deprecated) from ManageUser.xhtml
  • Update - expand the column width in ThermoSleuth, Consensus, and PanelPlex jobs.xhtml pages so the ID is not cut off or word-wrapped
  • Update - copyright date from 2022 to 2024
  • Update - the event_log filenames to be in 24 hour format


DEV-2710 Fix job queueing issue

Application Portal WebUI

  • Fixes null pointer in queue handling code
  • Fixes probe display in coverage window
  • Makes ThermoSleuth main page tab order match PanelPlex and Consensus


DEV-2713 Update pipeline for v6.1.11 release

Application Portal WebUI

  • Update policies and documentation


DEV-2719 Increase timeout for api call

Application Portal WebUI

  • Increase api call timeout limit
  • Remove deprecated file link
  • Update policies and documentation


v6.0.0 - Start of PanelPlex Major Update Project

DEV-262 DNAS Help Desk Portal Link in WebUI
Application Portal WebUI
  • Added "Get Help" button to portal menu bar that will open DNAS Help Desk Portal in a new tab.
  • Replaced mailto: support@dna... at bottom of page with DNAS Help Desk link to bottom
  • Updated Copyright to 2022

v6.0.1 - BIOTYPE testing portal

DEV-212 WebUI Diagnostics Dashboard app - Application Portal WebUI
Application Portal WebUI
  • Add a link from the PPngs results page to a new tab for the diagnostic content
  • Created a 'Diagnostics Dashboard' page
DEV-299 Change Solution label to Design - Application Portal WebUI
Application Portal WebUI
  • In the WebUI PP results interface, update terminology in the bottom table (standardize with documented terminology)
DEV-301 Make Biotype portal header
Application Portal WebUI
  • Added "- for BIOTYPE development only" to portal base.xhtml header.

v6.0.2 - User input of oligo design set data

DEV-196 User input of oligo design set data - Application Portal WebUI
Application Portal WebUI
  • Added new data object for oligo user input.
  • Added parsers for Excel and CSV input files.
  • Implemented Singleplex to Multiplex, tying it into the backend.
  • Implemented design regions based on the new oligo format, tying it into the backend.
  • Implemented partial junction functionality, tying the most basic form into the backend.
  • Updates the UI to allow user access to the new features.

v6.0.3 - If ThermoSleuth cannot place one of the Singleplex to Multiplex primer pairs, it spoils the run

DEV-319 If ThermoSleuth cannot place one of the Singleplex to Multiplex primer pairs, it spoils the run - PanelPlex_main
  • Prevents failure, allowing solution to just drop out.


DEV-314 Diagnostics Dashboard middle-layer and backend support

Project Behemoth (PanelPlex)

  • Add DiagnosticsDashboardBean and Loader classes to support loading a reaction set with Hibernate
  • Add a helper object for the loading/organizing/display of oligo related data
  • Export oligo data as CSV


DEV-205 Oligo evaluation panel in a new Diagnostics Dashboard feature
Application Portal WebUI
  • Update NGS (PanelPlex) results page to pass selected reaction to the new dashboard page
  • Populate dashboard page with oligo details table with basic functionality (sorting, hide columns)
  • Button to download the oligo table
  • Tabs (placeholders) for bimolecular/cross hybridization matrices


DEV-202 Constrain designs by control oligos and control amplicons
  • Adds ability for the user to specify control oligos that will be incorporated into the PanelPlex analysis.


DEV-1995 Fix more detailed issues introduced by Develop Merge
  • Fixes interamplicon generation problem caused by merge, as well as other misc merge conflicts.


DEV-1992 Generate Design Set output files
  • Has PanelPlex generate output files using the DesignOligo format.


DEV-200 Generate SAM design output files
  • Has PanelPlex call the Python process to create the SAM file


DEV-325 Provide WebUI-PP access to SAM design output files
Application Portal WebUI
  • Adds button to download SAM file


DEV-1996 Update checked in template files
Infrastructure & Server Config
  • Updates files


DEV-1997 Have the portal call the SAM generator with all accession lengths
  • Sends all accessions and lengths to the Python SAM generator


DEV-1998 Update DesignerOligo CSV format
  • Updates column names and values to latest schema


DEV-1999 Add radio button to enable target regions to be run without generating new oligos
Application Portal WebUI
  • Adds radio button to restrict run to controls


DEV-1990 User interface for Primer and Probe vs Amplicon matrix of binding parameters
Application Portal WebUI
  • Adds primer and probe vs amplicon matrix


DEV-2000 Ensure that oligo names are unique
  • Updates name creation code to ensure uniqueness


DEV-2001 Fix indexing for control primers
  • Ensure that primers are positioned on the correct strand


DEV-2002 Make blanks wildcards for control oligos
  • Runs blank control oligos against every target


DEV-2004 Indexing for the substring to cut out the amplicon region is off when creating CSV
  • Fixes indexing


DEV-2003 Download Cross-Hybridization matrix and other minor fixes
Application Portal WebUI
  • Activate download button (try the Primefaces DataExporter.)
  • Change column headers to “ - AMPLICON” as the other oligo names.
  • Center data/values in the columns
  • “Cross-hybridization” (hyphenated, not one word or separate words)
  • Note to users regarding "n/a" values


DEV-2005 Translate ThermoSleuth indexing into Designer indexing when using TS values to replace Designer ones
  • Shifts to using correct indexing


DEV-2018 PP-NGS Results page refactor
Application Portal WebUI
  • Refactor the PanelPlex NGS results page, consolidating results.xhtml and batchresults.xhtml with 3 interactive tables (panels), based primarily off of ngs/results.xhtml


DEV-2019 Results Reaction Sets Panel
Application Portal WebUI
  • Rename the first panel/dataTable to Reaction Sets
  • Rename Solution column to Reaction Set Id
  • Add Number of Reaction Sets column
  • Add Reaction Set Ids column


DEV-2020 Results Reaction Set panel content
Application Portal WebUI
  • Reaction id column
  • comma separated Target Ids column
  • Reaction score column


DEV-2021 Results Reaction Designs Panel
Application Portal WebUI
  • Rename table as 'Reaction Design Set'
  • Add columns
  • Design Id
  • Target Id
  • Total Design Score
  • Remove data (redundant from Designs Dashboard)
  • oligo sequences
  • list of primers and probes


DEV-2032 Update Oligo loader and UI to operate under new constraints
Application Portal WebUI
  • Updates UI and workflow in order to enable full control functionality
  • Adds explicit control for specifying Singleplex to Multiplex runs


DEV-2031 Track filtering of input oligos
  • Saves logs for user oligo filtering to S3


DEV-2051 Update Extension Temperature Default
Application Portal WebUI, ThermoSleuth
  • Changed default TS Extension Temperature to 63C (was 72C).
  • updated version


DEV-2013 Migrate improved Simulator wrapper code from the Cephied branch
  • Imported improved Simulator code


DEV-2012 Update Simulator wrapper to save its results matrix to a file
  • Shifts Simulator to output a full matrix to JSON.


DEV-2015 Call Simulator wrapper in NGS code path
  • Make the simulator call from the PanelPlex main workflow


DEV-2070 Refactor Designer calls to split generation and scoring of oligos
  • Refactors Designer wrapper into a single classes
  • Splits Designer call into two versions


DEV-2016 Update Design Dashboard to read from matrix file


Application Portal WebUI

  • Load Simulator run results (JSON) in PanelPlex results
  • Populate the Designs Dashboard cross-hybridization matrix with simulator data
  • Removed previous cross-hybridization matrix


DEV-229 Generate modified oligos for design consideration


Application Portal WebUI

  • Adds call to tool to modify oligos that overlap user-specified positions accordingly.
  • Saves input and output files to cloud with new more general interface.
  • Fixes minor issue with an error if there was a blank in the outermost cell of the oligo import.
  • Makes it so that junctions only generate the forward or reverse regions if they are not already given.


DEV-2076 Pre-create the oligo filtering file


  • Creates the oligo filtering file at the start of the run.


DEV-2078 PP Dashboard change to Target Tm


  • Change Oligo Details Tm value to Target Tm
  • Update column headers to reduce ambiguity (Tm and Fraction Bound), resize to show name


DEV-2084 Create new JSON Data Objects


  • Adds new objects


DEV-2088 PP Results backend support


  • Translating the data paradigm to reaction-based to enable a uniform results (page) presentation


DEV-2066 PanelPlex Step 2 Refactor

Application Portal WebUI

  • Move advanced settings to collapsable containers on steps 2 and 4
  • Address wording a white space
  • Group like settings


DEV-2104 Generate and select best probe for user input Junction Oligo_sequence


  • Design probes with defined mutants for specificity


DEV-2092 Integrate new JSON objects to PanelPlex workflow


  • Initial incorporation of the JSON backed storage into PanelPlex, replacing the database backing


DEV-2106 Update Simulator calls to work with new JSON data structures


  • Additional fixes to make Simulator work properly with the DEV-2092 fix.


DEV-2107 Reconnect PP Designs Dashboard with JSON

Application Portal WebUI

  • Set the PanelPlex results page to load from the JSON schema
  • Set the Designs Dashboard page to load from the JSON schema


DEV-2108 Allow mix and match to provide multiple probes for a given design


  • Update the mix and match to populate designs with multiple probes.


DEV-2109 Include amplicons in Cross-Hybridization tables and standardize names


  • Cleans up naming conventions, including issues that were hampering Cross-Hybridization table.


DEV-861 On Hybridization Conditions page, User should be able to remove a custom kit and also be able to change the order of kits

Application Portal WebUI

  • User created kits at the top of the list - starting with the newest


DEV-2117 JSON generator and parser


  • Initial incorporation of JSON backed input parameters for PanelPlex workflow


DEV-2123 Amplicon Fraction Bound Percent to Decimal


  • Convert Minimum Amplicon Fraction Bound (Inclusivity) from percent to fraction (decimal)


DEV-2119 Implement Shared Primers in UI

Application Portal WebUI

  • Adds user interface for semicolon separation and shared primers.


DEV-2124 serialize JSON input

Application Portal WebUI, PanelPlex_main

  • User inputs to JSON constraints, serialized


DEV-2128 Export constraints JSON

Application Portal WebUI, PanelPlex_main

  • Allow the user to download PanelPlex constraints for a job from the results and job pages


DEV-2114 JSON input function for PanelPlex WebUI

Application Portal WebUI


  • Default PanelPlex constraints/input parameters to a single resource
  • User imported PanelPlex constraints from JSON
  • Reset PanelPlex input parameters to default


DEV-2099 Update user input parser for advanced design constraints against target regions/positions

Application Portal WebUI


  • Update oligo- and target-related column headers in input files and web UI (Step 2 and Designs Dashboard)
  • Add target-specific constraints to input file parsing, oligo output json


DEV-2095 PP Example Input File

Application Portal WebUI

  • New example input target file (Step 2)
  • Clean up web UI instructions regarding the input file


DEV-2126 Update User Input parser for Target specific constraints

Application Portal WebUI


  • Parse input target-specific constraints into input oligos


DEV-2120 Implement Shared Primers in Workflow Layer


  • Update algorithm to handle cases where the primers are set to be shared


DEV-2127 Apply user input target constraints over WebUI inputs


  • Apply target-specific constraints on the oligo level where applicable, overriding general job constraints


DEV-2141 Allow adding multiple playlists to a playlist through the search feature at one time


  • Update the search-based playlist add feature to allow multiple playlists to be added at once


DEV-2142 Fix minor errors hindering build


Application Portal WebUI

  • Fixes minor errors


DEV-2143 Log key data to S3


  • Updates logging to write new Json structures to S3


DEV-2144 Show S3 Logs in UI

Application Portal WebUI

  • Adds link to view S3 logs in job page


DEV-2145 Fix bugs in S3 log upload/download


Application Portal WebUI

  • Fixes bugs.


DEV-2219 Remove comment

Application Portal WebUI

  • Remove commented code captured by table exporter


DEV-2230 Target Specific Primer Length Range


  • Simplify variable naming


DEV-2277 Fix run status bars in results page


  • Adjust status bar to pull from new source that reflects an accurate state of the run.


DEV-2221 Add Amplicon to Dashboard-Oligo Details


  • Bug fix - restore amplicon details to the Designs Dashboard - Oligo Details table


DEV-2214 Change label for data download button

Application Portal WebUI

  • Update - change button name for accuracy


DEV-2278 Shift Consensus over to JSON based data structures


  • Reworks Consensus workflow to use new data structures.


DEV-2328 Fix failures that occur when uploading very large Fasta files

Application Portal WebUI

  • Updates test condition for scanning mode to return the correct results at all times.


DEV-2325 Update Consensus to use new Simulator calls


  • Alters the calling code for Consensus to use the new Simulator code.


DEV-2067 PP Step 4 refactor

Application Portal WebUI

  • Update - move PanelPlex input parameters from step 4 to step 2, and rearrange for an intuitive flow.


DEV-2340 Ignore ^ in NCBI feature parsing

Application Portal WebUI

  • Adds ^ to the list of characters parsed out of the NCBI variation entries.


DEV-665 Allow user to specify for each target: min_amplicon_gap, max_amplicon_gap, minimum nucleotides on ether side of junction


  • New feature - Add amplicon gap range (min and max) as a user input parameter on the target level


DEV-2334 Update Consensus UI to pull data from JSON data structures for "Solutions" column


  • Updates "Solutions" column to take data from the new JSON data structures.


DEV-2139 Target input row split on select columns


  • Updates ";" parser for the target input file to restrict 'splitting' or 'duplicating' of rows to the Shared Primers feature related columns


DEV-2223 Set precision in Dashboard


  • Updates PanelPlex Dashboard oligo details precision to relevant digits


DEV-2353 Update SQL creation scripts to match latest database schema

Infrastructure & Server Config

  • Updates SQL scripts so that the blank database can be generated from scratch.


DEV-2368 Fix RT Primer Functionality

PanelPlex_main, PanelPlex-Consensus_main

  • Fixes RT primer calls to generate them again.


DEV-2371 Update AWS Util calls to make region configurable


  • Makes the AWS region configurable.


DEV-2382 Update S3 calls to make region configurable


  • Makes the AWS region configurable for S3 Calls.


DEV-2369 Update Consensus UI to pull data from JSON data structures for "Options" column


  • Updates Consensus display for exclusions and crosshybridizations.


DEV-2369 Invoke user input local constraints for designer jobs


  • Update source of DesignerJob input parameters with constraints JSON


DEV-2367 Fix Tail functionality

PanelPlex-Consensus_main, PanelPlex_main, Application Portal WebUI

  • Re-enable the running of the tail generation step.


DEV-2389 Fix rebase error in constraints calls

PanelPlex-Consensus_main, PanelPlex_main, Application Portal WebUI

  • Adjust the constraint calls to use the new approach.


DEV-2222 Additional metrics in Oligo Details


  • Add unimolecular metrics to the designs dashboard oligo details


DEV-2290 Run setup Target Strand help text

Application Portal WebUI

  • Add tooltip help text to Consensus and PanelPlex step 2 (target)


DEV-2023 Consensus Input Param File update

PanelPlex-Consensus_main, Application Portal WebUI

  • Include Consensus parameters to Constraints structure
  • Create a Consensus default values file
  • Tidy up Web UI


DEV-2399 Consensus Input Param File update

Application Portal WebUI, PanelPlex-Consensus_main

  • New feature - reset parameters buttons on Consensus steps 2-4
  • Bug fix - preserve user input whole_target_range when uploading Consensus input file


DEV-2392 Update file output for Consensus

Application Portal WebUI, PanelPlex-Consensus_main

  • Links Consensus user output files to JSON data store and adds new output for PanelPlex input.


DEV-2232 Ensure Interoligo Hits Matrix has correct values for all cells

Application Portal WebUI, PanelPlex-Consensus_main, PanelPlex_main

  • Fixes Simulator calls to more accurately reflect the calculated situation.


DEV-2276 Add init/prop outputs to results WEBUI

Application Portal WebUI

  • Let Consensus call the Designs Dashboard, and make the initiation oligos toggleable in the Designs Dashboard


DEV-221 Save original user target input file to S3 run folder

Application Portal WebUI

  • New feature - Save the user's target input file along with other run-related files


DEV-379 Add ability for user to save their primer/probe list as .csv file

Application Portal WebUI

  • New feature - Download button for designs in the Oligo per line format (same as target input file format)


DEV-2405 Update DataReaction scoring to include crosshybridization penalties

PanelPlex-Consensus_main, PanelPlex_main

  • Adds cross-hybridization penalties to the reaction score calculation.


DEV-2400 Update WebUI product words

Application Portal WebUI

  • Change PanelPlex-Consensus to Consensus, PanelPlex-NGS to PanelPlex, and qPCR CopyCount to CopyCount


DEV-2207 Update design and reaction scoring with gap and exclusion scores

PanelPlex-Consensus_main, PanelPlex_main, Application Portal WebUI

  • Adds gap and exclusion scores, incorporating the new equation for the exclusion gap adjustment


DEV-2387 Standardize retention of MP input/output files for a design run

PanelPlex-Consensus_main, PanelPlex_main

  • Update temporary local working path for component input and output storage


DEV-2409 Standardize retention of Designer input/output files for a Consensus run


  • Bug fix - update Designer to expect targan input files in the targan component folder


DEV-2411 Address null pointer errors

Consensus_main, PanelPlex_main

  • Bug fix - handle optional sequence definition for an oligo as optional
  • Bug fix - manage loading the local constraints for a specific oligo over the global constraints


DEV-2410 Add function to "kill" a TS, PanelPlex, Consensus run in the job queue

Consensus_main, PanelPlex_main

  • Updates the Java process to look for the presence of a "" file and to terminate itself if it sees it.


DEV-2347 Bring forward PanelPlex run validation


  • Updates the callback functions for PanelPlex step 2 and 3 to validate parameters and submit the run at the appropriate web pages


DEV-2388 Move temporary component-specific formatted input/output files for a design run to s3


  • New feature - preserve working files for debugging


DEV-2416 Update Consensus to use Constraints input file

Consensus_main, Application Portal WebUI

  • Exposes Constraints file via the Consensus interface, and tweaks handling of its input.


DEV-2204 Add WebUI button for user to "kill" a TS, PP, Consensus run

Application Portal WebUI

  • New feature - cancel a queued or currently processing PanelPlex, or Consensus run from the web UI
  • Update the delete button from PanelPlex, Consensus, or ThermoSleuth jobs page to only appear on completed runs


DEV-2408 Update scoring to take weights and tail penalties into account

Consensus_main, PanelPlex_main, Application Portal WebUI

  • Returns the weight calculation to match the way it originally was, adjusting the data structures accordingly.


DEV-2422 Implement "kill" a ThermoSleuth run with web UI button

Thermosleuth_main, Application Portal WebUI

  • New feature - cancel a queued or currently processing ThermoSleuth run from the web UI


DEV-2407 Update scoring to include coverage penalties

Consensus_main, PanelPlex_main

  • Re-implements penalties based on the coverage statistics.


DEV-2224 Change "Delete" button to "Clear" button

Application Portal WebUI

  • Bug fix - 'Delete (Row)' button in PanelPlex - Step 2 deletes all targets


DEV-2227 DeltaH Cross-hybridization data


  • New feature - pull Delta H data for results output


DEV-2423 Code Cleanup - DesignerResults

Application Portal WebUI

  • Housekeeping - code cleanup


DEV-2058 Add user log messages for failed PP target designs from excessive interamplicon hits


  • Adds log messages and a file to store rejected designs, while moving all run directory uploads to unzipped


DEV-2426 Move Target Strand drop down to Probe section of UI

Application Portal WebUI

  • Moves dropdown and reworks style and ajax update to work in the new location


DEV-2218 Bimolecular homodimer values for Designs Dashboard

Consensus_main, PanelPlex_main

  • New feature - provide homodimer values in the Designs Dashboard cross-hybridizations matrices


DEV-797 PP scoring should show ALL terms used in getting the final score

Application Portal WebUI

  • Exposes all necessary scores required to calculate the final scores


DEV-2131 Copy run logs from local OS to S3 storage run folder

Consensus_main, PanelPlex_main, Thermosleuth_main

  • Uploads the server logs after every run


DEV-2429 Remove deprecated DesignerTarget functions and fix the places that still used them

Consensus_main, PanelPlex_main

  • Fixes exclusion code to look at the right values, and updates the target functions to pull from the oligo data


DEV-2412 Update file management to decouple components and workflows

Consensus_main, PanelPlex_main

  • Consolidate file management handlers to a consistent standard


DEV-2424 Apply new storage configs to legacy EC2

Consensus_main, PanelPlex_main, Thermosleuth_main

  • Update config references


DEV-2421 Make fast-compare the default option

Consensus_main, Application Portal WebUI

  • Update - change default aligner for Consensus to FastCompare


DEV-2226 Delta H cross-hybridization table

Consensus_main, Application Portal WebUI

  • New feature - display DeltaH cross-hybridizations in the Designs Dashboard


DEV-2425 Change statuses to "Completed"

Consensus_main, Application Portal WebUI

  • New Feature - For Consensus and PanelPlex runs that complete without results, the status is set to "Completed"


DEV-2337 Update example Target Input file

Application Portal WebUI

  • Update - update probe coordinates to realistic values


DEV-2444 Updates to enable E1 DEV pipeline

ThermoSleuth_main, Consensus_main, PanelPlex_main

  • Update - add console logs related to file management with AWS S3


DEV-2444 Updates to enable E1 DEV pipeline

ThermoSleuth_main, Consensus_main, PanelPlex_main

  • Update - playlist file path correction for AWS S3 objects


DEV-2444 Updates to enable E1 DEV pipeline

ThermoSleuth_main, Consensus_main, PanelPlex_main, Application Portal WebUI

  • Update - playlist file path correction for AWS S3 objects, add playlist status logging
  • Restore genome viewer for ThermoSleuth webUI


DEV-2444 Updates to enable E1 DEV pipeline


  • Update - adding thermosleuth logging


DEV-2444 Updates to enable E1 DEV pipeline

ThermoSleuth_main, Consensus_main, PanelPlex_main

  • Update - remove server logging


DEV-2445 Workflow run tracking

ThermoSleuth_main, Consensus_main, PanelPlex_main

  • Update - store tracking information with the run data


DEV-2437 Tidy up user target input file ingestion

PanelPlex_main, Application Portal WebUI

  • Update - clean up code relating to loading a target input file
  • New feature - expand a target junction oligo to target region oligos
  • New feature - display junction(s) and related target region oligos in step 2
  • New feature - add probe_primer_overlap_limit, junction_padding_minimum, and primer_design_range_minimum to webUI, constraints
  • New feature - Recalculate target design regions on button click, run submission


DEV-2446 Add Intelliqube data format parser to CopyCount


  • Adds Intelliqube data processor


DEV-2440 Combine targets logic


  • Update - implement new calculations to determine which junctions should be combined, if any


DEV-2451 Fix Intelliqube parser to handle ROX data


  • Adds extra filters to ignore unused channels


DEV-2105 Update Thermosleuth product WebUI to accept modified nucleotides in input seqs

Application Portal WebUI

  • Loosens checks on valid sequences to allow bracket codes
  • Updates ThermoSleuth query length calculations to count nucleotides instead of characters
  • Minor fix to file output where strand type could be output incorrectly


DEV-2450 Fix bug in combine targets logic


  • Bug fix - separate combined target design regions and shared target feature
  • Bug fix - update the user-facing list of targets


DEV-2238 Code Cleanup - billing services

Application Portal WebUI

  • Housekeeping - code cleanup


DEV-2206 Add new scoring rule for fluorophore

Consensus_main, PanelPlex_main

  • Adds new scoring term for Taqman cleaving at the five prime end


DEV-2396 Consensus design range param for junctions


  • Fixes data flow and misc bugs preventing Consensus from running successfully


DEV-2461 Add UI Components for Fluorophore Taqman Cleaving penalty

Application Portal WebUI

  • Adds output displaying the penalty, as well as the weight sliders, for the Fluorophore Taqman Cleaving penalty


DEV-2460 Maintain tiling feature

Application Portal WebUI, PanelPlex_main

  • Fixes regressions in the Tiling code due to v6
  • Fixes regression in coverage calculations when there are multiple options for coverage
  • Makes FAILED default for no-result jobs, but allows COMPLETED to be set if it did get to the end


DEV-2238 Develop portal signin and product access check from new user license objects

Application Portal WebUI

  • Update - switch login service to api
  • Housekeeping - remove deprecated code


DEV-2238 Develop portal signin and product access check from new user license objects

Application Portal WebUI, PanelPlex_main, Consensus_main

  • Debug - decouple deprecated fields


DEV-2481 Fix problems in Controls and Predesigns

Application Portal WebUI, PanelPlex_main

  • Fixes regressions preventing PanelPlex from running Control/Predesign jobs.


DEV-2365 Invalid double quote symbol throws error

Consensus_main, PanelPlex_main

  • Replaces invalid double quote symbol with generic escaped one.


DEV-199 Store JBoss log

Consensus_main, PanelPlex_main, ThermoSleuth_main

  • Reactivates storage of server log to new location.


DEV-2459 Clarify status of runs

Consensus_main, PanelPlex_main, Application Portal WebUI

  • Makes "Completed" and "Done" display differently to the user.
  • Cleans up the Results column on the results page.


DEV-2384 Add product page header with institution AWS hours used/remaining

Application Portal WebUI

  • Update portal user to match user access api, display processing hours usage
  • Update Consolidate end user permissions


DEV-2384 Add product page header with institution AWS hours used/remaining

Application Portal WebUI

  • Bug fix - Display when not viewing a specific product


DEV-2486 Fix error in mix and match thin-out code

Consensus_main, PanelPlex_main

  • Calculates overlap correctly


DEV-2487 Fix errors discovered while investigating bug in thin-out code

Consensus_main, PanelPlex_main

  • Fixes bug preventing playlist creation
  • Fixes bug using probes as input oligos
  • Fixes bug where control input oligos would not make it past the UI checks
  • Fixes bug where empty columns could generate Null Pointer exceptions before giving a proper error


DEV-778 Maintain filter to force all designs to have either FP or RP end at the junction position

Consensus_main, PanelPlex_main

  • Fixes bug in amplicon gap calculation affecting endpoint junction calculation.


DEV-2238 Develop portal signin and product access check from new user license objects

Application Portal WebUI

  • Bug fix - update junit tests to latest API version


DEV-2492 Add check to prevent lockout spiral in License Manager

Application Portal WebUI

  • Does not perform license checks on logged out user


DEV-2493 Remove API-referencing unit test

Application Portal WebUI

  • Removes the module


DEV-2484 Remove API-referencing unit test

Application Portal WebUI

  • Bug fix - navigation and error handling
  • Bug fix - update links to configured addresses
  • Bug fix - login attempt messages
  • Bug fix - PanelPlex values do not auto-reset


DEV-2494 Fix Consensus runs that use exclusivity playlists


  • Fixes file paths and temporarily deactivates individual FastCompare score for oligos


DEV-2338 Update validation of input target design regions

Application Portal WebUI

  • Adds new validation checks and tweaks the text for existing ones
  • Updates minor predesign check to no longer require five prime and three prime coordinates


DEV-276 Misleading instructions ("or") on the Consensus web portal

Application Portal WebUI

  • Removes incorrect Consensus controls UI


DEV-2057 Add error message for target designs outside user input amplicon size constraints

Application Portal WebUI

  • Adds an extra validation error message, and refines existing message


DEV-2428 Display ThermoSleuth Cart

Application Portal WebUI

  • Bug fix - display ThermoSleuth Cart


DEV-2497 Put run logs and processor logs in different subdirectories

Consensus_main, PanelPlex_main

  • Splits the server logs and run logs into two non-nested directories


DEV-2496 Add the run_id (runDirectoryId) to product Job Lists

Application Portal WebUI

  • New feature - add the run_ID to PanelPlex, Consensus, ThermoSleuth results list (jobs.xhtml) pages


DEV-620 Add user name and email to the Stack Trace

Application Portal WebUI

  • Update - hide the stack trace from the user


DEV-620 Add user name and email to the Stack Trace

Application Portal WebUI, PanelPlex_main

  • Update - remove link to deprecated output file


DEV-2404 Add link to confluence software docs into Portal WebUI

Application Portal WebUI

  • New feature - add a link to DNAS (all) product documentation


DEV-2498 Debug logout of the application web portal

Application Portal WebUI

  • Bug fix - forward and redirect for relative and absolute page paths


DEV-2501 Remove Completed Status

Consensus_main, PanelPlex_main

  • Removes Completed status
  • Tidies up logging


DEV-2491 Develop web UI to reset user password

Application Portal WebUI

  • Update - switch password reset service to api


DEV-2506 Allow ThermoSleuth owner and admins to view a run

ThermoSleuth_main, Application Portal WebUI

  • Bug fix - load ThermoSleuth results


DEV-2503 Reattach FastCompare and Targan runs and statistics to Consensus


  • Adjusts the Consensus workflow to use the FastCompare generated runs
  • Fixes the Targan file generation to offset for subregions


DEV-2511 Debug transaction error to persist password reset request

Application Portal WebUI

  • Bug fix - track password reset requests


DEV-2502 Ensure all Consensus design solutions are included in output PCR_designs.csv

Application Portal WebUI, Consensus_main

  • Fixes indexing errors in the CSV creation and the amplicon calculation
  • Removes old code for result file recalculation


DEV-2507 Allow Designer run owner and admin to view results

Application Portal WebUI, Consensus_main, PanelPlex_main

  • Bug fix - load Designer results


DEV-2512 Turn off multiplex for batch singleplex mode in panelplex

Application Portal WebUI, PanelPlex_main

  • Removes unnecessary checks from Multiplex and batch singleplex, allowing partial results
  • Fixes other minor issues preventing batch singleplex from running


DEV-2427 Add warning column in reaction sets table for uncovered targets

Application Portal WebUI

  • Adds column alerting user to any targets that the multipick reaction set does not cover


DEV-2505 Address null InputStream for S3 object creation

Application Portal WebUI, Consensus_main, PanelPlex_main, ThermoSleuth_main

  • Replaces null value with input stream on S3 cancellation call
  • Replaces old timeout code with new job cancellation call


DEV-2509 Remove deprecated download buttons

Application Portal WebUI

  • Remove "Download Temporary Fasta File" and "Download Reaction Designs" from the PanelPlex results view


DEV-2495 Add Fluorophore and quencher on TaqMan Probe selection

Application Portal WebUI

  • Updates UI to properly display flourophores and quenchers


DEV-2275 Implement feature access controls in WebUI

Application Portal WebUI

  • Updates UI and processor server queue management to consider new license model on specific features


DEV-2508 Address error on constraints file upload

Application Portal WebUI

  • Update location of user's custom global_constraints for Designer projects to Step 2/target definition
  • Update input parameters preview in results view for Designer projects


DEV-2508 Address error on constraints file upload

Application Portal WebUI

  • Housekeeping - code cleanup


DEV-2508 Address error on constraints file upload

Application Portal WebUI, Consensus_main

  • Update move maxPrimerPairDepth to global_constraints


DEV-2540 Change PP results view IDs to names from user

Application Portal WebUI, Consensus_main, PanelPlex_main

  • Replaces ids with user-parsable names


DEV-2554 Fix oligo names

Application Portal WebUI, Consensus_main, PanelPlex_main

  • Fixes ingestion of target names and updates oligo name generation to construct it from the base oligo


DEV-2525 Ensure PanelPlex WebUI constraint field values

Application Portal WebUI, PanelPlex_main

  • Bug fix - Store all PanelPlex Step 2 input field values on update
  • New Feature - on updates to fields relating to junction target region calculation, allow user to use recalculate targets feature
  • Update default PanelPlex values (detection_mode, primer_design_range_minimum)
  • Update - reorganize fields in PanelPlex Step 2 with updated labels and tooltip text
  • Update - user-facing labels, messages in web UI


DEV-2548 Ensure PanelPlex WebUI constraint field values

Application Portal WebUI

  • Update main and CopyCount landing pages' navigation paths to distinct tiles


DEV-2538 Fix ingestion and display of modified nucleotides in ThermoSleuth WebUI

Application Portal WebUI

  • Removes number removal, and loads run info in ThermoSleuth jobs


DEV-2550 Subtract 1 from gap calculation in exclusion scoring

Consensus_main, PanelPlex_main

  • Adjusts the gap calculation


DEV-2556 Fix Consensus crash when loading ThermoSleuth job


  • Adds check for sub-ThermoSleuth jobs


DEV-2563 Remove 'view errors' hyperlink from Status column

Application Portal WebUI

  • Remove hyperlink from Failed status for both Consensus and PanelPlex


DEV-2519 Update Raw Design Sets to Include IDs

Application Portal WebUI

  • New Feature - the Download Raw Design Set Data in PanelPlex results now includes reaction data


DEV-2390 Export amplicon details

Application Portal WebUI

  • Bug fix - display amplicon coordinates and sense in the Designs Dashboard


DEV-2573 Debug parsing local constraints


  • Debug - persist local constraints downstream


DEV-2537 Replace deprecated code in Consensus iteration feature


  • Fixes Consensus iteration feature


DEV-2559 Add outstanding Consensus constraints to global_constraints object

Consensus_main, PanelPlex_main

  • Add ThermoSleuth load throttle config value to constraints ("candidate_oligo_search_limit")


DEV-2566 Update Step 2 page on constraints upload for Consensus

Application Portal WebUI

  • Debug - update form values on custom global_constraints selection


DEV-2579 Implement candidate oligo search limit parameter for component ThermoSleuth runs

Consensus_main, PanelPlex_main

  • Adds logic to inclusivity analysis to respect the candidate_oligo_search_limit parameter


DEV-2560 Re-add probe_modifications to global_constraints object

Consensus_main, PanelPlex_main

  • Adds probe modifications to exported global_constraints


DEV-2585 Sort before ThermoSleuth cut


  • Sorts the candidate designs before running ThermoSleuth to only grab from the best designs


DEV-2527 Update target_name for junctions and probes when PanelPlex combines target junctions


  • Updates the target name for junctions


DEV-2558 Fix multiple probe feature validation when generated from overlapping junction design regions


  • Debug - correctly apply license control on combined junction regions with probes


DEV-2557 Misc one line WebUI fixes

Application Portal WebUI

  • Center product tiles on welcome page
  • Display product name on results page
  • Debug Gray-out "Next" button if unlicensed features are attempted


DEV-2527 Update target_name for junctions and probes when PanelPlex combines target junctions


  • Updates oligo names


DEV-2562 Provide download link for target input file

Application Portal WebUI

  • New feature - download the user's target input file from the PanelPlex results page (Input Parameters tab)


DEV-2571 Fix null pointers found during v6 testing

Consensus_main, PanelPlex_main

  • Fix various errors that led to Null Pointer exceptions in Consensus and PanelPlex


DEV-2551 Add "Reporter Email" field to portal WebUI bug encountered page

Application Portal WebUI

  • New feature - new field in the error report for a user to supply their email


DEV-2561 Display playlists used in webUI (Consensus and PanelPlex)

Consensus_main, PanelPlex_main

  • New feature - display playlists used in Consensus and PanelPlex


DEV-2555 Debug reload function for PanelPlex design target regions


  • Debug target input file reload


DEV-2587 Generate broken down json files from run_results.json

Consensus_main, PanelPlex_main

  • Adds code for reaction-only interoligo hit json files


DEV-2583 Revert TS to use genome viewer


  • Debug restore genome viewer and structure viewer in ThermoSleuth


DEV-2580 Remove amplicons from columns of Design Dashboard cross-hyb tables

Consensus_main, PanelPlex_main, Application Portal WebUI

  • Removes amplicon data from columns of interoligo matrix data storage
  • Updates web UI to accept the asymmetric matrix


DEV-2584 Solve AWS TLS 1.2 errors in webserver

Consensus_main, PanelPlex_main

  • Updates portal to request TLS 1.2 usage when it sends mail


DEV-2588 Separate Consensus setup step 3 RESET button from "Back" button

Application Portal WebUI

  • Updates button placement at the top of Consensus and PanelPlex products for consistency


DEV-2587 Generate broken down json files from run_results.json

Consensus_main, PanelPlex_main

  • Alters the save functionality to remove the independent upload for the interoligo matricies


DEV-2591 Fix Null Pointer Exception in ThermoSleuth emails


  • Bug fix - load run_info


DEV-2593 Fix Json load error

Consensus_main, PanelPlex_main, Application Portal WebUI

  • Fixes load issue in Json
  • Fixes null pointer error when not giving a probe region to a probe design
  • Fixes missing forward and reverse labels for no-probe designs
  • Makes the order of the tabs in the playlist selection consistent between Consensus and PanelPlex


DEV-2592 Load reaction crosshyb on dashboard load

Consensus_main, PanelPlex_main, Application Portal WebUI

  • Updates the Designs Dashboard to only load the needed interoligo matricies on Dashboard view


DEV-2552 In ThermoSleuth add Forward Primer DG and Reverse Primer DG columns to amplicons.csv file


  • New feature - export forward primer DG and reverse primer DG to amplicon output


DEV-2598 Fix Null Pointer Exception in Consensus results page

Application Portal WebUI

  • Fixes null pointer


DEV-2567 Fix PP junction variant probe feature

Application Portal WebUI, PanelPlex_main

  • Adds link between probe regions and their junctions
  • Removes mutant probes from inclusivity thermoblast, uses more accurate Designer data instead
  • Removes mutant oligo sequence from cloned forward primer, reverse primer and probe regions


DEV-2543 Sort Consensus design results in WebUI by "solution score" to be consistent with PCR_designs file

Application Portal WebUI, Consensus_main

  • Bug fix - Default view in Consensus results now sorted properly by Total Score


DEV-2457 Update rules for negative amplicon gaps to include


  • Debug - filter ThermoSleuth results to remove overlapping primers (negative amplicon gap)


DEV-2568 Add specific run log for designer failures

Application Portal WebUI, Thermosleuth_main, PanelPlex_main, Consensus_main

  • Improves logging and error handling to give better information about status and errors


DEV-2603 Refine selection of second+ inclusivity sequence to increase Consensus Inclusivity Coverage

Application Portal WebUI, Consensus_main

  • Fixes error in iterative keystone selection
  • Fixes associated null pointer errors
  • Adds extra logging and cleans up target names


DEV-2611 Update Oligo Name and appearance in Consensus Designs Dashboard

Application Portal WebUI, PanelPlex_main, Consensus_main

  • Updates the design, amplicon and oligo names to match requirements
  • Sorts designs dashboard crosshyb tables so that the amplicon oligos are on the bottom


DEV-2595 Debug Tiling Mode

Application Portal WebUI, PanelPlex_main, Consensus_main

  • Bug fix - tiling mode
  • Load default values based on Design Mode selection


DEV-2602 Fix off-by-one coordinate errors in ThermoSleuth v6 Product

Application Portal WebUI, Thermosleuth_main

  • New feature - update coordinate reporting to both ends in the industry standard
  • Update - increase width of primer selector


DEV-2620 Update pom resource specification to explicitly load entire resources directory


  • Makes the base resource directory for the processor pom explicit


DEV-2609 Rounding of numbers needed in Thermodynamic details pages

Application Portal WebUI, Consensus_main

  • Update - reduce precision of thermodynamic values in Consensus


DEV-2610 Update name of Consensus oligo_details.csv with "PanelPlex" in the name

Application Portal WebUI, Consensus_main

  • Bug fix - Correct product name in generated filename download


DEV-2581 Ensure only shared designs are produced in PP results


  • Fixes bug in the loading of designs for the pruning multipick run
  • Adjusts filtering of interamplicon exclusions to allow for shared primer restrictions


DEV-2612 Add reaction tracking info to top of design dashboard

Application Portal WebUI, Consensus_main, PanelPlex_main

  • Add project, reaction set, and reaction information to the Designs Dashboard


DEV-2614 Update Consensus k-mer analysis validation


  • Update validation messages related to Target Characteristics


DEV-2626 Ensure values in Consensus results downloads are not object references


  • Bug fix - export exclusion oligo sequences in coverage output csv


DEV-2623 Remove partition percent bound result


  • Update - remove Partition Percent Bound from ThermoSleuth results page


DEV-2628 Update Exclusion Score for consistency


  • Bug fix - export false amplicon score in the Consensus coverage csv


DEV-2630 Update tiling validation


  • Bug fix - catch error when tiling design region is too small
  • Bug fix - apply default values on design mode selection


DEV-2594 Differentiate Predesigns from Controls

PanelPlex_main, Application Portal WebUI

  • Runs grouping feature whenever there is only one design for all multiplex targets
  • Fixes oligo names and numbering
  • Don't penalize predesigns for not being in non-existent regions
  • Fixes problem with predesigns in designs dashboard
  • Fixes bug where empty input file rows could crash input reading
  • Fixes wildcard functionality
  • Don't accept user-defined primers outside the region designated for them


DEV-2632 Fix inconsistencies and errors in false amplicon calculation

PanelPlex_main, Consensus_main

  • Fixes several interrelated bugs that were causing inconsistencies in the false amplicon report


DEV-2633 Fix Null Pointer Exception in Playlist emails

Application Portal WebUI

  • Passes run info through so that the Playlist creation and edit emails can use it


DEV-2631 Fix Show Initiation filter

Application Portal WebUI

  • Updates Show Initiation button to call a specific reload function


DEV-2635 Make target file validation fail predesigns with accessions not in inclusivity

Application Portal WebUI

  • Makes target file validation more restrictive


DEV-2629 Correct INIT/PROP Amplicon coordinates

PanelPlex_main, Application Portal WebUI

  • Update naming of, coordinates, sequence splicing of the gap for amplicons Ref_Fragment and Prop_Amplicon
  • Update SAM file management and download to a zipped file


DEV-2636 Flatten "playlist of playlist" import

Application Portal WebUI

  • Removes playlist-of-playlist linking in the data structure
  • Makes playlist-of-playlist import UI put the accessions directly into the main playlist


DEV-2638 Replace duplicate removal comparison with hash comparison

Application Portal WebUI

  • Moves ambiguity tally to sequence creation
  • Creates md5 digest hash for sequence at creation
  • Checks for duplicate sequences based on digest hash rather than direct comparison


DEV-2641 Update wrapper to read new Multipick grouping output format

PanelPlex_main, Application Portal WebUI

  • Updates the multipick wrapper code to parse new information from the multipick executable
  • Removes reaction set total penalties in PanelPlex UI, renames the panel/interpanel penalties


DEV-2642 Fix primer/probe Target_Accession in Consensus Designs Dashboard-Design Oligos table

PanelPlex_main, Consensus_main, Application Portal WebUI

  • Switches Target_Accession in the designs dashboard to the hit value


DEV-2596 Fix positioning of reverse sense primer/probe modifications and mutations


  • Update input parameters to the sequence tools to modify oligos
  • Update interpretation of results from the sequence tools to modify oligos


DEV-2646 Remove 3-prime metrics from Consensus results WebUI

Application Portal WebUI

  • Removes unused columns from result page


DEV-2651 Fix array out of bounds error

PanelPlex_main, Consensus_main

  • Sets the correct minimum value for the genomic slicing


DEV-2645 Remove 3-prime NET Score and k-mer score (FC) from Design Total Score

PanelPlex_main, Consensus_main, Application Portal WebUI

  • Relegates the 3 prime NET score and k-mer scores to the earlier heuristic score value
  • Fixes bug in playlist load code


DEV-2521 Re-Develop microservice for getting institution active products

Application Portal WebUI

  • Update processor server spooling from user-based to institution-based
  • Added API and JSON utilities


DEV-2652 Remove extra character string from Consensus amplion fasta files


  • Removes extraneous string


DEV-2267 Display release notes in web UI

Application Portal WebUI

  • Update release notes page to display formatted markdown files


DEV-2655 Fix cancel requests executed while generating modified oligos

PanelPlex_main, Consensus_main

  • Fixes cancel request


DEV-2656 Fix amplicon len off by one error in Consensus results


  • Debug amplicon length value in Consensus results


DEV-2653 Include target input oligo_name in name of primer/probe candidates

PanelPlex_main, Consensus_main

  • Update primer and probe candidate names to include the target input oligo_name


DEV-2657 Add a note in the WEB UI file upload limit

PanelPlex_main, Consensus_main

  • Update - inform users on file upload limit


DEV-2658 Fix PP modified oligos functionality

PanelPlex_main, Consensus_main

  • Bug fix - remove obfuscating double quote characters from modifier input csv file
  • Bug fix - use oligo name instead of oligo id


DEV-2660 Filter junction probes to force junction overlap

PanelPlex_main, Consensus_main

  • Adds filter to force probes to overlap junction
  • Fixes error in Excel input of region files
  • Removes incorrect failure on no results found


DEV-2653 Include target input oligo_name in name of primer/probe candidates

PanelPlex_main, Consensus_main

  • Bug fix - use oligo_function abbreviation in oligo_name


DEV-2662 Fix error writing zeroes in Json

PanelPlex_main, Consensus_main

  • Changes Jackson settings to no longer strip zeroes


DEV-2663 Fix prefiltering and sorting in mix and match

PanelPlex_main, Consensus_main

  • Removes positional filtering for probes prior to mix and match
  • Sorts Reverse and RT primers by their five prime end for mix and match


DEV-2665 Create oligos from modified sequences early

PanelPlex_main, Consensus_main

  • Bug fix - add modified sequences to compete with generated candidates


DEV-2666 Fix Null Pointer Exception in Oligo name creation


  • Alters Consensus naming to use the proper data it has access to


DEV-2669 Change "Target Strand" to "Probe binds to"

Application Portal WebUI

  • Update wording of the label for which strand a probe binds to


DEV-2648 Set weight to zero for "Off-target-hits" penalty

Application Portal WebUI

  • Changes the default scoring weight for the raw off-target hits


DEV-2667 Consensus cross-hyb table missing primer/probe Tms

PanelPlex_main, Consensus_main

  • Bug fix - report two-state melting temperature in the Designs Dashboard


DEV-2670 Store Consensus-specific settings

PanelPlex_main, Consensus_main

  • Bug fix - port remaining Consensus input parameters to the new structure for import


DEV-2671 Fix Consensus Coverage:Alignment sequences displayed and used for stats


  • Bug fix - correct offset error in Consensus coverage display for alignment


DEV-2572 Ensure that runs fail gracefully after database connection loss

PanelPlex_main, Consensus_main, Thermosleuth_main, Application Portal WebUI

  • Forces a run to a failed state if it failed unable to do so from the processor
  • Adds extra logging for mix-and-match
  • Removes last vestiges of the old error reporting code


DEV-2678 Fix attempt to get run directory from ThermoSleuth sub-jobs

Application Portal WebUI

  • Prevents the failure check from loading ThermoSleuth sub-jobs


DEV-2676 Adjust TS amplicon sequence displayed

Thermosleuth_main, Application Portal WebUI

  • Bug fix - show exact sequence of the amplicon in export functions and genome viewer


DEV-2680 Fix evaluation for whether controls are in targets


  • Fixes coordinate checking for whether control oligos are in a given target


DEV-2677 Fix Design Dashboard DG, DH values

Application Portal WebUI

  • Adjusts DH table to pull from the correct data


DEV-2679 Ensure PP tiling run can start multiple jobs


  • Bug fix - preserve user's contact email throughout tiling runs


DEV-2050 Update portal with new v6 EULA

Application Portal WebUI

  • Update - add latest EULA and policy policies
  • Bug fix - fix 'not forwarding' bug


DEV-2590 Debug EULA acceptance API call

Application Portal WebUI

  • Bug fix - update API call
  • Bug fix - remove out-dated reference links


DEV-2681 Update probe filtering during Mixnmatch

PanelPlex_main, Consensus_main

  • Adds positional short circuiting for probes
  • Makes probe junction filtering use correct overlap padding
  • Fixes error in positional sort
  • Allows cancelling job during mix-and-match


DEV-2590 Debug EULA acceptance API call

Application Portal WebUI

  • Bug fix - extract policy version from file name


DEV-2688 Address null pointer error when checking predesign parent oligo


  • Bug fix - Predesign probes are not generated from a junction input


DEV-2694 Fix creation of amplicon string for negative sense runs

PanelPlex_main, Consensus_main

  • Correct the creation of the amplicon strings on negative sense runs
  • Fix null pointer exception running with no probes


DEV-2691 Update pipeline for v6.1.0 release

Application Portal WebUI

  • Update policies and documentation



DEV-2080 Fix error where ThermoSleuth results improperly pruned
  • Adjusts code to remove incorrectly applied pruning.


DEV-2082 Fix race condition in playlist saving
Sequence Playlists
  • Removes race condition.


DEV-2091 Update Portal to use latest version of EUtils
Sequence Playlists
  • Updates library.



DEV-209 Incorporate updated primer-dimer prediction algorithm
  • Makes enzyme homodimer check conditional on initial target strand type.


DEV-1993 Fix CopyCount to handle GOI and control in the same channel
  • Update CopyCount to distinguish between GOI and control even in the same channel.



DEV-320 Update Targan to use new playlist format
  • Adds the ability to index the new Playlist format on the fly for Targan usage



DEV-297 Add missing queries to update MySQL scripts
Application Portal WebUI
  • Added new tables and update existing tables to support 4.6.0 and 5.0.0 functionality in the SQL migration files, thus avoiding a manual work-around


DEV-306 Interamplicon test in PanelPlex is Broken
  • Updated the temporary playlist generation code to properly interface with ThermoSleuth, and made the amplicon gap generation key off of the keystone alone


DEV-277 Doxygen code documentation trial
  • Added initial documentation (via Doxygen) with config file.


DEV-302 Clean up Behemoth with .gitignore
Infrastructure & Server Config, Project Behemoth
  • Consolidated and updated .gitignore for IDE related files. Cleaned up files that should have been ignored


DEV-303 Replace source of percent bound result
  • Gets PB from TS
  • Altered PB from TS (/100) and limiting it to 4 decimal places
  • Changed all methods which access percent Bound to Two State Fraction Bound
  • Changed DB column name from PercentBound to TwoStateFractionBound


BHM-2905 Filter out and ignore improbable (e.g. low percent bound) TB hits.
  • Updates code to use the new MaxHitsPerOligo parameter


DEV-315 Have ThermoSleuth run multiple primers and probes in a single execution.
  • ThermoSleuth runs will now run multiple primers/probes at a time.


DEV-316 Update release notes for 5.0.20 release
Infrastructure & Server Config
  • Updates release notes.


DEV-317 Fix default for number of PanelPlex results
  • Sets the default number of multipick solutions to the lesser of panels+1 or a configurable number.

Version 5.0.12

February 2022

Changes made to Playlist Creation:
  • Users will be provided with options regarding letters other than IUPAC and agct's in playlist preperation.
  • Remove slashes from playlist name.
  • Fix playlist creation table lock issue.
Changes made to PanelPlex™-NGS:
  • Regions .csv will have all the amplicons, synchronized the code block.
  • Checks for null pointers on PanelPlex file.
  • Fixes race condition that was resulting in missing amplicon data in PanelPlex CSV output.
Changes made to PanelPlex™-Consensus:
  • Removes checks against Ns in region, and adds them for Ns in amplicon instead.
  • Corrects update of 3' and 5' positions for control primers from inclusivity run.
  • Improves coverage penalties in solutions with multiple primer pairs, so that the penalty is not overly excessive.
  • Don't prohibit ambiguity codes if using FastCompare.
Changes made to ThermoBLAST-CE:
  • Remove the empty sequence and notify the user.
  • Updates ThermoBLAST to ThermoSleuth
Changes made to qPCR CopyCount:
  • Users will be able to delete managed assays.
  • Fixes error in CopyCount CNV channel selection.
  • Improves CNV channel defaults.
Changes made to Infrastructure:
  • Don't simply return least loaded server if there are no available servers with enough capacity.
  • Updates to make the code compatible with newer MySQL versions.
  • Adds config variable that can set a webserver to not check for jobs to forward to a processor server.

Version 4.1.1

September 2018

Changes made to qPCR CopyCount since the previous (4.0) release:
  • Added QuantStudio 3 Data processor
Changes made to PanelPlex™-NGS since the previous (4.0) release:
  • Added performance and efficiency enhancements.
  • Updated the NGS input format to specify a junction range instead of a single position.

Version 4.0

May 2018

Added new product: PanelPlex™-NGS
  • Allows for multiplexes up to 50plex (later versions will increase this limit)
Changes made to PanelPlex-MDx since the previous (3.2.1) release:
  • Changed name of product from PanelPlex to PanelPlex-MDx. Clarifies that this product is for the consensus design of molecular diagnostics for infectious diseases.
  • Added functionality to save all the input parameters for a given run. This allows accurate documentation of how each run was performed.
  • Added functionality to run PP-MDx using the input parameters file. This allows runs to be repeated exactly with minimal opportunities for user input error.
  • Improved default settings in PP-MDx.
  • Scoring weight for G-quartet penalty increased.
  • Added functionality to download all results as a .zip file.
  • Page load times improved.
  • Improved layout of Next and Back buttons on each page.
  • Genomes with lower case letters (such as Zika virus) now correctly shown in the Coverage section of the output.
  • Improved automatic keystone selection
Changes made to ThermoBLAST-CE since the previous (3.2.1) release:
  • Increased number of CPU cores devoted to ThermoBLAST jobs from 14 to 33. Resulting in runtime improvement.
  • Fix ability to add and remove accessions from an existing ThermoBLAST playlist
  • Fixed issue where downloaded amplicon had 1 extra nucleotide on the 5’-end and was missing 2 nucleotides at the 3’-end.
  • Functionality for automatic detection and deletion of duplicate accessions.
  • Fixed functionality for combining pre-existing playlists.
  • Increased memory limits to allow for larger playlists to be handled.
  • Amplicon detection algorithm improved to both go faster and also to detect more amplicons. In the previous version some weak binding primers would not be detected as amplicons.
  • Minor bug fixes and optimizations
  • Several new playlists added (e.g. Vaginal microbiome, GEBA).
  • Known remaining issue: Within the “View Playlist” page if you try to edit the playlist then the program terminates. Workaround: Log back in and edit the playlist from the “Playlists you created” page.
Changes made to qPCR CopyCount since the previous (3.2.1) release:
  • Added support for MJ Research data format.
  • Non-permanence of data implemented for CNV
  • At rest encryption added for CNV data

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