Version 5.0.26 (July 2022)
Changes made to ThermoSleuth:
- [DEV-2080](https://dnasoft.jira.com/browse/DEV-2080) Fix error where ThermoSleuth results improperly pruned
Changes made to Playlist Creation:
- [DEV-2082](https://dnasoft.jira.com/browse/DEV-2082) Fix race condition in playlist saving
- [DEV-2091](https://dnasoft.jira.com/browse/DEV-2091) Update Portal to use latest version of EUtils
Version 5.0.24 (May 2022)
Changes made to PanelPlex™-Consensus and PanelPlex™-NGS:
- [DEV-209](https://dnasoft.jira.com/browse/DEV-209) Incorporate updated primer-dimer prediction algorithm
Changes made to qPCR CopyCount:
- [DEV-1993](https://dnasoft.jira.com/browse/DEV-1993) Fix CopyCount to handle GOI and control in the same channel
Version 5.0.22 (March 2022)
Changes made to PanelPlex™-Consensus:
- [DEV-320](https://dnasoft.jira.com/browse/DEV-320) Update Targan to use new playlist format
Version 5.0.21 (March 2022)
Changes made to PanelPlex™-NGS:
- [DEV-306](https://dnasoft.jira.com/browse/DEV-306) Interamplicon test in PanelPlex is Broken
- [DEV-317](https://dnasoft.jira.com/browse/DEV-317) Fix default for number of PanelPlex results
Changes made to ThermoSleuth:
- [DEV-303](https://dnasoft.jira.com/browse/DEV-303) Replace source of percent bound result
- [BHM-2905](https://dnasoft.jira.com/browse/BHM-2905) Filter out and ignore improbable (e.g. low percent bound) TB hits.
- [DEV-315](https://dnasoft.jira.com/browse/DEV-315) Have ThermoSleuth run multiple primers and probes in a single execution.
Changes made to Infrastructure:
- [DEV-297](https://dnasoft.jira.com/browse/DEV-297) Add missing queries to update MySQL scripts
- [DEV-277](https://dnasoft.jira.com/browse/DEV-277) Doxygen code documentation trial
- [DEV-302](https://dnasoft.jira.com/browse/DEV-302) Clean up Behemoth with .gitignore
- [DEV-316](https://dnasoft.jira.com/browse/DEV-316) Update release notes for 5.0.20 release
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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