--------------------------------------------------------------------- Version: 2.3.3 Date: 04/20/2026 (i) Fixed polisher bug where the per-job constraint-violation cache returned stale results. --------------------------------------------------------------------- Version: 2.3.2 Date: 03/13/2026 (i) Updated home page news items --------------------------------------------------------------------- Version: 2.3.1 Date: 02/26/2026 (i) Added predefined dicodon usage tables for Phanerochaete chrysosporium (RP-78 v4.0, JGI MycoCosm) and Pleurotus ostreatus (PC15 v2.0, JGI MycoCosm) (ii) Dicodon usage table dropdowns now default to Coprinopsis cinerea and are sorted alphabetically --------------------------------------------------------------------- Version: 2.3.0 Date: 02/19/2026 (i) Added dicodon optimization feature: codon juggling can now use dicodon usage tables (codon-pair frequencies) instead of single-codon usage tables. Uses a Viterbi/HMM algorithm (ported from dicodon_optimizer by Florian Finkernagel, MIT License) to find the globally optimal codon-pair sequence for each gene. (ii) Added dicodon polishing: when a dicodon usage table is provided, the Polisher derives per-codon weights from the dicodon pair frequencies to guide codon replacements at violation sites. --------------------------------------------------------------------- Version: 2.2.17 Date: 02/13/2026 (i) Fixed bug where sequence pattern constraints in coding regions were not being removed during polishing when feature (e.g., gene, CDS) coordinate annotations overlapped --------------------------------------------------------------------- Version: 2.2.16 Date: 02/11/2026 (i) Fixed critical bug in Gibson/Chewback and Yeast assembly final construct generation where overlap regions were being duplicated, resulting in incorrect sequence lengths and potential introduction of spurious restriction sites (ii) Implemented overlap-aware building block concatenation using SequenceRegion coordinates to detect and prevent duplication of homologous recombination overlap regions --------------------------------------------------------------------- Version: 2.2.14 Date: 01/30/2026 (i) Added Similarity Check module that runs automatically as the final task in every workflow; can also run standalone. (ii) Added Similarity Check section to Manual page --------------------------------------------------------------------- Version: 2.2.13.1 Date: 01/29/2026 (i) Fixed bug related to rerunning jobs with destination vector sequence --------------------------------------------------------------------- Version: 2.2.13 Date: 01/09/2026 (i) Added support for inputting destination vector sequence and outputting complete genbank file. --------------------------------------------------------------------- Version: 2.2.12 Date: 10/14/2025 (i) Added more information about duplicate sequences to user message --------------------------------------------------------------------- Version: 2.2.11 Date: 08/26/2025 (i) Fixed issue with re-introducing sequence pattern constraints especially (but not solely) when checking for vendor constraints. (ii) Fixed issue w/ sequence ID clobbering when duplicate sequences appear in a job --------------------------------------------------------------------- Version: 2.2.10 Date: 02/28/2025 (i) Update max BB length for twist clonal and non-clonal to 5kb (ii) Update boost output globally to 4 digit p numbers, p001 -> p0001 --------------------------------------------------------------------- Version: 2.2.9 Date: 01/10/2025 (i) Simplified for workflows only (ii) Updated some default input values for Juggler, Polisher, Partitioner (a) Codon default from Arabidopsis to Escherichia coli (b) BB max length from 1700 to 3000 (c) Primer min length from 23 to 26 --------------------------------------------------------------------- Version: 2.2.8 Date: 06/06/2024 (i) Updated to conform with Golden Gate API v0.21.0 --------------------------------------------------------------------- Version: 2.2.7 Date: 06/05/2024 (i) Added academic usage confirmation check --------------------------------------------------------------------- Version: 2.2.6 Date: 05/03/2024 (i) Bug fix setting constraint class --------------------------------------------------------------------- Version: 2.2.5 Date: 05/03/2024 (i) Bug fix updating job cache --------------------------------------------------------------------- Version: 2.2.4 Date: 04/26/2024 (i) Handling of minimum fragment length for golden gate API --------------------------------------------------------------------- Version: 2.2.3 Date: 04/23/2024 (i) Fixed bug in Golden Gate multi-sequence/multi-error handling --------------------------------------------------------------------- Version: 2.2.2 Date: 04/04/2024 (i) Implemented NEB API to use whitelist authentication --------------------------------------------------------------------- Version: 2.2.1 Date: 01/09/2024 (i) Updated JIRA issue collector URL --------------------------------------------------------------------- Version: 2.2.0 Date: 09/06/2023 (i) Golden Gate assembly integration --------------------------------------------------------------------- Version: 2.1.1 Date: 07/31/2023 (i) Updated license --------------------------------------------------------------------- Version: 2.1.0 Date: 05/24/2023 (i) BOOST v2 logo updated (ii) Preserve source sequence case --------------------------------------------------------------------- Version: 2.0.0 Date: 05/15/2023 (i) Yeast assembly implemented (ii) Scaffolding for fine-tuning logging implemented (iii) Keycloak authentication integration (iv) CSV output file bug fixes (v) Add'l GenBank file generation w/o yeast assembly info (vi) Updated default building block lengths depending on assembly type (vii) Updated manual section (viii) Removal of Builder and Codon Merger tool --------------------------------------------------------------------- Version: 1.3.13.7p (prod) Date: 11/11/2022 (i) Fixed bug when rerunning jobs with uploaded partitioning parameters --------------------------------------------------------------------- Version: 1.3.13.7 (dev) Date: 11/11/2022 (i) Fixed bug when rerunning jobs with uploaded partitioning parameters --------------------------------------------------------------------- Version: 1.3.13.6p (prod) Date: 11/10/2022 (i) REVERSE_TRANSLATION added to rerun job types --------------------------------------------------------------------- Version: 1.3.13.6 (dev) Date: 11/10/2022 (i) REVERSE_TRANSLATION added to rerun job types --------------------------------------------------------------------- Version: 1.3.13.5p (prod) Date: 11/08/2022 (i) BOOST database work --------------------------------------------------------------------- Version: 1.3.13.5 (dev) Date: 11/04/2022 (i) BOOST database work --------------------------------------------------------------------- Version: 1.3.13.4 (dev) Date: 10/24/2022 (i) BOOST job management release patch --------------------------------------------------------------------- Version: 1.3.13.3 (dev) Date: 10/21/2022 (i) BOOST job management improvements --------------------------------------------------------------------- Version: 1.3.13.2 (dev) Date: 08/19/2022 (i) Fixed API examples appearing in manual section --------------------------------------------------------------------- Version: 1.3.13.1 (dev) Date: 05/02/2022 (i) JIRA ref: SYNBIO-816 - Creation of dynamic messaging banner for BOOST, which can be used to warn of upcoming downtime, for example. (ii) JIRA ref: SYNBIO-828 - BOOST to purge data files after 90 days. Messaging for the user appears on the job results page, near the zip file download button. (iii) Small bug fix - Build phase order adjusted --------------------------------------------------------------------- Version: 1.3.12 (dev) Date: 04/28/2022 (i) JIRA ref: SYNBIO-815 - Copyright year updated across application (ii) JIRA ref: SYNBIO-819 - Server/build information available to see in build (iii) JIRA ref: SYNBIO-829 - Contact page altered to citation information page (iv) Reverted temporary changes made for VM migration --------------------------------------------------------------------- Version: 1.3.11 (dev) Date: 03/22/2022 Version (dev) built expressly for migration to new servers. --------------------------------------------------------------------- Version: 1.3.10 (dev) Date: 03/11/2022 (i) Bug fix - NullPointer occurring in Polisher module --------------------------------------------------------------------- Version: 1.3.9.3 (prod) Date: 07/07/2022 (i) Fixed JIRA issue tracking links --------------------------------------------------------------------- Version: 1.3.9.2 (prod) Date: 07/01/2022 (i) Added 90-day data purge notification --------------------------------------------------------------------- Version: 1.3.9.1 (prod) Date: 03/22/2022 Version built expressly for migration to new servers. --------------------------------------------------------------------- Version: 1.3.9 Date: 05/10/2021 (i) Partitioner Module - Is able to generate _PAR csv using the _REV file output from the Polisher Module as part of Workflow - In _PAR csv file generated, the naming convention for Building Block IDs now match with corresponding partition numbers i.e. BatchName_p001. - The 001 after _p, for each sequence will be used to maintain mapping in the output [NOTE: Current partitioner naming convention only supports 3 characters after '_p'. i.e. 0001 will cause unexpected behavior] (ii) Juggler Module - First and Last 3 codons of a CDS in sequences will not be modified by the Juggler Module (iii) Bug fix - BOOST is able to read files uploaded containing Custom Codon Table and Restriction Sites (iv) Bug fix - Only jobs selected for deletion are deleted on the Job List page instead of random jobs (v) Polisher Module - Sequences who violations occurred in non-modifiable regions will also be written to output files (These were previously not written to output files causing them to not get partitioned as well) --------------------------------------------------------------------- Version: 1.3.8 Date: 05/04/2020 BOOST does not modify * regions of two (or more) overlapping mutable features, i.e. features annotated as CDS or gene, and * the start codon when optimizing mutable features for synthesis --------------------------------------------------------------------- Version: 1.3.7 Date: 02/20/2020 (i) input of initial value in Partitioner (ii) bug-fix in Jobs table (select and delete) --------------------------------------------------------------------- Version: 1.3.6 Date: 10/29/2019 (i) updated default values for Chewback/Gibson assembly BB length 350/1700 Overlap 25/30/40 Primers 23/40/62 (ii) bug-fix in logging mechanism on back-end --------------------------------------------------------------------- Version: 1.3.5 Date: 10/23/2019 (i) bug-fixes in invocation of vendor APIs --------------------------------------------------------------------- Version: 1.3.4 Date: 03/07/2019 (i) bug-fixes in Partitioner --------------------------------------------------------------------- Version: 1.3.3 Date: 02/21/2019 (i) various bug-fixes in Partitioner (ii) warnings in case of degenerate sequence input (iii) error messages in case of processing degenerate sequences --------------------------------------------------------------------- Version: 1.3.2 Date: 02/12/2019 (i) Sequence patterns in Polisher app: - support of Ns in degenerated sequences - output of the sequence pattern in case of violations (ii) Various bug fixes in Partitioner app, such as keeping the features of the input sequences in the GenBank output --------------------------------------------------------------------- Version: 1.3.1 Date: 01/19/2019 (i) Update calls to API of Twist for clonal products up to 5kb --------------------------------------------------------------------- Version: 1.3.0 Date: 12/11/2018 (i) Integration of GenScript (https://www.genscript.com/) as DNA synthesis vendor in Polisher and Workflow-Manager apps --------------------------------------------------------------------- Version: 1.2.0 Date: 10/12/2018 (i) Check for sequence duplicates (ID and nucleotides of sequences) and display of warnings in case of duplicates --------------------------------------------------------------------- Version: 1.1.1 Date: 10/10/2018 (i) Bug-fix in provenance tracking of reverse-translation tasks --------------------------------------------------------------------- Version: 1.1.0 Date: 08/15/2018 (i) Bug-fixes (ii) Addition of "Codon Usage Tables Merger" App --------------------------------------------------------------------- Version: 1.0.4 Date: 05/22/2018 (i) Bug-fixes regarding Twist API integration (ii) Storing request data and results for each job in JSON format. --------------------------------------------------------------------- Version: 1.0.3 Date: 05/07/2018 (i) Integration of new version of Twist API (ii) Initial version of "Builder" app --------------------------------------------------------------------- Version: 1.0.2 Date: 11/01/2017 (i) Web UI: -- removed "Forum" -- added "Account" for displaying user information --------------------------------------------------------------------- Version: 1.0.1 Date: 09/30/2017 (i) Partitioner: ** Inputs: -- vector name, resistance marker, and origin of replication -- vector linearization method and corresponding parameter values - digestion using a restriction enzyme - amplification using 5' and 3' primers ** Outputs: -- Tree-View and Tabular-View of input sequences, their building blocks, and their 5' and 3' primers, as well as Download of a CSV file containing this information -- design.xml avoiding duplicate primer sequences -- build.sbol, which is JGI's new version of design.xml The new Partitioner inputs are also available in the Workflow Manager qpp. (ii) Manuals: ** updated description of Partitioner inputs ---------------------------------------------------------------------