--------------------------------------------------------------------- Version: 1.3.13.7p (prod) Date: 11/11/2022 (i) Fixed bug when rerunning jobs with uploaded partioning parameters --------------------------------------------------------------------- Version: 1.3.13.7 (dev) Date: 11/11/2022 (i) Fixed bug when rerunning jobs with uploaded partioning 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 ---------------------------------------------------------------------