37 Version change log Version 2.2.2 (09-MAR-15) Upon loading a DeviceEditor XML design file, the start/stop BPs are now checked for errors. Added links to the DeviceEditor and j5 manuals in the help menu. When re-mapping sequences to parts, sequence files that are no longer in use are removed from memory. Version 2.2.1 (09-JAN-15) Fix for bug affecting part -> right click -> Import multiple DNA sequences process, which resulted in multiple new parts incorrectly being assigned the same part IDs. Version 2.2.0 (26-NOV-14) Minor changes from http:// to https:// in warning/error message dialogs, following change to SSL for the public j5 web server. Version 2.1.9 (29-JUL-14) Implemented the display of a warning message for people using the Pepper Flash plugin in Chrome, Genbank support in import multiple DNA sequences, improvements for part preferred overhangs (give user feedback after updating, and not showing button if mock assembly). Minor bug fix for extracting sequence from GenBank files. Version 2.1.8 (03-JUL-14) Implemented access to part internal preferred overhang settings, and enabled the user to update these part internal preferred overhang settings following each j5 design run. Implemented access to forced relative overhang inequality settings. Fixed a bug that was preventing copy/paste of parts between standalone and DIVA DeviceEditor. Version 2.1.7 (09-MAY-14) The j5 parameter APPEND_UUID_TO_PLASMID_OLIGO_AND_SYNTHESIS_NAME has been added to the j5 parameters interface. Access to the j5 method Distribute Split and Pool PCR reactions has been added to the Downstream Automation tab of the j5 interface. Sequences mapped from ICE-tethered VE are now displayed in the part info tab. Minor bug fix to re-enable copy/paste between DeviceEditor tabs. Minor update for importing j5 parts list files. The DeviceEditor design file XML schema has been updated. Version 2.1.6 (22-JAN-14) Minor change to the DeviceEditor j5 xml-rpc interface for condense assemblies and downstream automation functionality. Version 2.1.5 (19-DEC-13) Minor change to the DeviceEditor j5 xml-rpc interface, as well as a minor bug fix to not throw an uncaught error when encountering an invalid SBOL iconID when importing a DeviceEditor XML design file. Version 2.1.4 (11-DEC-13) Minor change to the DeviceEditor XML v4.2 design file import process, in that if the attribute has not been set for a given j5Bin id, DeviceEditor will set the attribute automatically. Version 2.1.3 (02-DEC-13) DeviceEditor XML schema updated to v4.2. An additional minor change that enables user access to setting a new additional j5 parameter: SUPPRESS_PRIMER_ANNOTATIONS. DIVA-specific changes: added mechanisms to save designs to and retrieve designs from the DIVA backend, and to call j5 through the DIVA backend instead of the j5 server. Unsaved design changes are detected. Added a simplified j5 Controls dialog.   Version 2.1.1 (04-SEP-13) Generated j5 input files now use j5-standardized file names: j5parameters.csv, mastersequences.csv, masterzippedsequences.zip, partslist.csv, targetpartsorder.csv, and eugeneruleslist.eug. Version 2.1.0 (13-AUG-13) New features implemented include multi-entry FASTA file import (DNA sequences only) and multiple sequence files import (FASTA DNA sequences only). This functionality is accessible by either right-clicking a grid location on the design canvas (row/column) or selecting the grid location and then via the File menu. Version 2.0.9 (08-APR-13) SBOL Visual icons updated to v1.0.0. DeviceEditor XML schema updated accordingly. Version 2.0.8 (13-MAR-13) Minor bug fix coinciding with Adobe Flash update to version 11.6.602.171 which appeared to break proper mapping parts from the clipboard and copy/cut/paste functionality in some browsers in some operating systems. Version 2.0.7 (07-FEB-13) Minor change that enables user access to setting two new additional j5 parameters: HOMOLOGY_MIN_LENGTH_BPS and HOMOLOGY_MAX_FRACTION_MISMATCHES. Version 2.0.6 (01-Nov-12) When a DNA sequence is mapped from VectorEditor to DeviceEditor via the system clipboard (i.e., copy/paste), any illegal characters (such as whitespace or special characters) in the name of the source sequence (i.e., part source) are now converted into underscores.   Version 2.0.5 (03-Oct-12) SBOL Visual icons updated to latest versions. Version 2.0.4 (11-Sept-12) Minor fix for bug that in some situations resulted in SBOL XML not being recognized as a valid sequence output format. Minor fix for bug that resulted in j5-ready status not being updated following the addition or removal of columns in the design canvas. Version 2.0.3 (25-Jul-12) Minor bug fix when importing designs from j5 files. Version 2.0.2 (12-Jul-12) "SBOLXML" added as j5 output sequence file format option. Version 2.0.1 (6-Jul-12) Copy, cut, paste, and delete keyboard shortcuts are again functional. Minor bug fixes including: column direction arrows are now correctly set after loading from j5 files, prohibited characters in file name are checked before opening the save dialog box, and extracting sequence files from j5 files is now more robust. Minor aesthetic change from "Map Genbank" to "Map from Genbank". Version 2.0.0 (30-May-12) Major user interface overhaul. The design canvas has been migrated to a spread-sheet like grid interface. Each part is now associated with a row/column, with each column representing a combinatorial bin, and each row within a column representing an alternative combinatorial variant. SBOL Visual icons are no longer associated with parts, but rather a SBOL Visual icon may be associated with each column. Access to newly available j5 features (e.g. expanded set of Eugene design specification rules, (combinatorial) mock assembly design, annealed oligos forced assembly strategies, and revised default j5 parameters) has now been implemented. The design file XML xsd, generator, and parser have also been updated accordingly. Version 1.2.5 (22-FEB-12) Forced Assembly Strategy and Eugene rule indicator lights are now displayed for part icons with forced assembly strategies and Eugene design specification rules. Forced Assembly Strategy warnings are no longer issued (obsoleted by the indicator lights). There is now support for running Combinatorial SLIC/Gibson/CPEC assembly designs on the j5 server, specifying extra 5' and 3' CPEC overlap bps, and for specifying a circular or linear assembly product type. Combinatorial SLIC/Gibson/CPEC and Golden Gate built-in examples have been added. 7 new j5 design parameters have been added, and functionality for retrieving and loading j5 parameters from the j5 server has been implemented. The design XML xsd, generator, and parser have also been updated accordingly. Version 1.2.4 (23-DEC-11) Icons have been updated to SBOLv 1.0, and their corresponding images are tracked by ID instead of paths. The design XML xsd, generator, and parser have also been updated accordingly. Version 1.2.3 (15-DEC-11) Importing Eugene design specification rules from a file has now been implemented, and several minor changes to Eugene rules creation dialog box behavior have been made. The default for the j5 parameter "Golden Gate Term Extra Seq" is now "CACACCAGGTCTCA". Version 1.2.2 (22-NOV-11) The DeviceEditor design file XML schema has been updated to associate Eugene design specification rules with overall design rather than with individual parts. In the Part Info panel, the list of Eugene rules that apply to the selected part now includes those rules for which selected part is the Operand2 of a NOTWITH rule. A minor change has been implemented to address incorrect part icon directions. Version 1.2.1 (07-NOV-11) The DeviceEditor design file XML schema has been updated, along with the built-in examples, parsers and generators. The "Part Info" tab has been modified in a minor way. Version 1.2.0 (19-OCT-11) The forced assembly strategy for a combinatorial bin is now set more consistently, and is now displayed in the collection object panel. On Windows and Linux computers, when opening a file, there is now an option to consider all files (beyond the default expected file extension). When loading a design from j5 files, the start and stop bp for each part defaults to the beginning and end of the corresponding sequence if the start and stop are not specified, mimicking j5 behavior. Additional error checking routines implemented. When mapping a sequence to a part from the clipboard, mapping the whole sequence is now an option. Right click -> Delete is now implemented for parts and collection objects. After running a j5 assembly design, jbei-seq and FASTA format output sequences are now displayed. Version 1.1.9 (28-SEP-11) After running a design on the j5 server from within DeviceEditor, the user can now click on hyperlinks provided for each of the resulting j5-designed sequences. These hyperlinks will open the corresponding sequences in VectorEditor, allowing the user to immediately visually assess if the desired sequences were designed as envisioned. Version 1.1.8 (05-AUG-11) Minor bug fixes including ensuring that part source sequence file names do not contain whitespace characters, and that no two part source sequence file names are case-insensitive matches of each other (e.g. "ntcA.gb" and "Ntca.gb") which can cause problems in Windows and Mac OSX operating systems. Version 1.1.7 (11-JUL-11) Added support for importing (j5) zipped sequence files whose contained sequence files are located within a directory structure.   Implemented user-interface modifications to the j5 Controls dialog (removed the expand/collapse button functionality), to the Condense Assembly Files and Downstream Automation dialogs (added stop waiting buttons), and to the design canvas (no longer provides internal software status information at the bottom of the display). Version 1.1.6 (13-JUN-11) Example design files are now available through File -> Load Design -> Example Design. The Run j5 on Server dialog box now has the option to generate empty Master (Plasmids, Oligos, Direct Syntheses) List files. Version 1.1.5 (02-JUN-11) Initial change log reporting coinciding with release of j5.jbei.org public web server.