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Latest improvements in CLC Main workbench

CLC Main Workbench 7.5

Release date: August 28, 2014

New features and improvements

  • Workflows:
    • The input information is now shown in the preview dialog and also exported to all formats.
    • It is now possible to edit the workflow input name by right-clicking on the input name in the workflow.
    • Workflows as such can have multiple inputs (though this will disable the batch functionality).
    • Data can now be directly bundled with a workflow installation. This means that reference data can be packed and shared together with a workflow (only recommended for small data).
    • A workflow input can be pre-configured. If kept unlocked, it can be used to give a default when executing the workflow.
    • A text field has been added to the side panel, where you can search for elements in the workflow. A found element will be centered and highlighted.
    • A new editor was added to the workflow to make it easier to check the configuration. The new editor can be accessed from the lower left corner of the View Area and lists all configuration parameters.
    • Workflows can be packaged with a plugin and will get installed with the plugin simultaneously.
    • Workflows installed on the server now have an overlay icon in the workbench, to make them easily distinguishable from workflows installed in the workbench.
    • The execution of a workflow in the workbench and on the server have been unified to have the same behavior regarding logs, intermediate results and output naming.

    • Locked settings in the workflow wizard are now again hidden per default when executing the workflow, to give a cleaner, simpler look to the configuration. When expanding, all parameters are displayed.

  • Protein Analysis, Pfam domain search:
    • Pfam Domain Search now uses HMMER3 and the latest Pfam database that can be downloaded with the new tool "Download Pfam Database".
    • Searching multiple sequences is significantly faster.
    • New filters are available in the improved Pfam Domain Search tool to enable generation of the same results as the online tool.
  • Local Search enabled from the menu bar now includes filtering on "Path".
  • Advanced filtering on tables now includes the option to filter for a space, comma or semi-colon delimited lists of terms.
  • Zoom tools redesign: The “Zoom to selection” feature is now also available for sequences, sequence lists, alignments and read mappings.
  • The tracks info panel, with track names in the left side of the track, now wraps information instead of showing a scroll bar.
  • Saving/applying side-panel settings for tables now works for different tables that share some columns. 
  • Copy operations can now be stopped.
  • Output from "Reverse Translate" can now be a Sequence List.

  • Import of Example Data and imports done through dragging files into the workbench and dropping them in the Navigation Area will no longer block the user interface while executing. Instead, the import happens as a background process that can be monitored and controlled via the Processes tab in the lower left corner.

  • CLC workbenches now support high resolution displays such as Apple retina displays of all data shown in the View Area (including tooltips).
  • Improved error message in the Empirical Analysis of DGE tool in case of invalid expression values in experiments (occurs rarely).
  • More informative naming of coding region translations produced by the tool Translate to Protein. The name for a coding region translation consists of the name of the input sequence followed by the annotation type and finally the annotation name.
  • Genetic codes: The list of NCBI translation tables has been expanded to include  translation table 25 "Candidate Division SR1 and Gracilibacteria" (See: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c).
  • Improved error messages due to low disk space.

 

Bug fixes

  • The right-click menu on certain annotations in tracks was not working when viewing a single track. This has been fixed.
  • Icons in the workflow editor are now scaled consistently when zooming in or out.
  • Several issues with the validation display in the workflow editor have been fixed.
  • A bug has been fixed in the workflow configuration wizard. Previously the input was not taken into account when deciding which parameters were enabled.
  • Fixed problem where the "space" key did not trigger "Find Conflict" in the stand-alone read mapping editor.
  • Fixed stand-alone read mappings not showing mismatches and insertions in the overflow graph.
  • 'Replace input sequences with result' in Cloning Editor no longer fails.
  • Multi-sequence BLAST search results (BLAST tables) are now exportable as plain text.
     

Changes

  • Due to upgrade to Java 7,  Windows Server 2003 and OSX 10.5.8, 10.6 are no longer supported by Oracle. Hence, the system requirements are now: Linux, Windows Vista, Windows 7, Windows 8 or Windows Server 2008, or Mac OS X 10.7 or later.

CLC Main Workbench 7.0.3

Release date: May 14, 2014
  • Fixed error that caused selections in views not to be centered in the middle of the view.
  • Fixed bug that caused a crash in the Reassemble Contigs tool
  • Fixed bug that made the Workbench crash when viewing tables under certain circumstances
  • Fixed problem with "Find" on stand-alone read mappings with a circular reference and sequence lists containing circular sequences.
  • Fixed problem with some parts of workflow not being executed if there was multiple branches in workflow.
  • CLC Main Workbench 7.0.2

    Release date: March 18, 2014

    Bug fixes

    • Fixed problems causing an error when trying to uninstall plugins.
    • Fixed issue with pausing and resuming running processes

    CLC Main Workbench 7.0.1

    Release date: March 14, 2014

    New features and improvements

    • Fasta export:
      • Fasta export with trimming is now much faster and consumes less memory
      • Fasta export now reports progress while executing
      • When the "Remove trimmed regions" option is set, the Fasta export will ignore sequences in which all nucleotides are covered by a Trim annotation
    • Translate to Protein (Batch Process):
      • The wizard now has options for specifying whether to translate the coding regions or extract translations from the annotations
      • The log has been made more detailed and informative
      • If the result is just a single protein sequence, the output will be just that, otherwise all sequences are output as a list
      • If the tool estimates that the number of protein sequences to be produced is greater than 1.000.000, it will create protein sequences without history, and it will not copy the common name, latin name, and taxonomy fields
    • The PDB importer has improved support for custom residues

    Bug fixes

    • Fixed missing icon for "Metadata Import" in the phylogenetic tree table
    • Multi BLAST results table: the missing "Description (E-value)" field is displayed again in the table output
    • Fixed a bug that made PDB import fail on workstations with Turkish Locale settings

    CLC Main Workbench 7.0

    Release date: February 11, 2014

    New features and improvements

    • New functionality for phylogenetic trees (was previously part of a beta plugin)

      • Greatly enhanced viewer for visualizing and working with phylogenetic trees. The viewer allows the user to rapidly create high-quality, publication-ready figures of the trees.

      • Large trees are made easy to explore using different zoom functionalities and a small minimap of the entire tree. The viewer also comes with two alternative tree layouts, namely circular layouts and radial layouts, which are great for visualizing very large trees.

      • Supports importing, editing and visualization of metadata associated with nodes in phylogenetic trees.

      • Tool to reconstruct phylogenetic trees based on k-mers. This approach avoids the computationally intensive step of constructing a multiple alignment of the input sequences. The k-mer based reconstruction tool is especially useful for whole genome phylogenetic reconstruction where the genomes are closely related.
      • Tool performing a statistic evaluation of different substitution models to be used with maximum likelihood tree construction. The output of this tool is a report that lists the recommended settings to be used when constructing phylogenetic trees based on maximum likelihood.

      • Added an option for using the Kimura 80 substitution model when creating trees with distance based methods.
      • Distance-based tree reconstruction methods can now reconstruct trees from protein alignments using the Jukes-Cantor substitution model or the Kimura protein ML distance estimate.
      • A user defined start tree can now be supplied to the ML inference tool.
    • Complete redesign of the graphical user interface including:
      • New tool bar graphics
      • New product logos and colors, including splash screen
      • New background graphics on canvas and in dialogs
      • Tool bar has been re-organized
      • New tab design. Aligning the look and feel across platforms, which is particularly important to mac-users as split screen used to take up a lot of screen space.
    • New concept for Side Panels and Views:
      • Support for multiple screens: views can be moved to a different screen by dragging the tab of the view
      • Side Panels now consist of palettes that can be organized in group and the order can be customized
      • Palettes can be detached and placed anywhere on the screen
      • Navigation Area and Toolbox can be minimized to allow more pixels for displaying data
    • Zoom tools redesign:
      • The zoom tools have been re-organized and placed closer to the data
      • A zoom slidershows the present zoom level and can be used to adjust zoom
        • Detailed zoom is a new feature that allows zooming in and out in very small increments by dragging the zoom slider and moving the cursor above it. An expert feature for e.g. large tracks.

      • New zoom tools. Easy adjustment of zoom speed for improved zooming of huge sequences.

      • Detachable Side Panel editors. A Side Panel editor can be dragged from the main workbench window and dropped outside the workbench, making a separate window e.g. on a second screen, if available.

    • Copying data in the Navigation Area runs much faster and uses less memory than before. This is a great improvement which also kicks in when moving data between a CLC Genomics Server and a Workbench.

    • Workflows:
      • Possibility to have bulk configuration of elements. This enables to set the same reference data for multiple elements at once.
      • Workflows can be added inside a workflow. The inner workflow is "unfolded" into the single elements.
      • Parameters can now be renamed in the editor by the creator during configuration of the elements.
      • Workflows with invalid/unknown elements are laid out nicer and more consistent.
      • The sidepanel has now an option to display rulers in the editor to indicate better the size of a workflow (particularly when exporting)
      • Fit Width now fits the entire workflow in the editor by zooming out.
      • The sidepanel has a new section "Minimap" which shows an outline of the whole workflow. It allows to navigate the workflow in the view and also supports zooming
      • One can change the design of the workflow editor via the sidepanel (removed the old designs in the preferences)
      • Better validation when configuring parameters in workflows
      • If a tool receives inputs from at least two tools, the inputs can now be ordered via the context menu on the connections or the input part of the target element.
      • The name of an output in the workflow can be set by configuring the output element
      • Parameters of a workflow run can now be exported to various formats via the wizard
      • It is now possible to reset a reference parameter. Before it was only possible by removing the whole element and add it again.
      • In the workbench the installed workflows are now sorted alphabetically.
      • The graphics export of a workflow now knows about the scale and one can now export the whole workflow or only the current view.
      • A cpw file can now be dragged into the workflow manager and will be installed.
      • Further speed improvements on working with larger workflows in the editor
      • New tools that are now workflow-enabled:
    • 3D structure viewer:
      • Property viewer - a new tab in the Side Panel. Shows detailed information about the atom under the mouse pointer. If multiple atoms are selected (Ctrl-click), the distance (two atoms selected), angle (three atoms selected), dihedral angle (four atoms selected) formed by the selected atoms, is shown in the Property viewer. If a molecule is selected in the Project Tree, meta-data relating to the molecule is shown in the Property viewer.
      • Issues List. Issues related to the molecule structures and their chemistry representation is listed in the Issues List view on Molecule Projects. If seen in split-view with the 3D viewer, a selected issue will zoom to the atoms involved in the issue and select them in the 3D view.
      • General improvements to the PDB importer
      • Double-clicking an entry in the Project Tree will zoom-to-fit on the molecule or atom group.
      • When selecting atoms (by mouse clicking or from sequence), the atom context (whole residue or molecule) will also be shown in the 3D view. From context menu on 'Current' selection, an atom group can be generated either from the exact selection or from the selection plus the context (whole residues or molecules).
    • Extract consensus sequence is now able to copy annotations from both existing consensus sequence and the reference sequence.
    • When extracting consensus sequence from a mapping, conflict and low coverage annotations now include the position on the reference.
    • Trim annotations can be used to trim off sequences when exporting to fasta.
    • Secondary peak calling has been improved: it now only detects peaks that have a distinct peak shape, only peaks that fall within the same interval as the top peak are called. In addition, trim annotations are taken into account so that no peaks are called within trimmed regions. This greatly reduced false positive calls. Finally, the annotations now include information about the secondary peak's fraction of the maximum peak height. 
    • Advanced table filter now includes an option to search for "starts with" in addition to just "contains"
    • Limitations on export of Excel 2010 files (xlsx) are removed:
      • Multiple tables can be exported to one xlsx file
      • Reports can be exported to xlsx
      • Hyperlinks are preserved in xlsx files
    • SignalP prediction has been updated to be server-, batch- and workflow enabled.
    • Folder contents view: subfolders will display how many items they have
    • Assemble Sequences tools now accept sequence lists as input.
    • REBASE restriction enzyme list updated to version 310.

     

    Bug fixes

    • Workflow:
      • In the editor the "Fit Width" zooming was active, but behaved as "100%" zooming. Therefore the "100%" zooming is now active instead of the "FitWidth"
      • Added or connected elements are now placed near where you connect or add them, even when zoomed near or far.
      • It was possible to Undo the action of adding a workflow output, but it was not possible to Redo afterwards.
      • The right-hand icons in an element now scale with zooming.
      • The log of a workflow run on the server contains now the same information as when run in the workbench.
      • When configuring elements in the editor, the "Reset to CLC Standards" button is now functional and will reset the parameters to their default values. When configuring during installation or execution the button is disabled.
      • The log of a server executed workflow now states when the workflow has been cancelled.
      • A workflow with elements which provide additional inputs could not be batched.
    • Crash when adding data to experiments (e.g. by running any of the statistical analysis tools) has been fixed.
    • Various bugs in the extract consensus sequence tool have been fixed.
    • When translating to protein, ambiguous nucleotides potentially resulting in stop codons were not translated properly, and only the codons resulting in an amino acid were represented in the protein. Now the stop codons are also represented by an X in the protein sequence.
    • A problem with filtering and sorting the BLAST output table has been solved. Some of the columns were treated as text instead of numeric.
    • Restriction maps, histogram data, and primer tables could not be exported to csv or similar. This has been fixed.

    • When using the “Find Open Reading Frame” tool, the input sequence was reported incorrectly in the ORF table. This has been fixed.

    • Fixed problems with Excel export that failed when special characters were used in the name.

    Changes

    • The two tools in the "Multiplexing" folder in the toolbox category have been changed:
      • "Process Tagged Sequences" has been removed..
      • "Sort Sequences by Name" has been moved directly into the Sequencing Data Analysis folder.
    • Motif search: annotations created by the motif search are of type "Motif" instead of "Region"

    CLC Main Workbench 6.9.2

    Release date: January 23, 2014

    Bug fixes

    • Fixed: Error message when running analysis on experiments (statistical tests, clustering etc.)
    • The folder used by the Workbench for storing log and settings files on Windows 8 has been updated to follow conventions for Windows 8 which is identical to Windows 7. Any existing settings will be copied to the new location automatically. 
    • Fixed various problems related to launching the Workbench through Java Webstart.
    • Fixed: Opening a search view for searching sequences at NCBI would sometimes fail.
    • Fixed various stability and performance problems of Maximum likelihood phylogeny.
    • Fixed problem that caused a crash with extract consensus sequence tool with certain parameter configurations and with read mappings with no reads.
    • Fixed a bug in the Assemble Sequences tool causing some data sets to produce inferior contigs.

    CLC Main Workbench 6.9.1

    Release date: October 21, 2013

    New features

    • Heat maps: It is now possible to show a legend on a heat map.

    Changes

    • When importing Genbank nucleotide sequences, the Workbench will determine whether it is DNA or RNA based on the sequence rather than the description in the file.

    Bug fixes

    • Fixed: Trimming sequencing data for vector contamination from UniVec failed
    • Fixed: GFF export failed.
    • Fixed: Copying information from the Folder Contents view did not work.
    • Fixed: out of memory error when performing bootstrapping with ML tree construction methods.

    CLC Main Workbench 6.9

    Release date: August 21, 2013

    New features

    • Workflows:
      • Automatic adjustment of layout in workflows . It is now (again) possible to adjust the connected workflow elements automatically. Right click in the workflow editor to access a menu with the option "Layout". Clicking on "Layout" will adjust the layout of the workflow. The layout can also be adjusted with the quick command Shift + Alt + L.

      • Automatic update of tools in workflows . Tools in existing workflows will automatically be updated when opened from the Navigation Area. If new parameters have been added to the updated version of the tool, these will be used with their default settings. A workflow can be kept in its original form by saving the updated workflow with a new name as this will ensure that the old workflow is kept rather than being overwritten.

      • Information: In the “Manage Workflows ” dialog a new tab has been added providing information about the workflow (such as when it was built and which version of the workbench was used).

      • Highlight used elements : In the Side Panel under “View mode” it is now possible to select “Highlight used elements”, which will show all elements that are used in the workflow. Unused elements are grayed out. The “Highlight used elements” can also be activated with the quick command Alt+ Shift + U.

      • Highlight Subsequent Path: Is a further development of the old option “Mark Subsequent Path”.  If you right click on the name of one of the tools in a workflow, it is possible to select “Highlight Subsequent Path”, which will highlight the path in the workflow from the tool that was clicked on and further downstream.  All other elements in the workflow will be grayed out.

      • Create Installer: A workflow can now be installed directly from the workbench. This can be done with the “Create Installer” button (or the quick command Alt + Shift + I). Three options exist in the “Create Installer” dialog: 1) Install the workflow on your local computer, 2) Install the workflow on the current server (requires that you are logged on to the server and that you are the administrator), and 3) Create an installer file to install it on another computer.

      • Export can now be part of workflows.
      • Workflow enabled elements can be dragged directly from the Toolbox into the workflow editor.

      • Workflow images can be copied from the editor by using Ctrl + C (copy) and pasted into the desired destination with the Ctrl + V command.

      • All elements can be removed from the workflow with the shortcut Alt + Shift +R.

      • Reinstallation of modified workflows can now be done directly with the “Create Installer” function. A pop-up dialog provides the option to make "forced import" of an already installed workflow.

      • Speed improvements in the workflow editor means that the user experience when editing large workflows has been greatly improved.
      • New tools that are now workflow-enabled:
    • 3D Molecule Viewing : The integrated viewer of structure files, the 3D Molecule Viewer, has been completely redesigned. The Molecule Viewer offers a range of tools for inspection and visualization of proteins and other molecules stored in structure files from the Protein Data Bank (PDB).

    • Export framework redesigned
      • Export of multiple files: you can export several files in one go. The naming of the file will default to the name used in the Navigation Area of the Workbench, but the user can specify a naming pattern to use instead.
      • Export formats: A new column “Exports selected” has been added to the “Select exporter” table that indicates with a “Yes”, “No” or “Partly” whether the currently selected element can be exported with the given exporters. Partly means that you have made a selection of elements where only some of them can be exported by the selected exporter.

      • Improved usability with a quick-select dialog for choosing the right export format. The dialog includes a  description of each exporter that can be quickly filtered.
      • Export can be integrated into workflows
      • Support for direct compression of exported files in zip and gzip.

    •  The folder view has been improved with the following:
      • It is now possible to drag and drop objects from the folder editor. This will create a copy of the objects at the selected destination.
      • Attribute columns will be left empty if the attribute has not been defined (previously attribute values that had not been defined were set to 0 and checkboxes were shown as unchecked).
      • A new column showing the first 50 residues of each sequence has been added as an option.
      • The column with the name “Length” has been renamed to “Size”.
      • The column “Size” shows the length of a sequence, or for sequence lists, the number of sequences e.g.:
        • Sequence or contig lists: the number of sequences/contigs
        • Read mappings: the length of the consensus sequence
        • Alignments: the length of the alignment
    • The Side Panel “Save/Restore Settings” function has been expanded with a new feature:
      • The “Save/Restore Settings” function (found at the top of the Side Panel) has been redesigned. It is now possible to save settings in two different ways. 1) The settings can be saved for this element type in general, e.g. for a track it would be save settings “For Track View in General”. In this way the settings will be applied each time you open an element of the same type, which in this case means each time one of the saved tracks are opened from the Navigation Area, these settings will be applied. These “general” settings are user specific and will not be saved with or exported with the element. 2) Settings can be saved with the specific element only e.g. for a track it would be save settings “On This Track Only”. The settings are saved with only this element (and will be exported with the element if you later select to export the element to another destination).

    • Alignments: If you have one particular sequence that you would like to use as a reference sequence, it can be useful to move this to the top. This can now be done automatically by right clicking on the sequence name and then selecting “Move Sequence to Top ”.

    • The Sequence List Table has been improved with a new feature. A new column showing the first 50 residues of each sequence has been added as an option.
    • Phylogenetic trees:
      • Create Tree now support the Kimura 2-parameter substitution model for DNA sequences and Kimura's distance estimate for protein sequences (Kimura 1983).
      • Construction Maximum Likelihood phylogenies from protein sequences.

    Improvements

    • Scrolling in read mappings: The mouse scroll speed through read mappings can now be performed with increased speed. Shift + Alt + Mouse wheel scroll makes the scroll 10x as fast as when using Alt + Mouse wheel scroll. When zoomed all the way in, each mouse wheel step scrolls 10 rows.
    • Sort Sequences by Name : The multiplexing tool now allows a delimiter between group names in the “Sort Sequences by Name” wizard. This means that the selected group names are separated by an underscore. Previously all selected group names were merged without any delimiter.

    • Cloning: The cloning editor can now work without having a designated vector. In essence this means that when no vector is selected you go directly in “Stitch mode” when a fragment has been selected, whereas you go in “Cloning mode” when a cloning vector and a fragment are selected.

    • Renaming of data in the Navigation Area by clicking twice has been improved. Previously, you could accidentally enter rename mode when the intention was to get focus in the Navigation Area. Now, you can only trigger rename by clicking when the Navigator has focus.
    • Extract consensus sequence tool :
      • It is now possible to use the quality scores when resolving conflicts or disagreements between reads with “Insert ambiguity codes”. Previously, “Use quality scores” could only be selected when using the “Vote” option for conflict resolution.
      • Low coverage regions are now annotated in the consensus sequence produced.
      • The Extract Consensus Sequence dialog is now shown when extracting the consensus sequence when right-clicking a selection on the reference sequence in the mapping view, enabling the user to extract part of the consensus sequence.
      • The Extract Consensus Sequence dialog is now shown when extracting the consensus sequence when right-clicking the name of the consensus or reference sequence, or when clicking the Extract Consensus button in the mapping table. The right-click menu option on the consensus to Open Sequence Including Gaps has been removed, since this functionality is now covered by the Extract Consensus Sequence tool.
    • When using the “Translate to protein ” tool, the max limit has been raised to 1GB.
    • The sequence action "Open Copy" has been removed and "Open This Sequence" has been renamed to "Open Sequence ".

    • The alignment tool is now more memory efficient.
    • Tables: Improved auto-adjustment of the column width (based on content and number of columns).

    • Read mapping: The status bar in the lower right corner now shows the corresponding positions on the reference/contig sequence.

    • BLAST has been upgraded to BLAST+ 2.2.28 that includes a number of improvements and bug fixes. A full list of BLAST+ 2.2.28 changes can be viewed at http://www.ncbi.nlm.nih.gov/books/NBK131777 .

    • Usability improvement of simple table filtering :
      • A dedicated filter button has been added to apply the filter directly without having to wait until the filter is automatically applied
      • For tables with more than 10000 rows, the filter will not be applied automatically after a delay. Instead, there is a helping text asking the user to apply the filter through the "Filter" button. This avoids premature filtering before entry of the filter text has completed. Since filter can take some seconds for large tables, this used to be an annoyance because the user would have to wait until filtering was done to complete the entry.
    • Phylogenetic trees:
      • Bootstrapping with the "Maximum Likelihood Phylogeny" is now possible.

      • Bootstrap values are now displayed in percent instead of absolute numbers.


    Bug fixes

    • Numbering of amino acids when calculating amino acid changes was wrong for coding regions spanning the starting point of circular chromosomes. We recommend running amino acid calculation again. Please note that the actual amino acid change is called correctly, only the numbering is affected.
    • PDF export of the history of a result did not include the name and version number of the Workbench that produced the result.
    • Phylogenetic trees:

      • The Juke-Cantor distance estimate now ignore all positions containing gaps in pairwise alignments.

      • Disabled substitution rate estimation when the corresponding option is deselected by the user in the Maximum Likelihood Phylogeny tool.

      • Fixed a bug that caused branch lengths to be estimated incorrectly for ML trees.

    Changes

    • System requirements for Linux has changed. From this release, SuSE is supported from version 10.2. This was previously version 10.0.
    • Secondary Peak Calling : The parameter “Fraction of max peak height for calling”, in the “Secondary Peak Calling” wizard,  has been changed to use the interval 0-1with 0.2 as default setting. Previously the interval was 0 – 100 with 20 as default setting.

    CLC Main Workbench 6.8.4

    Release date: May 15, 2013

    Bug fixes

    • Fixed problem in workflows: it was not possible to configure all elements when running a workflow that branched after the input element.

    CLC Main Workbench 6.8.3

    Release date: May 8, 2013

    Bug fixes

    • Description text in progress area is now making full use of available width of the progress area
    • Handling of line breaks in annotation notes improved
    • On Linux: User interface text has been changed to not use bold font to make a better visual appearance
    • Annotation tracks and variant tracks created in CLC Genomics Workbench can be displayed in a table

    CLC Main Workbench 6.8.2

    Release date: March 19, 2013

    Improvements

    • Fragments generated from restriction site analysis can now be opened in batch. When multiple rows in the fragment table are selected, the right-click menu option will now create a sequence list with all the selected fragments.
    • For alignments, mappings, BLAST results and other sequence views, the right-click options to Open Copy of Sequence and Open This Sequence have been merged to Open Sequence. If a copy should be created, use Save As with the new sequence, or drag it into a folder in the Navigation Area.

    Bug fixed

    CLC Main Workbench 6.8.1

    Release date: January 23, 2013

    Improvements

    • Added Legal and Tabloid formats for printing

    Bug fixes

    • Fixed an error when translating DNA to protein. When more than 10 sequences were produced, the resulting protein sequence included X instead of * as stop symbol. We advice customers to re-run any analyses with the translation tool when using more than 10 sequences as input.
    • Various minor bug-fixes

    CLC Main Workbench 6.8

    Release date: January 8, 2013

    New features

    • Workflow: there are several important new features for workflows
      • It is possible to control which parameters should be locked or unlocked. This means that the creator of the workflow can decide which parameters should be left open for adjustment when the workflow is executed.
      • Usability of workflow editor greatly improved
        • There is a grid for helping layout
        • Visual indication of the number of possible connections as input to a workflow element
        • Visual indication to show if parameters have been changed
        • Handles for dragging and connecting elements have been made more clear
        • Side Panel for controlling grid layout and switching on compact visualization of workflow elements
        • You can high-light selected paths in a workflow
      • It is now an option to attach the workflow design file with the installer to allow users edit the workflow
      • There is a special icon for workflows in the Toolbar to make the creation and installation of workflows more visible
      • Several tools are now workflow-enabled:
    • Toolbox improvements:
      • New Favorite Toolbox: A new tab next to the Toolbox holds
        • Frequently used tools. This is automatically updated based on which tools are used most frequently.
        • Favorite tools: Right-clicking a tool in the Toolbox allows you to add a tool to your favorites list.
      • Quick launch of tools: Pressing Ctrl + Shift + T shows a dialog for easy typing and launching tools.
    • Relevant view settings are now copied when switching between different views of the same data. As an example: if you have specified a set of restriction enzymes to display in the circular view of a sequence and switch to the linear view, these enzymes will also be listed in the Side Panel here. Note that the Side Panel settings are only copied to the new view if they have been changed by the user in the old view.
    • Performance when sorting of large tables has been improved
    • Rename can now be done through right-click menu in Navigation Area.
    • Annotations on circular sequences:
      • When shown in linear view they have a cleaner appearance. Before, there was a line from beginning to end of the annotation, and this has now been removed.
      • When shown in circular view, it is no longer displayed as a joined annotation over the start point but as a continuous annotation.
    • Alignments: The performance of the algorithm for running multiple alignments has been improved and now runs on multiple cores.
    • Find Open Reading Frames can be run in batch and workflows
    • Translate to protein can be run in batch and workflows
    • Restriction map: Excel export now creates a sheet for both the cut sites table and the restriction map.
    • Alignments can be used as input for finding primer binding sites.
    • Export now has progress and can be canceled. 
    • BLAST results and 3D structures can be exported as text.
    • Batching: Previously, results where saved in the same folder as the input data. This can now be changed and a new save folder can be specified. Sub-folders will be created for each batch unit.
    • The limit for the cloning editor has been increased to 6,000,000 bases (from 4,000,000 bases).

    • Create Expression Clone (LR) from Gateway Cloning produces sequence object rather than a list

    • Shortcut key for Translate to Protein has changed from Ctrl + Shift + T into Ctrl + Shift + P.
    • Bug fixes

      • Fix to the proxy settings recognition meaning that Download of BLAST databases now work when there is a proxy setup.
      • Fixed problem of not correctly formatting qualifiers in EMBL export.
      • Fixed a problem sorting sequence lists on modification date.
      • Test on proportions: Fixed an error caused by the wrong group being used as reference, which means that the positive values should have been negative and vice versa.
      • Various bug fixes.

    CLC Main Workbench 6.7.2

    Release date: December 7, 2012

    Bug fixes

    • Fix to the proxy settings recognition meaning that download of BLAST databases now works when there is a proxy setup.
    • Fixed problem of not correctly formatting qualifiers in EMBL export.
    • Fixed a problem sorting sequence lists on modification date.
    • Test on proportions: Fixed an error caused by the wrong group being used as reference, which means that the positive values should have been negative and vice versa.
    • Various bug fixes.

    CLC Main Workbench 6.7.1

    Release date: September 5, 2012

    Bug fixes

    • Fixed: Workflows would fail when intermediate results were empty (e.g. if no variants were found and a variant track was used for subsequent analysis).
    • Various bug fixes

    CLC Main Workbench 6.7

    Release date: August 9, 2012

    New features

    Workflow

    • Workflows can be built in the Workbench to combine various tools from the Toolbox into one analysis, connecting the output from one tool to the input from another
    • In the first release, the gateway cloning tools are the only tools that can be incorporated into workflows.
    • Workflows can be distributed and installed either in the Workbench or in the CLC Genomics Server
    • The creator of the workflow can configure parameters for the workflow and these will be fixed when the workflow is distributed and installed
    • The creator of the workflow decides which of the output from the tools that should be saved and which should be discarded
    • Workflows can be run in batch, making it a powerful tool for crunching high numbers of samples through the same pipeline.

    Plugin updates

    Grid integration plug-in is integrated into the general server plug-in. If a grid preset is present on the server, the Grid option becomes available in the Workbench dialog.

    CLC Main Workbench 6.6.5

    Release date: July 25, 2012

    Improvements

    • Support for Mac OS X 10.8, Mountain Lion

    Bug fixes

    • Fixed: Problem with online BLAST at NCBI

    CLC Main Workbench 6.6.2

    Release date: April 11, 2012

    Improvements

    • Aligned fasta import and export is now supported (see http://www.bioperl.org/wiki/FASTA_multiple_alignment_format). A consequence of this is that the standard fasta import of sequences will reject to import sequences that contain gaps, assuming they should be imported as alignments instead.
    • The license order ID is visible in the License Manager, both for static and network licenses. For security reasons, the last 10 characters of the ID are masked. This will prevent unauthorized persons from copying the license order ID to another computer, but will allow the CLC staff to identify the license used.

    Bug fixes

    • Fixed: Cloning bug: when performing restriction cloning in regions with single-stranded DNA, you would get an error.

    CLC Main Workbench 6.6.1

    Release date: February 23, 2012

    New features

    Translate to protein creates sequence lists as results when more than 10 sequences are produced. This greatly improves performance when translating large amounts of proteins It is now possible to specify the number formatting in tables in the View Preferences.

    CLC Main Workbench 6.6

    Release date: February 13, 2012

    New features

    • Printing and pdf export of assemblies: the assemblies are now wrapped to make better use of the paper.
    • Usability of Close icon on tabs has been improved. Both in terms of responsiveness and making it impossible by accident to initiate a drag and drop movement when you hit the close icon to try to close a tab.
    • "Show" submenu has been removed from File Menu, and the right-click menu now includes only the relevant views and editors. This provides a better overview.
    • The behavior of the Close Other Tabs function has changed so that it will close all views, regardless of the way the view area is split.
    • The most common annotation types are assigned a special color per default. Other annotation types previously got the same color. This has been extended so that the Workbench attempts to find a special color for each type.
    • VectorNTI import is no longer in a separate plug-in but part of the Workbench. The functionality remains unchanged.

    New plug-ins and plug-in updates

    • Additional Alignments Plug-in updated
      • The algorithms have been updated to the most recent versions
      • The list of algorithms has been reduced to two for compatibility reasons

    Old Releases

    View older releases in our CLC Main Workbench release archive