Latest improvements for CLC Bioinformatics Database

Changes

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

Bug fixes

• Fixed: Unresponsive administration interface when connected to Active Directory systems with many users
• From CLC Server Command Line Tools It is now possible to export to a local folder.

New features

• 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 can be integrated into workflows
  • Support for direct compression of exported files in zip and gzip.

Bug fixes

• When setting up user authentication, a help button was missing in the “Server User and Group Management” dialog.  This has now been fixed.

• PDF export of the history of a result did not include the name and version number of the Workbench that produced the result.

Changes

• System requirements for Linux has changed. From this release, SuSE is supported from version 10.2. This was previously version 10.0.
• The internal Audit Log is no longer archived automatically to prevent loss of disk space.

Bug fixes

• Fixed problem listing user groups from Active Directory

Bug fixes

• If the local hostname of the server computer did not resolve to an IP-address, it was not possible to connect to the Server from a Workbench. This has now been fixed.
• Various bug-fixes

Bug fixes

• New versions of the Chrome browser caused web interface to flicker
• Various minor bug-fixes

New features

• Support for LDAP authentication using GSSAPI /Kerberos

New features

• Audit log :
  • Removed external audit log
  • Added text audit log
    • A new log rolled every day
    • The last 31 logs are kept
    • Placed in webapps/CLCServer/WEB-INF/ and named like audit.%d{yyyy-MM-dd}.log

New features

• Possibility to import data from the Workbench on the Database Server. This was previously only possible with NGS data import.
• Support for redirecting non-SSL port to SSL port when accessing the database server’s web interface.
• Command Line Tools: it is allowed to provide CLC urls with full path including the .clc file extension.

New features

• Core features and improvements
  • For Oracle databases: There are now two ways of connecting to an Oracle database. One is the traditional using SID style and the other is using thin-style service name. Existing installations do not need to be changed.
• Algorithm features and improvements
  • Exporting fastq format no longer includes redundant name of the read in the quality score line. Now the name only appears once per read.

Bug fixes

• Various minor bug fixes

New features:

• Check set-up tool for diagnostics of database server setup Read more
• Support for exporting tables as tab-delimited files.
• New way of getting a license based on Order ID and automatic download of a license file. This makes it much easier to set up the database server.

New features:

• Improved memory management in general: lower memory footprint and shorter management overhead pauses.
• Improved memory handling of large tabular data sets.
• When searching data from the Workbench, the results did not list the custom attributes of the data. Read more.
• Copy operations on server locations are now performed completely on the server side, eliminating client processing and network traffic
• A number of import and export formats have been included on the database server, including csv, ace and excel.
• Progress when downloading files from the database server using the web interface is shown in browser
• Performance of export of data via the Workbench from a database server location has been improved
• Index server status added under User Statistics in the Admin tab of the web interface.
• Possibility to report server-side bugs from both web interface and Workbench, including log and configuration files. Read more
• Improved usability of user interface for adding locations in the web interface. Read more
• Server home path has been removed from configuration panel in the web interface (it now resides in a properties file in the settings directory). This makes it easier to deploy a job node installation in a mixed environment.

Bug-fixes:

• Added support for viewing data attributes in web browser for enzyme lists.
• Display of folder structure was not right in special cases involving differentiated permission on folders
• Changed order of custom attributes was not reflected in search drop-down menu
• Searching for data entered as custom attributes required specification of which attribute to search in
• Genbank import: sequence name (LOCUS) was truncated to 18 characters

New features

• 3 tier data communication. Data communication/management is now based on communication through the Server middleware.
• Option for File locations on server.
• Index Server for stability/scalability.
• Administrators can close user sessions. Read more…
• Option to automatically log in to the server when the Workbench starts Read more…
• The order of attributes can now be changed. Read more…
• General import and export
  • Export tables and reports in Excel format.
  • Import section of user manual re-structured to provide better overview Read more…. Expression data importers are now described in technical details in a separate section Read more….
  • You can now export multiple sequence lists in fasta format
  • Forced import of zip files is now supported (it will force import the contents of the zip file)
  • The standard import now accepts gzip and tar files as well as zip
  • Genbank importer now makes several attempts at naming genes that do not have a gene name. It will iteratively try the following qualifiers: “product”, “locus_tag”, “protein_id” and “transcript_id”
  • When importing genbank files where the length stated does not match the actual sequence, a warning is shown but the sequence is accepted.

Bug-fixes:

• Fixed an error opening external files from a server location

New features

• Creation of customizable metadata – an extra layer of information on top of other data. Examples could be freezer position, amount of sample left, LIMS identifier, project Number ID, etc., etc.
• Definition of metadata fields of different types like hyperlinks, lists, text, number etc.
• Advanced searching in metadata.
• Enhanced API that fully supports custom metadata (create/remove definitions etc)
• Thin client access to the database from an Internet browser. This enables Internet based
  • searching in data and metadata
  • viewing of data and data logs
  • upload/download of data in any supported format
  • editing of metadata

New features

The solution now includes an Application Programming Interface (API). It enables the following features that can all be implemented outside a CLC Workbench:

• Import/export of data to/from the database by creating your own client scripts or applications. CLC bio provides a library of example command line tools
• Access and modification of any data structure and data content in the database
• Powerful and easy data searching
• Migration of data from existing databases to CLC Bioinformatics Database
• Integration of third party technologies/tools with the database

Other Improvements:

• More advanced and more flexible user access rights management
• The user authentication now supports LDAP server directories
• Support of more data formats