BioNumerics version 7.6.2

Update 7.6.2 build 3894.32288 of BioNumerics is now available for download.

Instructions for installation

  1. Click on the link to download the update.
  2. Close BioNumerics.
  3. Double-click on the executable to run the setup. Please note that this action will require administrator privileges.

List of improvements

Improvements in version 7.6.2 build 32288:

The only change in this update is a fix for the CE Store Uploader issue which appeared recently on some systems and is likely caused by Windows security updates.

New functionality in version 7.6.2:

Functional genotyping of E. coli

The E. coli genotyping plugin provides an easy way to predict serotype, virulence and antibiotics resistance based on whole genome sequences. Genotyping results are presented in an interactive and customizable report and can be analyzed in combination with other data stored in the BioNumerics database. This plugin is offered as a free online plugin (see below) and is the first in a series of organism-specific functional genotyping plugins.

New distribution mechanism for plugins

The new concept of online plugins makes it easy to download, install and update plugin functionality. Different from installing a BioNumerics software update, the installation of a plugin or script in the database does not require administrator rights. With online plugins, you gain quicker access to new plugins or plugin versions, in order to benefit from the latest developments.

Minor improvements and bug fixes in version 7.6.2:

  • Improvement to the Whole Genome Sequencing (WGS) tools plugin:
    • Installation of plugin is now easier and faster.
    • Better defaults: the default settings for assembly-based allele calling and automatic submission of new alleles are now curator-defined, ensuring that optimal organism-specific thresholds are used.
    • New option to treat multiple allele calls as absent values in the wgMLST character experiment type.
    • Only the active entry view is taken into account when submitting jobs to the Calculation Engine, avoiding accidental job submission for selected entries outside the current view.
  • New .crv file import option for fingerprint curves, providing an alternative for import of Beckman-Coulter raw chromatograms (.scf files). Since .crv files are corrected for spectral overlap, their use is recommended with multi-channel experimental setups.
  • Easier way to manage user defined views. In previous versions, drop-down lists become unwieldy when many (>100) views are present. Now, a maximum number of items to show in a list can be specified in the preferences and the desired view can easily be picked from a long list.
  • An example import template was added for sequence read sets, which parses the sample identifier from the file name.
  • Whe re-importing a sequence read set as link, the quality statistics are reset.
  • The Power Assembler now also determines a consensus sequence in regions with extremely high (>2666) coverage.
  • Improved stability of the wgMLST Quality Assessment window.
  • Improved stability when loading an advanced cluster analysis from a comparison.
  • Significant performance improvements when loading comparisons that contain sequence read set data.
  • The Sequence extraction tools plugin now deals with renamed sequence experiment types.
  • Fixed issues with auto numbering when working with Oracle relational databases in a multi-user environment.
  • Improved stability of the SNP analysis window.
  • Assembly comments are now correctly saved during batch assembly of Sanger sequences.
  • Fixed export of a sequence multiple alignment from the Alignment window to the Comparison window.
  • More flexible options to export character data from a comparison.
  • Fixed issue with the import of Bruker MSP spectra.
  • Improved stability when using local composite data sets in a comparison.
  • The fingerprint OD range is not overwritten anymore during import of fingerprint curves.
  • The Export fields and characters functionality now also employs character views and exports entry field names instead of IDs.
  • The command Sequence > Reload sequence from database... now works on the selected entries in the comparison.
  • Improved visualization of charts in the Charts and statistics window.

Improvements in version 7.6.1 build 3075.31949:

This update ensures compatibility with NCBI moving all web services to HTTPS. This change from HTTP to HTTPS protocol is scheduled for September 30th, 2016 and affects following BioNumerics functionality:

  • Importing sequence read sets as link from the NCBI Sequence Read Archive (SRA) and submitting Calculation Engine jobs with SRA links via the WGS tools plugin. A hotfix for this issue is available that can be applied without administrator privileges.
  • BLAST searches against one of the online NCBI databases, as available e.g. from the Sequence editor, Annotation and Chromosome comparison window.
  • Downloading sequences from NCBI GenBank or RefSeq via their accession numbers.

After September 30th, the above functionality will likely stop working in older builds, hence we recommend users to update to the latest version.

Improvements in version 7.6.1 build 2992.31893:

  • Fix for "unsupported protocol" error when importing sequence read sets as links from NCBI's Sequence Read Archive (SRA). Alternative to installing this update, a hotfix is available that can be applied without administrator privileges.
  • Resolved issue with editing a character color scale, which occurred exclusively on Dutch 32-bit Windows 7 operating systems.

Improvements in version 7.6.1 build 2833.31796:

The only change in this update is the fix of a bug introduced in the original release of version 7.6.1, which prevented sequences to be downloaded from online repositories (EBI, NCBI or NIG).

New functionality in version 7.6.1:

Direct upload of short reads to the Calculation Engine

Used in whole genome sequence (WGS) analysis, be it wgSNP or wgMLST, this functionality provides an easy and robust way of making short read data available to the Calculation Engine without having to make this data publicly available, store it in BaseSpace or manually upload it to cloud storage. The actual fastq(.gz) file upload is performed by a separate executable, meaning that you can continue working with BioNumerics while the files are being transferred.

Sequence extraction plugin

This new plugin offers functionality to extract a particular subsequence of interest from any genome sequence, including unannotated draft genomes. The extraction protocol is based on a BLAST similarity search, optionally combined with start/stop codon detection or forward/reverse primer detection. Sequence extractions are ran in batch for the selected entries and for a set of user-defined genes or partial gene sequences (e.g. in case of MLST).

Minor improvements and bug fixes in version 7.6.1:

  • Whole genome single nucleotide polymorphism (wgSNP) analysis:
    • Sequence curves can be created for the reference sequence from a text file containing start and end positions and subsequently used for SNP filtering based on position masks.
    • An additional predefined SNP template "Strict SNP filtering (closed SNP set)" is available. This SNP template always creates a closed SNP set, i.e. a SNP matrix from which no values are missing.
    • The labeling of SNP positions in the Comparison window is more flexible and now also includes reference sequence base or annotation.
    • Improved export functionality for SNP matrices (now optionally exports reference sequence bases) and for SNP graphs from the Genome panel.
    • When performing a SNP based clustering directly on sequence data, the SNP dendrogram is shown by default as distances instead of similarities.
    • Improved visualization of SNPs in the circular genome viewer with many entries.
    • Improved printing of wgSNP data.
  • Additional option to import spectrum data from mzXML files.
  • When importing sequences from EMBL/GenBank files, sequences can be concatenated per file and imported as multiple contigs in the same sequence experiment.
  • The layer functionality in the Matrix mining window is restored.
  • Fixed issue with printing of composite data sets, where the character ordering is taken over from the Comparison window instead of the original ordering.
  • Sequence editor: the correct number of contigs is displayed in the Contigs panel, also for sequences that contain gaps.
  • Sequence type experiments can again be created on-the-fly, i.e. during import of sequences.
  • A performance issue with Minimum Spanning Trees for large data sets is resolved.
  • In the Data matrix panel of the Advanced clustering window, entry keys no longer duplicated.
  • Fixed issue that prevented dendrograms calculated from character data to be displayed on geographical maps.
  • Database repository: SQLite is made the default database solution in all situations.
  • The SNP calling plugin now supports an additional file format for BMG LabTech micro plate readers.
  • Diversilab plugin: solved import problems with non-European Windows system locale.
  • Stable sorting in all object grid panels, including the Database entries panel in the Main window.
  • Various other small fixes.