BioNumerics version 7.6.3 (64-bit)

Improvements in version 7.6.3 build 7.6.13738.35510:

• In addition to Amazon S3 and BaseSpace, sequence read sets can now also be imported from Alibaba Cloud Object Storage Service (OSS).
• A long-standing issue with the import routine from BaseSpace, in which sequence reads sets were sporadically duplicated or omitted, is fixed.
• Additional columns (E-value and Summed alignment length) are displayed in the Hit view panel of the BLAST window.
• The BLAST executables that are shipped with BioNumerics are updated.
• When a SNP analysis is performed, the command File > Export > Export sequences (fasta) in the Comparison window exports again the SNP set instead of the complete sequence.
• The Antibiotics resistance plugin now correctly deals with manually deleted decision networks.
• The Chinese language pack is updated with missing translations.
• A larger number of pie charts and bar graphs can be shown on a geographical map.

An additional improvement worth mentioning is that, since our recent Calculation Engine maintenance, the synchronization with public wgMLST nomenclature is sped up considerably. This avoids timeout issues with larger subschemas such as cgMLST schemas. The improvement is available in all BioNumerics version 7.6.3 builds.

Improvements in version 7.6.3 build 7.6.12519.34990:

• Fixed import issues with whole-genome sequences from EBI and NCBI online repositories.
• Restored functionality of the Geographical mapping plugin by specifying additional parameters when loading the Google Maps API.
• Improved import of mzml files, containing raw spectra or spectrum peak tables. This greatly facilitates the import of VITEK MS mass spectrometry data.
• Fixed issue with import of TIFF files via the data exchange tools.
• Import templates created by specialized plugins, such as the Antibiotics susceptibility, Riboprinter, Import Fingerprint tools and WGS tools plugin can now be managed and shared.
• The WGS tools plugin now only submits a new allele for a non-CDS locus (e.g. one of the classical MLST loci) if the allele sequence is full-length.
• The SNP calling plugin now imports SNP data files generated by Douglas Scientific IntelliQube format and has an improved logic for marking SNP calls as manual or automatic.
• Improved export of sequences in FASTA format from the Comparison window.
• Fixed import of single-column text files.
• The import from MS Excel now handles sheet names that end with a space.
• The Chinese language pack is updated and now includes WGS functionality.

New functionality in version 7.6.3:

wgMLST and the WGS tools plugin:

• Wherever possible, subschemas from the wgMLST schemas on the BIONUMERICS Cloud Calculation Engine are now synchronized with public nomenclature. This means that for samples analyzed using wgMLST in BioNumerics, allelic profiles can be retrieved for e.g. the 7 housekeeping gene MLST schemas or core genome MLST (cgMLST) schemas from services such as BIGSdb or Enterobase. When available (e.g. for MLST schemas from PubMLST), public sequence types can be retrieved as well.
• wgMLST curators can push a synchronization of client databases with the allele database, e.g. when critical settings are changed or when subschemas are added, ensuring that clients immediately have the latest features and improvements at their disposal.
• Improved curator-defined and organism-specific thresholds facilitate the interpretation of wgMLST quality control parameters.

wgSNP:

• The new SNP similarity coefficient (indicated as Categorical (SNPs) under multi-state character coefficients) takes IUPAC ambiguous bases into account for an accurate calculation of phylogenetic distances from SNP matrices, obtained via wgSNP analyses.
• The Ambiguous bases SNP filter has an additional option Take into account transitional bases, that does not remove ambiguous bases corresponding to a transition between the reference base and one of the non-ambiguous SNPs.

Other:

• The Power Assembler now works on sequence read sets imported as links to local fastq or fastq.gz files. This allows you to keep your database lightweight and makes it easier to mix and match sequence read set analyses on your own computer with analyses performed on the Calculation Engine.
• The default settings for trimming, reference mapping and de novo assembly of sequence read sets were optimized for the characteristics of present-day sequence data sets in the corresponding Power Assembler templates.
• The new character comparison option Ignore zero values is extremely useful for TaqMan-based SNP calling and any other character sets in which a distinction needs to be made between absent values (i.e., the experiment was not performed) and undetermined values (i.e., the experiment was not conclusive).
• The Antibiotics susceptibility plugin is reworked and features a new and more flexible import routine for antibiotics resistance data (MIC values or inhibition zone diameters), which is especially improved for import from MS Excel files. Editing of antibiotics breakpoints has also been made easier and more intuitive.
• New sequence export options (FASTA/EMBL/GenBank) options are available to save contigs as separate sequences in the same file and to save contigs into separate files.
• The new sequence import option Minimum sequence length with Concatenate sequences per file allows filtering based on contig length.
• In the SNP calling plugin, reference panels can be assigned to SNP markers. These reference panels are plotted in the background and allow you to cross-check calls with historical data, which is particularly useful in case not all call types are represented on the plot.

Minor improvements and bug fixes in version 7.6.3:

• The “timestamp out of range” error that occurred on some Citrix systems is solved in the Import plugin.
• The MLST online plugin does not use the deprecated PubMLST SOAP web services anymore; allele and profile information is stored locally instead.
• The wgMLST assembly-based allele finder optionally uses alternative start/stop codons and calculates a “repeat score”, which can be used to filter out repeated loci.
• Automatic annotation against online databases is adjusted to match the new BLAST efetch FASTA format.
• An easier way to re-submit failed jobs to the Calculation Engine job queue via Jobs > Resubmit in the Job overview window.
• SPAdes is now the default de novo assembler on the Calculation Engine.
• Sequence read sets from the European Nucleotide Archive (ENA) can be accessed again by the Calculation Engine.
• Locally stored fastq.gz files containing non-Latin characters in their file names can be uploaded to the CE Store.
• The CE Store Uploader, a separate executable used to upload sequence read set data to the CE Store, is now compatible with 32-bit Windows versions.
• The Sequence extraction plugin works with non-Latin characters in experiment names.
• When a Power Assembly project is deleted, all associated data is removed, freeing up maximal disk space.
• Fixed display issues with characters and composite data sets in the Comparison window and Print preview window.
• Character experiment types with open character sets can be replicated over database levels.
• Composite data set colors are more consistent with the underlying experiment colors.
• Improved stability of the “object picker” (called e.g. via Edit > Find object in list) in combination with non-Latin characters.

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 30^th, 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 30^th, 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.