Sybil Version: strepneumo-v1r19

Data Version: 15

Database updates:

• Added two genomes to the data set
• Streptococcus pneumoniae TCH8431/19A
• Streptococcus mitis B6

Site Changes:

• Added several help links to the site. They can be identified by a small blue '?' in a box or a '?' in a bubble. Hovering over these will bring up help information about that particular page/feature.

Sybil Version: strepneumo-v1r18

Data Version: 14

Database updates:

• No database updates for this release

Site Changes:

• Updated Sybil VM to use the latest code and data.

Sybil Version: strepneumo-v1r18

Data Version: 14

Database updates:

• Additional featuretypes
• Added antigenic protein regions from antigenic. The tool was run with a minlen parameter of 50
• Added B-cell epitopes predicted by BepiPred The tool was run with a threshold of 2.2.
• Additional Meta-data from GOLD
• Host Age
• Host Sample Site
• Isolation Country
• Additional database references with links
• GOLDSTAMP
• NCBI Project Page
• IMG Object Page

Site Changes:

• Added support for SVG/PDF exports from the new genomic comparative page.
• Added a dynamic organism table with meta-data and links to GOLD, NCBI and IMG on the home page
• Added metadata and external links to the individual organism pages
• Deployed themed mirrors to ILRI and ICRISAT
• Added display support for the new antigenic and b-cell epitope features

Sybil Version: strepneumo-v1r17

Data Version: 13

Database updates:

• Added homopolymeric tracts
• Added tandem repeat features as predicted by phobos. More info can be found at http://www.ruhr-uni-bochum.de/spezzoo/cm/cm_phobos.htm

Site Changes:

• Added support for bookmarking on the protein and cluster search pages.
• The 'new' genomic comparative view page has now replaced the old version
• Added link to the India Mirror hosted at ICRISAT

Sybil Version: strepneumo-v1r16

Data Version: 12

Database updates:

• Added pathogenicity islands data from IslandPath. More information on IslandPath can be found at http://www.pathogenomics.sfu.ca/islandpath/ and the original publication can be found at http://www.ncbi.nlm.nih.gov/pubmed/16299586.

Site Changes:

• Support for search/display of pathogenicity islands from IslandPath.
• Added support for atypical nucleotide plots in the synteny and whole genome displays.
• Many bug fixes

Sybil Version: strepneumo-v1r15

Data Version: 11

Database updates:

• Addition of IDEA results. These results currently are limited to clusters that exhibit evidence of positive selection. More information on IDEA can be found at idea.igs.umaryland.edu

Site Changes:

• Support for drawing protein subfeatures in Search Feature Image
• Cluster Search:
• Addition of 'Contains' filter like in the protein search form.
• Addition of IDEA filter for genes exhibiting positive selection
• Addition of clusters columns in the protein search
• Many bug fixes

Sybil Version: strepneumo-v1r14

Data Version: 11

Database updates:

• Addition of RepeatMasker simple repeats to the list of searchable/displayable features.
• Addition of psortb 3.0 search results. Final psortb predictions are now queriable on the protein search page and are viewable in the protein popups.

Site Changes:

• Support for querying out protein properties like psortb results.
• Addition of CloVR link to homepage
• Upgrade to ExtJS 3.1.1
• Many bug fixes

Sybil Version: strepneumo-v1r13

Data Version: 10

Database updates:

• No Data Updates for this release.

Site Changes:

• The size of the Sybil VM has been reduced from 3GB to 1.7GB by moving the database data directory off the virtual machine.
• A Strepneumo Sybil International Mirror has been added in Africa

Sybil Version: strepneumo-v1r13

Data Version: 10

Database updates:

• No Data Updates for this release.

Site Changes:

• Addition of the Sybil Virtual Machine to allow easy installation of the strepneumo system using VMWare player

Sybil Version: strepneumo-v1r13

Data Version: 10

Database updates:

• No Data Updates for this release.

Site Changes:

• Added several screencasts to the Sybil YouTube screencast channel and added a link from the Strepneumo homepage:
• Sybil Protein Search
• Sybil Cluster Search
• Sybil Protein Report
• Sybil Cluster Report
• Sybil Genomic Comparative View

Sybil Version: strepneumo-v1r13

Data Version: 10

Database updates:

• Clusters were run using a 70% coverage cutoff.

Site Changes:

• Added links from gene/cluster popups to the new genomic comparative view. These links allow the user to center on a feature in the genomic comparative view from other pages including the gene report page, cluster report page, synteny gradient view and whole genome view.
• Popups are now ExtJS powered and can be dragged around the screen and resized
• Added Zoom in/Zoom out buttons to the new genomic comparative region image form
• Several bugs have been fixed

Sybil Version: strepneumo-v1r12

Data Version: 9.1

Database updates:

• No new data updates for this release

Site Changes:

• Included several changes to the new genomic comparative display:
• Added Check All/Uncheck All buttons for feature selection
• Added ability to select/drag multiple sequences at once and place them in the grid
• Added a 'search mode' which allows a user to select a particular reference region and search for matching regions. The user can also slide left/right along the reference and the system will re-search the selected sequences.
• The 'edit mode' allows the user to modify the results of a search or generate a totally custom image with specific regions of interest.
• Added backend support for cluster analyses to be ordered before display. This provides uniformity in that the same cluster analysis will be selected by default in forms.
• Multiple sequence alignments (when regenerated) now include stop codons. This allows easier identification of frameshifted genes.
• Download links have been added to the homepage for multi-fasta files containing the entire data set as Genomic sequence, protein sequence or gene nucleotide sequence.
• Several bugs have been fixed

Sybil Version: strepneumo-v1r11

Data Version: 9.1

Database updates:

• No new data updates for this release

Site Changes:

• Sybil now works in Firefox 3.5, Safari 4, Google Chrome and Internet Explorer 8!!
• Added shift left/right buttons to New Genomic Comparative View.
• Added pan-genome data page which includes:
• A brief description of the pan-genome analysis steps
• Graphs of new/core gene counts and analysis
• A graph of the pan-genome and analysis
• Raw data used to generate the graphs
• A list of Pan-genome references pertinant to the analysis run

Sybil Version: strepneumo-v1r10

Data Version: 9.1

Database updates:

• Repeat and pmark searches were fixed for the following organisms:
• Taiwan19F-14
• Hungary19A-6
• 700669
• capsular loci

Site Changes:

• New features for the genomic comparative view page
• Server-side cached parameter sets allow for use of the forward/back and refresh pages as well as allowing for a URL to be bookmarked. Each URL will refer to a specific image by way of the input parameters.
• Upgrade to ExtJS 3.0
• Integration of Christian Effenberger's amazing cvi_map_util package to allow mouseover highlighting of image features. Check out Christian's website at http://www.netzgesta.de/
• Ext.Window style popups that attempt to position themselve intelligently. They are also draggable and resizable.
• Bug fixes including repair of the timeout

Sybil Version: strepneumo-v1r9b3

Data Version: 9.0

Database updates:

• 6 new genomes from The Center for Genomic Sciences at the Allegheny-Singer Research Institute added:
• BS292
• BS293
• BS397
• BS455
• BS457
• BS458
• New repeat features added:
• BoxA
• BoxB
• BoxC
• RUP
• pmark spacer features added for all genomes that are pseudomolecules (contigs ordered along a reference). These features define the boundaries of a contig and contain start and stop codons in all 6 reading frames

Site Changes:

• Minor bug fixes
• Addition of the training session survey page

Sybil Version: strepneumo-v1r9b2

Data Version: 8.0

Database updates:

• Several genomes have been updated to match the most current genbank entries:
• AE005672 - TIGR4
• CP000936 - Hungary19A-6
• CP001033 - CGSP14
• AE007317 - R6
• CP001015 - G54
• CP000410 - D39
• CP000918 - 70585
• CP000919 - JJA
• CP000920 - P1031
• CP000921 - Taiwan19F-14
• FM211187 - ATCC 700669

Site Changes:

• Added length filter to protein search page
• Improved layout of new genomic comparative region form
• Replaced new genomic comparative region pixel offset with a basepair offset. This offset should work reasonably well even when the image is resized.

Sybil Version: strepneumo-v1r9b1

Data Version: 7.0

Database updates:

• No new data for this release.

Site Changes:

• All features from old search forms migrated to new search forms
• Cluster filtering by length, cluster member count, and cluster organism membership counts
• Selectable 'representative annotation' source
• Tab-delimited and detailed cluster reports with logical file names
• Drag and Drop organism filtering on protein cluster form
• Improved layout for protein search page
• Full screen table browsing
• Initial version of a new Genomic Comparative Region form featuring:
• Drag and Drop sequence selection
• Drag and Drop reordering of selected sequences
• 'Search' mode which allows the definition of a reference sequence region and several target sequences and will return regions based on the search parameters (much like the current form)
• Custom regions are possible by reordering the sequences in the list and changing their fmin, fmax, stand and offset
• Sequences can be saved and new sequences can be added and searched
• Change references
• Leveraging ExtJS and custom code allows passage of complex data structures to and from the server providing a more powerful data mining tool
• Full screen image browsing

Sybil Version: strepneumo-v1r8b1

Data Version: 7.0

Database updates:

• No new data for this release.

Site Changes:

• Improved search functions for proteins and clusters
• Improved integration with ExtJS
• A more interactive search experience
• Protein/singleton/cluster searches all on 1 page
• Popup support for protein report page genomic context image
• Site wide popup support for blastp images

Sybil Version: strepneumo-v1r7b2

Data Version: 7.0

Database updates:

• Loaded new genomes:
• Streptococcus pneumoniae SP11-BS70
• Streptococcus pneumoniae SP14-BS69
• Streptococcus pneumoniae SP18-BS74
• Streptococcus pneumoniae SP19-BS75
• Streptococcus pneumoniae SP23-BS72
• Streptococcus pneumoniae SP3-BS71
• Streptococcus pneumoniae SP6-BS73
• Streptococcus pneumoniae SP9-BS68
• Streptococcus pneumoniae ATCC 700669

Site Changes:

• No new code changes for this release.

Sybil Version: strepneumo-v1r7b2

Data Version: 6.0

Database updates:

• Loaded additional protein data for search and display:
• Lipoprotein attachment sites
• LPxTG motifs
• Membrane surface motif (a collection of HMM's from Pfam and TIGRFAM)
• Bacteriocin protein motif
• Fibronectin binding protein motif
• Transmembrane Regions (tmhmm)

Site Changes:

• Bug fixes to the protein subfeature drawing
• Optimization of the subfeature query for caching

Sybil Version: strepneumo-v1r7b1

Data Version: 5.0

Database updates:

• No changes to the source data for this release.

Site Changes:

• 'Additional features' panel added to the protein report page.
• Added a protein search form page. This page is a first stab at using the extjs package within Sybil. This page will probably evolve quickly but for now it provides the following new features:
  • Search database references on transcript features (i.e. locus names)
  • Convenient paginated output
  • Filter search based on organism
  • Sort by any column
  • Find proteins with overlapping features
  • Download search results as a multifasta file

Sybil Version: strepneumo-v1r6b1

Data Version: 5.0

Database updates:

• Addition of SignalP analysis.

Site Changes:

• Addition of SignalP signal peptide and cleavage site features in the genomic comparative region image and protein cluster image. These features are not currently available on other views but will be in future releases.
• Optimizations to the popup data generation mechanism.

Sybil Version: strepneumo-v1r5b1

Data Version: 4.0

Database updates:

• Hungary19A-6 strain was loaded from its GenBank file.
• Refinements were made to the annotation of pseudogenes in: P1031, JJA, 70585 and Taiwan19F-14.

Site Changes:

• Addition of 'Add All Organisms' button in several of the forms.
• Optimization of the singletons blastp match filter query. This query was very very slow in previous versions.
• Addition of the CDS sequence in the protein report page.

Sybil Version: strepneumo-v1r4b1

Data Version: 3.0

Database updates:

• No changes to the source data for this release.

Site Changes:

• Asynchronous popups - These popup windows will now provide more information about the feature clicked and the data will not need to be loaded into the browser. Additionally these popups allow improved functionality in MS Internet Explorer and Apple's Safari browsers.
• Scrollable popups - Because of the increased volume of information in the asynchronous popups the popups will now be scaled according to the data they contain and their proximity to the bottom of the page. When a popup is very long or the click request happens near the bottom of the page the popup will utilize a scrollbar rather than overflowing the page.
• Gradient/Whole genome popups - The feature popups in the gradient and whole genome display have now been harmonized with the popups from the other views.

Backend Code Changes:

• Added the ability to specify site-specific data server/schema/vendor parameters. Previously these parameters were install-wide.

Sybil Version: strepneumo-v1r3b1

Data Version: 3.0

Database updates:

• MLST, serotype, sequencing method and sequencing status were all added as data types to the Chado database.

Sybil Version: strepneumo-v1r2b1 (new versioning for strepneumo tags.)

Data Version: 2.0

Database updates:

• New - Streptococcus pneumoniae CGSP14 added to the database from GenBank
• New - Streptococcus pneumoniae CDC1087-00 added to the database from the J. Craig Venter Institute
• New - Streptococcus pneumoniae CDC2088-04 added to the database from the J. Craig Venter Institute
• New - Streptococcus pneumoniae CDC1873-00 added to the database from the J. Craig Venter Institute
• New - Streptococcus pneumoniae CDC3059-06 added to the database from the J. Craig Venter Institute
• New - Streptococcus pneumoniae MLV-016 added to the database from the J. Craig Venter Institute
• New - Streptococcus pneumoniae SP195 added to the database from the J. Craig Venter Institute
• New - 90 Streptococcus pneumoniae capsular loci fragments added to the database from GenBank
• Updated - Streptococcus pneumoniae TIGR4: An A has been changed to a G in the SP_0668 locus, one of the seven loci used for MLST. This results in a change of sequence type for this strain from ST1982 (wrong) to ST205.
• Updated - Streptococcus pneumoniae G54: Several annotation updates including inspection of frameshifted and point mutated genes.

Additional draft Streptococcus pneumoniae genomes are available in Genbank, in particular those released by the Center for Genomic Sciences at the Allegheny-Singer Research Institute. These sequences will be incorporated in subsequent releases as we improve support for unfinished genome sequence.

Site Changes:

• Addition of serotype, MLST and sequencing data to the home page
• Apple Safari browser support
• Improved Microsoft Internet Explorer support (though not 100%)
• Improved standardization across forms
• Support for SVG output on more image generation pages
• Support for drawing intersequence paralog links in the Genomic Region Comparison Display
• Fixed a bug in the Synteny Gradient display in which paralogous query hits where not all being colored black
• Improved documentation for Synteny Gradient display and the sequence selection form
• Addition of a changes page (this page) for tracking releases

Sybil Version: 1.3.1

Data Version: 1.0

The initial release of the site is based on the v1r3b2 version of the Sybil code. Currently there are 10 S. pneumo genomes loaded. They are:

• Streptococcus pneumoniae TIGR4
• Streptococcus pneumoniae D39
• Streptococcus pneumoniae 70585
• Streptococcus pneumoniae JJA
• Streptococcus pneumoniae R6
• Streptococcus pneumoniae G54
• Streptococcus pneumoniae Taiwan19F-14
• Streptococcus pneumoniae P1031
• Streptococcus pneumoniae Hungary19A-6
• Streptococcus pneumoniae 670

The genome annotation was loaded which includes gene calls, associated polypeptides as well as gene product names and tRNAs. An all vs. all wu-blastp was also loaded. The detailed parameters set is available here: wu-blastp.

This wu-blastp was used to generate a set of paralog clusters and a set of ortholog clusters. These two cluster sets form the basis of the Sybil displays.

The currently available views/tools are:

• Whole Genome Display
• Gradient Display
• Region Comparison Display
• Shared Cluster Matrix
• List Protein Clusters
• List Protein Cluster Singletons