Xenbase Release Notes
Release 6.3.2
- Bug fixes
Release 6.3.1
- Bug fixes
Release 6.3.0
- Beta release of JBrowse2
- Bug fixes
Show Previous Releases [+]
Release 6.2.0
- GEO data updated from 10.x genomes
- Revamped UIs for creating and editing labs, organizations, and jobs
- Bug fixes
Release 6.1.0
- Overhauled person registration code
- Bug fixes
Release 6.0.2
- Bug fixes
Release 6.0.1
- Bug fixes
Release 6.0.0
- Major genome annotation improvements
- New GEO JBrowse tracks for version 10.x genomes
- Enhanced integration of partially supported amphibian species
- Revamped Search Gene
- Updated and restructured application code for improved performance and efficiency
- Bug fixes
Release 5.7.0
- Added KEGG Pathway names
- Multi-mutant gene support for lines
- Bug fixes
Release 5.6.2
- Bug fixes
Release 5.6.1
- Bug fixes
Release 5.6.0
- Support for InterPro gene search
- Zahn drawings added
- Bug fixes
Release 5.5.2
- Bug fixes
Release 5.5.1
- Morpholinos aligned with laevis 10.1 genome
- Bug fixes
Release 5.5.0
- X. laevis 10.1 genome
- Bug fixes
Release 5.4.2
- Bug fixes
Release 5.4.1
- Bug fixes
Release 5.4.0
- laevis 10.1 support added to BLAST and JBrowse
- Bug fixes
Release 5.3.0
- Phenotype tab on gene pages
- Bug fixes
Release 5.2.0
- Gene pages allow adding, rearranging, and removing species
- Improved phenotype interface
- Bug fixes and GUI updates
Release 5.1.1
- GUI update
- Bug fixes
Release 5.1.0
- Support for guide RNAs (gRNA)
- Improved morpholino support
- Bug fixes
Release 5.0.0
- Phenotypes!
- X. tropicalis genome version 10.0
- Redesigned landing page
- Bug fixes
Release 4.16.1
- Bug fixes
Release 4.16.0
- Morpholino alignment support for X laevis 9.2 and X tropicalis 10.0
- Added support for Rat orthologs (RGD)
- InterPro links added to UniProt IDs on protein gene page tab
- Bug fixes
Release 4.15.0
- Xenopus Phenotype Ontology (XPO 1.0) released
- Simplified search for accession IDs (e.g. www.xenbase.org/entry/XB-GENE-483693)
- XAO updated to version 9.0
- Bug fixes and GUI updates
Release 4.14.0
- Added support for rat (RGD) orthologs
- Added UniProt terms to gene pages
- Added MARRVEL, gnomAD, orphanet, GTR, dbVAR, COSMIC, and GHR to external disease links
- Added laevis 9.2 and tropicals 10.0 tracks to GBrowse
- XSMO and XBED ontologies available for download:
- New data statistics
- Bug fixes
Release 4.13.1
- Improved GUI support for smaller screens
- Bug fixes
Release 4.13.0
- X. tropicalis 10.0 support added to BLAST and JBrowse
- Added CRISPRscan tracks to gene pages
- Added mutants to gene pages
- Bug fixes and GUI updates
Release 4.12.3
- Bug fixes
Release 4.12.2
- Bug fixes and GUI updates
Release 4.12.1
- XAO updated to version 8.0
- Bug fixes and GUI updates
Release 4.12.0
- GEO GSE visualization
- Bug fixes
Release 4.11.4
- Added genes and videos to Latest Xenbase Content list
- Bug fixes and GUI updates
Release 4.11.3
- New GEO GSE tutorial videos
- New Anatomy and Histology Atlas
- Links to EctoMap, Tail Regen @ Cambridge, and SPRING @ Harvard
- Bug fixes
Release 4.11.2
- New JBrowse tutorial video
- Support for HTTPS
- Bug fixes and GUI updates
Release 4.11.1
- XAO updated to version 7.0
- Bug fixes
Release 4.11.0
- GEO expression data and JBrowse tracks
- X. laevis protein expression profiles
- Bug fixes
Release 4.10.2
- Bug fixes
Release 4.10.1
- Added link to single cell data at SPRING
- Bug fixes and GUI updates
Release 4.10.0
- Added the gene expression summary bar
- Tree browsing added to Disease Ontology pages
- New JBrowse tutorial videos
- Bug fixes and GUI updates
Release 4.9.2
- Added tropicalis ORFeome
- Bug fixes
Release 4.9.1
- Added the disease search page
- RNA-Seq Profile and heatmap data can be saved as CSV files
- Bug fixes
Release 4.9.0
- Added support for Disease Ontology
- Added disease pages for Disease Ontology
- Added disease pages for OMIM
- Added BLAST support for tropicalis 9.1 mRNA, CDS and protein
- Bug fixes
Release 4.8.2
- Java upgrades
- Bug fixes
Release 4.8.1
- Added mouse and fish Alliance links on gene pages
- Whole gene and CDS sequences are now displayed on gene pages
- New Xenopus development movies
- Bug fixes
Release 4.8.0
- New anatomy and developmental stage trees
- Morpholino snapshots are now generated by JBrowse
- BLAST allows longer sequences
- Support for ILAR lab codes
- Support for alumni lab membership
- GUI updates
- Bug fixes
Release 4.7.1
- Bug fixes
Release 4.7.0
- Added gene co-expression and co-regulation graphs
- Added Perron Lab retinal screen images
- BLAST search results now point to JBrowse (instead of GBrowse)
- Other amphibians: Added Rana catesbeiana, Nanorana parkeri, and Ambystoma mexicanum genomes to JBrowse
- Added a BLAST page for the above frogs
- Bug fixes
Release 4.6.0
- Added experimental regulation visualization
- Reworked stock center lines and strains
- Added XLRRI (US) and CRB (Europe) stock centres to the list of vendors
- Added links to laevis 9.2 and tropicalis 9.1 genome assemblies and gene models. Both are BLAST'able
- Replaced GBrowse gene snapshots with Xenbase images
- Increased support for JBrowse
- Added counts for mutant lines and available jobs to the landing page
- Bug fixes and enhancements
Release 4.5.0
- Human physical gene interaction visualization
- Isoform data added to tropicalis TPE visualization
- Bug fixes and enhancement
Release 4.4.0
- Visualization for tropicalis TPE data
- Visualization for laevis tissue data
- Gene-specific JBrowse links on gene pages
- Gene expression search results can be downloaded
- Bug fixes
Release 4.3.1
- JBrowse beta links
- Bug fixes
Release 4.3.0
- Added gene interaction visualization
- Added RNA-Seq stage expression graphs
- OMIM references in articles are displayed
- Recent articles added to Xenbase are displayed on landing page
- Article information now includes references
- Auto-suggest support for gene expression search's experimenter field
- Bug fixes
Release 4.2.0
- KEGG terms added
- GO Terms updated and a gene page tab added
- Added ability to search for GO terms
- XAO updated to version 5.0
- Separated UniProt IDs to Swiss-Prot and TrEMBL
- Added ability to BLAST sequences within GBrowse
- Bug fixes
Release 4.1.1
- Bug fixes
Release 4.1.0
- Added link to mouse pages on Allen Brain Atlas
- Added BLAST page for Xenopus Mitochondrial genomes
- Xenbase now supports gene page URLs using gene symbols (e.g. geneSym=pax8 instead of geneId=483692)
- Bug fixes
Release 4.0.0
- Extensive gene page additions and corrections
- Added laevis 9.1 genome
- GUI updates
- Bug fixes
Release 3.11.2
- Added Veenstra Lab UCSC track hub
Release 3.11.1
- Bug fixes
Release 3.11.0
- Gene pages now contain the corresponding transgene links
- Stockcentre line, transgene, and strain names are displayed in the correct format
- Antibodies can now be assigned RRIDs
- Image curation enhancements
- Reformatted "Cite Xenbase" page
- Bug fixes and enhancements
Release 3.10.0
- Xenbase accession strings can be used to search for Stockcentre Transgenes, Lines, Strains, as well as ORFeomes
- Moved some Expression URLs from the Summary tab to the Expression tab
- Added links to expression profile data from Owens, Blitz et al. 2016.
- All options are now enabled for Gene search
- Enhanced gene search in the upper-right hand minibar, including search for genes with a "+" in the symbol
- Bug fixes and enhancements
Release 3.9.0
- Added laevis- and trop-specific XenMine URLs
- Removed inbred generation and geo origin from srockcentre lines
- Added lab of origin, RRID, and catalogue number to stockcentre lines
- Bug fixes and enhancements
Release 3.8.0
- Added IMPC mouse phenotype gene page links
- Added PANTHER GO search links on gene pages
- Added XenMine links on gene pages (Data Mining section)
- Reformatted stock centre search and display
- Bug fixes and enhancements
Release 3.7.0
- Added fruit fly and worm ortholog links on gene pages
- Added XenMine links on the landing page
- Added GeneCards to the list of human MODs
- Added MalaCards, OMIM, DECIPHER, and KEGG Disease phenotype search links on gene pages
- Added Ensembl, Protein Atlas, Allen Brain Atlas, and Eurexpress links to the new ortholog "Gene Expression" column on gene pages
- Added Ensembl tropicalis link to gene pages' "expression" section
- Replaced gene page phenotype links for ZFIN (broken) and MGI with symbol search links
- Bug fixes and enhancements
Release 3.6.2
- Bug fixes and enhancements
Release 3.6.1
- Revised "Genomes" and "Download & Submit Data" menus
- Bug fixes and enhancements
Release 3.6.0
- More updates on the FTP landing page
- Added New Genomes! Xl9.1, Xl mitochondrial, Xt9.0
- Updated ORFeome search and search results
- Bug fixes and enhancements
Release 3.5.2
- Updated FTP landing page for data downloads
- Bug fixes and enhancements
Release 3.5
- Release of new feature ORFeome v1.0
- Migration of NCBI E-utilities from SOAP to REST
Release 3.4
- laevis-only genes now display on gene pages
- Latest XAO update added
Release 3.3
- Added new feature Morpholinos, a searchable database
Release 3.2
- Upgraded object-relational mapping (ORM) layer from iBatis to MyBatis
Release 3.1
- Improved image copyright handling
- GEISHA orthology imported into database and added to gene pages
- 10,000+ PubMed Central (PMC) article images added to Xenbase
- OMIM disorders associated with Xenopus genes added to gene pages
Release 3.0
- Redesigned site for improved look and feel
- New site is now responsive to mobile devices
- Added announcements carousel to landing page for promoting high impact Xenopus research, Xenopus researchers, and new Xenopus research technologies
- Added antibodies database
- New GBrowse server and software (2.55). New tracks added
Release 2.8
- Added antibody pages and search interface
- Added protein tab to gene pages
- Summary images on gene page summary auto-rotate
Release 2.7
- Added NCBI Entrez Gene ID as a searchable field for gene pages.
- Links to the Ensembl and UCSC genome browsers added for each gene page, where applicable.
- Gene page and clone page expression tab restructured. Expression images can now be sorted by various criteria, such as stage.
- Added the ability to exclude anatomy terms from a gene expression search.
- Added the ability to search clones by anatomy item.
- Added search all option to the literature search, along with the ability to filter queries by date range.
- Expression tab added to anatomy item pages, listing genes expressed in the tissue, along with expression sources.
- Reagents and protocols menu added to the main Xenbase menu bar
Release 2.6.5
- Implemented Textresso
for Xenopus. Textpresso is a powerful text-mining system for
scientific literature.
- Search paper titles, abstracts, results, discussion,etc using keywords or phrases.
- Selecting one or more Categories, which are pre-defined word-lists, increases the specificity of a search. Categories include Xenopus gene symbols and synonyms, the XAO, and GO terms.
- Pages created for XAO anatomy items and development stages.
- Includes a tab for displaying papers attributed to the XAO term via text matching.
- Includes a wiki tab for users to submit content.
- Xenbase secure login. Usernames and passwords are now encrypted when being sent from a user's computer to Xenbase.
- An image voting system to score images based on image quality
- To vote, click on an image of interest to bring up an enlarged view. Near the bottom of the popup are two icons, a thumbs up and a thumbs down, along with a comment box. Simply click one of the two icons to cast your vote. The user's choice is saved so it may be changed at a later date.
- Created a data statistics page for Xenbase which lists counts for various data types by year.
- Added a Sequence tab to gene pages which list associated mRNA and EST sequences.
- Added new tracks to the Xenbase
Genome Browser.
- EcRs for mouse, zebrafish and chicken
- Promoter regions for tropicalis
- Xenopus tropicalis genomic fosmids
- JGI 4.1 tropicalis gene and transcript model sets
- Xenopus stage development time / temperature charts have been added.
- Exact searches added for select literature queries.
- Clone name searches will now except partial matches.
- In the stockcentre, users can now copy a transgene under a new name.
- Xenbase movies have been added to Youtube so they no longer have to be viewed in Quicktime.
Release 2.6.1
- Ability to add, edit, and delete clones.
- Stockcentre now supports transgenes.
Release 2.6
- Xenopus wiki for community contributions of protocols, gene information, etc.
- New version of Gbrowse (2.0.5) including tracks for: Unigene, Gurdon EST, cDNA clones and methylation
- Clone vector pages, including the ability to search clones by clone ID
- Clone, Vector and Library pages now have unique Xenbase accessions for searching
- Old Xenbase and XMMR have been decommissioned.
Release 2.5.5
- Search for clones via Gene symbol, NCBI accession, library name or clone name.
- Search for gene expression patterns by sequence.
- Search literature by Granting Agency or Grant Number
- New Xenbase cDNA library pages accessible through clone pages and gene expression search results
- Filter out ubiquitously expressed genes from gene expression search results
- Include Anatomical successor and predessor tissues in gene expression searches involving anatomy terms
Release 2.5
- Search Expression Patterns: Search Xenopus expression patterns by gene symbol, developmental stages, anatomical structures and experimenters
- Search gene pages by NCBI sequence accession for mRNA, EST and protein.
Release 2.4
- Search 'All': Search all of Xenbase from the minibar at the top of the screen
- Search suggestion ability added to mini bar for searches in: gene, person, lab, organization, authors and titles
- Expanded and updated Stockcenter for searching Xenopus frog lines
- Faster BLAST searches and new search databases added
- Faster gene 'Search All' searches
- Search genes by Affymetrix probe ID
- Ensembl models listed in gene pages and gBrowse
- Gene page link to literature referencing 'morpholinos'
- Gene expression images from AxelDB now available in the 'Expression' tab on gene pages
- Added thousands of expression images from community labs: Zorn lab, Papalopulu lab
- Over one thousand additional expression images automatically curated from literature sources
Release 2.3.1
- Gene page interactants tab added. This tab lists genes that are co-cited in the literature for a gene of interest.
- JGI Xentr4.1 filtered model transcript and protein databases are now available at the Xenbase blast site.
Release 2.3
- Animal lines section added. This section provides information on frog lines currently carried by the European Xenopus Resource Center (EXRC).
Release 2.2
- Gene pages are being populated with archetypal image(s) of gene expression patterns
- New Expression tab on Gene pages
- in situ images from XDB3 (presence of images is indicated by an icon on the Expression tab). Axeldb and community submitted images available soon.
- Anatomy terms and stages (expression data derived from EST/cDNA library representation). This is available for most genes even when they lack images.
- UniProt Knowledgebase links (alternative splicing information, protein domains and much more)
- Microarray data from GEO - view array data where the gene of interest displays differential expression
- Affymetrix probe sets for both trop and laevis
- Gene search
- Select number of results per page
- Literature section
- Publications with figures are flagged with a small icon. Load the paper to see the abstract, figures and legends, or click on the icon to see only the figures and legends.
Release 2.1
- Dramatically faster gene search and gene pages
- Literature tab added to gene page
- In-line links from article abstracts, titles and image captions to gene pages
- Improved gene search
- Now search shows how results were found
- New search by gene function
Release 2.01
- Addition of 7,600 + Metazome-curated gene models.