You can access Ensembl Genomes Release 16 through the Bio Portal:
You can access Ensembl Release 16 through the Bio Portal:
Release 10! New Spain CLL methylation data. 18 TCGA DBs updated & 2 new DBs. Updates to UK Breast and MDS. 432 new genomes, 7,022 in total. Click the link below for more info:
Research in the Computational Gene Regulation group within the Research Unit on Biomedical Informatics focuses on the development of computational methods to study the mechanisms of regulation of gene expression.
This group is also part of the European network of excellence on alternative splicing EURASNET.
"Predictive Models of Gene Regulation from High-Throughput Epigenomics Data" research paper can be accessed below:
http://www.hindawi.com/journals/cfg/2012/284786/#B34
GWAS Central provides a centralized compilation of summary level findings from genetic association studies, both large and small.
RhesusBase is a knowledgebase developed by Peking university to facilitate the primate research community.
The database was developed on the basis of the BioMart 0.8 framework to customize and facilitate data download.
It has also recently been featured in an article in Nucleic Acid Research:
http://nar.oxfordjournals.org/content/early/2012/09/08/nar.gks835.full
12 TCGA database updated and 6 new databases, includes new data from MAGIC and PedBrain projects. Data from 3,029 new genomes, 6,590 in total.
Rfam database of non-coding RNA families has been included into http://central.biomart.org
The Rfam biomart may be found at:
http://xfam-biomart.sanger.ac.uk/
Additional Biomarts for other Xfam resources, such as Pfam are currently in development and will be included in due course.
This release includes the new mouse assembly (GRCm38) as well as updated patches for the human assembly (GRCh37.p8).
We introduce the Chinese softshell turtle (Pelodiscus sinensis) as a new species and update the Dog genome to CanFam3.1.
The ground squirrel has been renamed to Ictidomys tridecemlineatus in line with recent taxonomic reassessments.
Version 8 includes 21 genomes assembled and/or annotated at the JGI, and 9 externally produced genomes.
Also included are early release access to the Panicum virgatum (switchgrass) genome and annotation, as well as the unannotated assembly of the Cotton D Genome.
Update genomes include Eucalyptus, Aquilegia, and the grasses maize, rice and Brachypodium. New JGI genomes include the aforementioned Panicum virgatum genome, as well as Capsella rubella,and Phaseolus vulgaris, while the external genomes Brassica rapa, flax, and apple make their first appearance in Phytozome.
We are pleased to announce the release of the new BioMart website, which has been completely redesigned with improved functionality and graphics. Your feedback is welcome and appreciated.
BioMart is a unique open source data federation technology that provides unified access to distributed databases storing a wide range of data. This DATABASE issue recognizes BioMart's outstanding contributions to bioinformatics and documents the achievements of the BioMart community, which has grown impressively over the last ten years to become what it is today, a collaboration between numerous database projects on five continents: Asia, Australia, Europe, North America and South America.
http://oxfordjournals-marketing.oup.com/q/1MozDkVONg1Q1p/wv
This release candidate offers the following features:
- Supports rudimentary Semantic Web features: OWL-ontologies and SPARQL-queries (details in Section 11.5, "Semantic Web" in the user manual)
- Automated command line deployment tool for ICGC nodes
- MartConfigurator (MC) supports importing configuration (sources and/or access points) from other 0.8 portal configuration xml file
- Improved usability in MC including list view of the access points in the right-hand panel
- Better support in backwards compatibility to handle linkouturl and default filter displayname
- Bug fixes
This release candidate offers the following features:
- client APIs: Java, REST, SOAP (details in user manual section 11)
- full plugin support including both client and server side components
- update of materialized mart is now fully supported
- better support for virtual mart (schema update and basic manipulations)
- improvement of MC usability
- user manual includes a dedicated section about ICGC deployment
This release is tested on Mac OS X (Leopard and Snow Leapord), Linux (Debian 4.1.1-21), Java 6. See docs for details.
This release candidate offers the following features:
- Materialize for 5 database platforms (MySQL, Oracle, PgSQL, MS SQL, DB2)
- Secure access for BioMart server to server communication
- Third party plugins framework for GUI developers
- Improved configuration management
The 0.8 release candidate 3 is now available for deployer testing. The new BioMart version is a Java based, out-of-the-box single integrated application to facilitate mart building, configuration and web server deployment.
This release candidate offers the following features:
- Support for 5 database platforms (MySQL, Oracle, PgSQL, MS SQL, DB2)
- Virtual Marts (non-materialised querying against source database)
- A range of different web interfaces from Basic Form to Advanced Querying interfaces (MartAnalysis, MartForm, MartWizard, MartExplorer) and a Report page (MartReport)
- Backwards compatibility for BioMart 0.7 sources
- Secure access
- Multi-dataset linking with Link-Indices for faster and scalable joins
- Processor framework for specialised data visualisations (e.g charts)
Features not available yet:
- Full Mbuilder component including source schema modifications
- Updates
- Processors (Genomic Sequence, GFF, DAS, WSDL, Gzip, Excel)
This release candidate offers the following features:
- MartBuilder is now a fully featured application with enhanced layout for schema transformation. It can also run in a server/client mode making it possible to monitor the mart building process through a MartRunner component.
- MartView layout has been improved. Programmatic access has been extended to include URL API functionality and mapping from XML queries to URL API. The long outstanding problem with MartEditor templates has been fixed.
This release candidate offers the following features:
- BioMart can now be used as a 1.5 DAS annotation server. The server can be configured using standard BioMart configuration tools without requiring to do any additional programming.
- MartView comes with an improved layout and better interactivity. The response times for the results panel have been considerably improved for datasets with large configuration, and the results come with an 'unique rows' option. In addition to the existing web service XML button, MartView now features a Perl button which shows the query in Perl API format.
- MartBuilder now allows you to execute, monitor and control your transformation SQL remotely. Improved schema diagrams provide more compact overviews, and improved dataset diagrams provide a clearer picture of the dataset structure. In addition, the user has more options for modifying created datasets and better information about them in 'explain dataset' and 'explain table' dialogs.