EMBL-EBI Web Services

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====== News (2010) ======

[[..:News|Current]]

==== 2011 ====

News for [[.:2011]].

==== 9th December 2010 ====

The JDispatcher based [[:services:pfa:iprscan_rest|InterProScan (REST)]] and [[:services:pfa:iprscan_soap|InterProScan (SOAP)]] services have completed their beta preview phase and can now be considered production services. As part of the transition between the old and new services, the Dispatcher based [[:services:interproscan|WSInterProScan]] service will be deprecated from the 15th February 2011 and will be decommissioned later in 2011. We recommend that used of the [[:services:interproscan|WSInterProScan]] web service begin migrating their usage to the new services as soon as possible. 

==== 26th November 2010 ====

Sample Java client using the [[https://jax-ws.dev.java.net/|JAX-WS RI]] SOAP tool-kit, included in Java 6, is now available for [[:services:pfa:iprscan_soap|InterProScan (SOAP)]].

==== 25th November 2010 ====

The [[http://genenames.org/|HGNC]], [[http://www.ebi.ac.uk/imgt/hla/|IMGT/HLA]], [[http://imgt.cines.fr/cgi-bin/IMGTlect.jv|IMGT/LIGM-DB]] and [[http://www.ebi.ac.uk/ipd/kir/|IPD-KIR]] databases have been added to the dbfetch services:
  * [[http://www.ebi.ac.uk/Tools/dbfetch|dbfetch]]
  * [[:services:dbfetch|WSDbfetch]]
  * [[:services:dbfetch_rest|WSDbfetch (REST)]]

==== 22nd November 2010 ====

**Please Note**: Due to essential system maintenance some services will be unavailable on Tuesday 7th December 2010 between 09:30 AM and 12:30 PM GMT. Apologies for any inconvenience caused.

While the RPC/encoded SOAP services for InterProScan, Sequence Similarity Search (SSS) and Multiple Sequence Alignment (MSA) will be affected by this downtime, the equivalent REST and document/literal SOAP services will not be affected. Please see the documentation for these services for further information:
  * Multiple Sequence Alignment (MSA)
    * [[:services:msa:ClustalW2 (REST)]]
    * [[:services:msa:ClustalW2 (SOAP)]]
    * [[:services:msa:Kalign (REST)]]
    * [[:services:msa:Kalign (SOAP)]]
    * [[:services:msa:MAFFT (REST)]]
    * [[:services:msa:MAFFT (SOAP)]]
    * [[:services:msa:MUSCLE (REST)]]
    * [[:services:msa:MUSCLE (SOAP)]]
    * [[:services:msa:PRANK (REST)]]
    * [[:services:msa:PRANK (SOAP)]]
    * [[:services:msa:tcoffee_rest|T-COFFEE (REST)]]
    * [[:services:msa:tcoffee_soap|T-COFFEE (SOAP)]]
  * Protein Functional Analysis (PFA)
    * [[:services:pfa:iprscan_rest|InterProScan (REST)]]
    * [[:services:pfa:iprscan_soap|InterProScan (SOAP)]]
  * Sequence Similarity Search (SSS)
    * [[:services:sss:FASTA (REST)]]
    * [[:services:sss:FASTA (SOAP)]]
    * [[:services:sss:FASTM (REST)]]
    * [[:services:sss:FASTM (SOAP)]]
    * [[:services:sss:NCBI BLAST (REST)]]
    * [[:services:sss:NCBI BLAST (SOAP)]]
    * [[:services:sss:psiblast_rest|PSI-BLAST (REST)]]
    * [[:services:sss:psiblast_soap|PSI-BLAST (SOAP)]]
    * [[:services:sss:psisearch_rest|PSI-Search (REST)]]
    * [[:services:sss:psisearch_soap|PSI-Search (SOAP)]]
    * [[:services:sss:wu_blast_rest|WU-BLAST (REST)]]
    * [[:services:sss:wu_blast_soap|WU-BLAST (SOAP)]]

==== 20th November 2010 ====

Due to a fault in the Hintxon data centre services were unavailable between 15:00 and 18:00 GMT. The fault has been addressed and we are working to restore normal service. Apologies for any inconvenience caused.

==== 18th November 2010 ====

The [[http://www.ebi.ac.uk/RESID/|RESID]] and [[http://www.ncbi.nlm.nih.gov/Taxonomy/|Taxonomy]] databases have been added to the dbfetch services:
  * [[http://www.ebi.ac.uk/Tools/dbfetch|dbfetch]]
  * [[:services:dbfetch|WSDbfetch]]
  * [[:services:dbfetch_rest|WSDbfetch (REST)]]

==== 2nd November 2010 ====

Our existing similarity and homology search services have been migrated to a new data centre and the older versions of these services have now been deprecated. For more information, please have a look at the following [[http://www.ebi.ac.uk/Tools/sss|page]] or contact [[http://www.ebi.ac.uk/support|EBI support]]. 

==== 21st October 2010 ====

The dbfetch web services have been updated providing:

  - Additional functionality
    * Option to suppress EMBL-EBI HTML header and footer (see [[http://www.ebi.ac.uk/Tools/dbfetch/syntax.jsp|dbfetch]]).
    * OBDA biofetch compatibility (see [[http://www.ebi.ac.uk/Tools/dbfetch/syntax.jsp|dbfetch]]).
    * Support for format and database aliases (e.g. using ''swissprot'' to access ''uniprotkb'').
    * Meta-information methods for REST service (see [[:services:dbfetch_rest|WSDbfetch (REST)]]).
    * Detailed meta-information for SOAP service (see [[:services:dbfetch|WSDbfetch (SOAP)]]).
  - New databases
    * [[http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#emblconexp|EMBLCONEXP]] (''emblconexp'').
    * [[http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#nrnl1|Patent DNA NRL1]] (''nrnl1'').
    * [[http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#nrnl2|Patent DNA NRL2]] (''nrnl2'').
    * [[http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#nrpl1|Patent Protein NRL1]] (''nrpl1'').
    * [[http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#nrpl2|Patent Protein NRL2]] (''nrpl2'').
    * [[http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#tracearchive|Trace Archive]] (''tracearchive'').
  - Additional formats:
    * ''annot'' for all sequence databases where annotation and sequence can be separated.
    * ''entrysize'' for all sequence databases where the source database can provide information about the entry size.
    * ''emblxml-1.2'' for EMBL-Bank databases (e.g. ''embl'', ''emblcds'', ''emblcon'', etc.).
    * ''mmcif'' and ''pdbml'' for PDB.

==== 11th October 2010 ====

  * The proteomes, genomes and wgs databases available in the FASTA services ([[http://www.ebi.ac.uk/Tools/sss/fasta|FASTA]], [[:services:sss:FASTA (REST)]] and [[:services:sss:FASTA (SOAP)]]) have been updated to their latest version.
  * The T-COFFEE services ([[http://www.ebi.ac.uk/Tools/msa/tcoffee|T-COFFEE]], [[:services:msa:tcoffee_rest|T-COFFEE (REST)]] and [[:services:msa:tcoffee_soap|T-COFFEE (SOAP)]]) have been updated to use version 8.9.3 of the program
  * The MUSCLE services ([[http://www.ebi.ac.uk/Tools/msa/muscle|MUSCLE]], [[:services:msa:MUSCLE (REST)]] and [[:services:msa:MUSCLE (SOAP)]]) can now generate log and tree output files
  * SGT results now have hyperlinks to their corresponding entry in the [[http://targetdb.pdb.org/|TargetDB website]]
  * New services for peptide fragment searches ([[http://www.ebi.ac.uk/Tools/sss/fastm|FASTM]], [[:services:sss:FASTM (REST)]] and [[:services:sss:FASTM (SOAP)]]) are now available in beta version.


==== 1st October 2010 ====

The FASTA services: [[:services:sss:FASTA (REST)]] and [[:services:sss:FASTA (SOAP)]], have been modified to remove the ''program'' options for ''fastf'', ''fastm'' and ''fasts''. This is due to an input incompatibility between these programs and the other FASTA programs. The peptide fragment searches provided by ''fastf'', ''fastm'' and ''fasts'' are still available in [[:services:fasta|WSFasta]] and are to be re-introduced in a separate service (FASTM) in the near future.

==== 21st September 2010 ====

The following RPC/encoded SOAP services are now deprecated and no longer maintained:

  * Sequence Similarity Search
    * [[:services:fasta|WSFasta]]
    * [[:services:ncbiblast|WSNCBIBlast]]
    * [[:services:psiblast|WSPSIBlast]]
    * [[:services:psisearch|WSPSISearch]]
    * [[:services:wublast|WSWUBlast]]
  * Multiple Sequence Alignment
    * [[:services:clustalw2|WSClustalW2]]
    * [[:services:kalign|WSKalign]]
    * [[:services:mafft|WSMafft]]
    * [[:services:muscle|WSMuscle]]
    * [[:services:tcoffee|WSTCoffee]]

Please use the equivalent REST or document/literal SOAP service (see [[:|Web Services]]).

==== 5th July 2010 ====

REST and SOAP Web Services for the PRANK multiple sequence alignment method are now available, see the following for details:
  * [[:services:msa:PRANK (REST)]]
  * [[:services:msa:PRANK (SOAP)]]

==== 17th May 2010 ====

The [[services:dbfetch|WSDbfetch (SOAP)]] service now provides a document/literal interface in addition to the RPC/encoded interfaces.

Sample clients for the new interface are provided for Java, Perl and Python.

==== 16th March 2010 ====

.NET clients are now available for the following sequence similarity search (SSS) services:
  * [[:services:sss:psiblast_soap|PSI-BLAST (SOAP)]]
  * [[:services:sss:psisearch_soap|PSI-Search (SOAP)]]

A Perl client is now available for the [[:services:sss:psisearch_soap|PSI-Search (SOAP)]] service.

==== 5th March 2010 ====

The following services have been updated to use FASTA 35.4.10:
  * [[:services:sss:FASTA (REST)]]
  * [[:services:sss:FASTA (SOAP)]]
  * [[:services:sss:psisearch_rest|PSI-Search (REST)]]
  * [[:services:sss:psisearch_soap|PSI-Search (SOAP)]]
  * [[:services:fasta|WSFasta]]
  * [[:services:psisearch|WSPSISearch]]

==== 5 February 2010 ====

.NET clients are now available for the following multiple sequence alignment (MSA) services:
  * [[:services:msa:ClustalW2 (SOAP)]]
  * [[:services:msa:Kalign (SOAP)]]
  * [[:services:msa:MAFFT (SOAP)]]
  * [[:services:msa:MUSCLE (SOAP)]]
  * [[:services:msa:tcoffee_soap|T-Coffee (SOAP)]]

==== 27 January 2010 ====

The [[:services:mpsrch|WSMPsrch]] and [[:services:scanps|WSScanPS]] services have been retired.

For equivalent functionality please use SSEARCH ([[:services:sss:fasta_rest|FASTA (REST)]], [[:services:sss:fasta_soap|FASTA (SOAP)]] or [[:services:fasta|WSFasta]]) or PSI-Search ([[:services:sss:psisearch_rest|PSI-Search (REST)]], [[:services:sss:psisearch_soap|PSI-Search (SOAP)]] or [[:services:psisearch|WSPSISearch]]).

==== 11 January 2010 ====

Updated sample clients are now available for the [[services:EB-eye|EB-eye service]]:
  * Java client using [[http://ws.apache.org/axis/|Axis]]
  * Java client using [[https://jax-ws.dev.java.net/|JAX-WS]]
  * Perl client [[http://www.soaplite.com/|SOAP::Lite]]

Users are advised to use the latest release of the available [[services:EB-eye|EB-eye clients]] to deal properly with forthcoming version of the implementation on the server side.


==== 5th January 2010 ====

Reminder: the hands-on course "[[http://www.ebi.ac.uk/training/handson/course_100222_webservicesperl.html|Programmatic Access To Biological Databases (Perl)]]" will be held on 22nd–26th February 2010 at the European Bioinformatics Institute. The registration deadline is Thursday 21st January 2010, see the [[http://www.ebi.ac.uk/training/handson/|Hands-on training at EBI]] pages for details of how to register.

==== 2009 ====

News for [[.:2009]].
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