eFamily
The Wellcome Trust Sanger Institute MRC- Medical Research Council

0.9 - January 3rd 2008 


* From now on SPICE will require Java 1.5+. If you still are using an
  old Java 1.4 installation on your system, please consider an upgrade.
  Java 1.4 is in the end of life process http://java.sun.com/j2se/1.4.2/

* updated the keyword search service to the latest version provided by MSD.

* performance improvements.

* the protein structure related DAS servers used by SPICE have been
  updated to the remediated PDB files already at some point last year.

0.8.6 - May 24th 2007 


* We recently defined a convention how to configure and display
  histogram style data in Ensembl and SPICE. 
  http://www.dasregistry.org/extension_stylesheet_histogram.jsp

* SPICE has now built in support for this and can display 
  histograms, line-plots and colour gradients.
  http://www.efamily.org.uk/software/dasclients/spice/histogram.shtml

0.8.5 - March 6th 2007 


* SPICE is being used for the visualisation of the CASP7 results
see  
http://www.predictioncenter.org/casp/casp7/public/cgi-bin/results.cgi

It is now possible to view the 3D alignments of the CASP Targets, the
submitted protein structure predictions, and the closest protein  
structures
from PDB, which could have been used as a template. It is possible to   
switch
between the results of the different alignment methods that have been  
used for
evaluation of the predictions.

* better Spice - Jmol integration (speedups, better recovery if Jmol  
fails)

* display of histograms e.g. for hydrophobicity plots

* feedback system to submit bug-reports via the logging panel

0.8.4 - 

* This was a series of incremental releases during the end of 2006 
  in preparation for the CASP-7 meeting.

0.8.3 - August 25th, 2006 

* now with improved display of annotated features
* if feature  <note> section contain HTML <img> tags, those images can be displayed
* better configuration of DAS sources
* user interface improvements

* several improvements when showing structure alignments:
* now starts with the first structure loaded in an alignment
* there is a feature display that shows the region used for the alignment
* the toggle full structure button now immediately triggers a reload of the alignment
* interaction between Jmol and Spice now also works with alignments (if the "active"
   model is clicked, for the others a message on the console is printed)

0.8.2 - July 14th, 2006 

* SPICE now supports visualization of multiple structure alignments
  for an example see:
  http://sisyphus.mrc-cpe.cam.ac.uk:8082/sisyphus/showspicejnlp.jsp?alignment=AL00069117

* alignment display now shows conserved/non conserved regions
* rainbow coloring mode added
* new tabbed browsing and open window functionalities
* smaller size (< 6MB)

0.8.1 - Feb 1, 2006 

Mainly a bug fixing release with only a few improvements in functionality

* improved communication between Jmol and spice.
* improved management of DAS sources
* fixed a threading problem in Jmol
* fixed bugs related to the correct display of  alignments
* some small things.

0.8.0 - Dec 20, 2005 

* SPICE now contains three panels to display annotations
  for PDB, UniProt and ENSP sequences.
* the alignment between these is visualized
* new way to choose between alternative alignments
* overall improvement of the design/layout
* it is now possible to attach DAS sources, which are running locally
* many other small things.

0.7.5 - Oct 26, 2005 

* the keyword search now suggests correct words,
  if a typo is made (thanks to Adel Golovin)
* the spice - startup script has been changed to now
  first display a documentation page, before launching the
  program. The user can hide this page, to directly proceed to spice,
  without showing docu first.
  e.g
  http://das.sanger.ac.uk/registry/showspice.jsp?pdb=1boi
* better documentation. e.g. about how to link SPICE to the
  Ensembl genome browser.
  http://www.efamily.org.uk/software/dasclients/spice/ensembl.shtml

0.7.4 - Sep 15, 2005 

* fixed a bug related to freezing threads
* if no structure is found for a uniprot sequence, now correctly clears 
  the structure display (e.g. P00123)
* and some other minor things

0.7.3 - Sept 9, 2005 

* Only one SPICE instance running: When a new SPICE instance is started 
  it tries to send the accession code to be displayed to another instance 
  listening at a high numbered port. If something is running there, the 
  first instance will take over, otherwise this instance will become the 
  main one.

  some other minor things:
* update to latest das-registry and Jmol libraries
* features are now displayed in the order returned by the server

0.7.2 - Aug 10, 2005 

* a keyword search to identify matching PDB codes using a webservice  
  provided by MSD
* support for DAS stylesheet command ( allows to control display of  
  features)
* new ways how to interact with SPICE from the outside - and affect the  
  first accession code to be loaded:
	* select regions to be selected at startup
	* send a rasmol scripts at startup

0.7.1 - Jul 28, 2005 

* Changed the mouse behavior - now does not auto-select features.
* fixed some minor bugs.

0.7.0 - Jul 12, 2005 

* plenty of work done on feature viewer
* enable/disable DAS sources through external startup link