-
Notifications
You must be signed in to change notification settings - Fork 1
/
HISTORY.txt
164 lines (110 loc) · 5.22 KB
/
HISTORY.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
0.9.1 - November 27th 2008
* added possibility to export multiple structure alignment as PDB file
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