<s>
UTOPIA	B-Application
(	O
User-friendly	B-Application
Tools	I-Application
for	I-Application
Operating	I-Application
Informatics	I-Application
Applications	I-Application
)	O
is	O
a	O
suite	O
of	O
free	O
tools	O
for	O
visualising	O
and	O
analysing	O
bioinformatics	O
data	O
.	O
</s>
<s>
There	O
are	O
two	O
major	O
components	O
,	O
the	O
protein	O
analysis	O
suite	O
and	O
UTOPIA	B-Application
documents	O
.	O
</s>
<s>
The	O
Utopia	B-Application
Protein	O
Analysis	O
suite	O
is	O
a	O
collection	O
of	O
interactive	O
tools	O
for	O
analysing	O
protein	O
sequence	O
and	O
protein	O
structure	O
.	O
</s>
<s>
Utopia	B-Application
Documents	O
brings	O
a	O
fresh	O
new	O
perspective	O
to	O
reading	O
the	O
scientific	O
literature	O
,	O
combining	O
the	O
convenience	O
and	O
reliability	O
of	O
the	O
Portable	B-Application
Document	I-Application
Format	I-Application
(	O
pdf	B-Application
)	O
with	O
the	O
flexibility	O
and	O
power	O
of	O
the	O
web	O
.	O
</s>
<s>
Between	O
2003	O
and	O
2005	O
work	O
on	O
UTOPIA	B-Application
was	O
funded	O
via	O
based	O
at	O
The	O
University	O
of	O
Manchester	O
by	O
the	O
Engineering	O
and	O
Physical	O
Sciences	O
Research	O
Council	O
,	O
UK	O
Department	O
of	O
Trade	O
And	O
Industry	O
,	O
and	O
the	O
European	O
Molecular	O
Biology	O
Network	O
(	O
EMBnet	O
)	O
.	O
</s>
<s>
UTOPIA	B-Application
's	O
CINEMA	O
(	O
Colour	B-Application
INteractive	I-Application
Editor	I-Application
for	I-Application
Multiple	I-Application
Alignments	I-Application
)	O
,	O
a	O
tool	O
for	O
Sequence	B-Algorithm
Alignment	I-Algorithm
,	O
is	O
the	O
latest	O
incarnation	O
of	O
software	O
originally	O
developed	O
at	O
The	O
University	O
of	O
Leeds	O
to	O
aid	O
the	O
analysis	O
of	O
G	O
protein-coupled	O
receptors	O
(	O
GPCRs	O
)	O
.	O
</s>
<s>
SOMAP	B-Application
,	O
a	O
Screen	O
Oriented	O
Multiple	O
Alignment	O
Procedure	O
was	O
developed	O
in	O
the	O
late	O
1980s	O
on	O
the	O
VMS	B-Operating_System
computer	O
operating	O
system	O
,	O
used	O
a	O
monochrome	O
text-based	O
VT100	B-Device
video	O
terminal	O
,	O
and	O
featured	O
context-sensitive	B-Protocol
help	I-Protocol
and	O
pulldown	O
menus	O
some	O
time	O
before	O
these	O
were	O
standard	O
operating	O
system	O
features	O
.	O
</s>
<s>
SOMAP	B-Application
was	O
followed	O
by	O
a	O
Unix	B-Application
tool	O
called	O
VISTAS	O
(	O
VIsualizing	B-Application
STructures	I-Application
And	I-Application
Sequences	I-Application
)	O
which	O
included	O
the	O
ability	O
to	O
render	O
3D	O
molecular	O
structure	O
and	O
generate	O
plots	O
and	O
statistical	O
representations	O
of	O
sequence	O
properties	O
.	O
</s>
<s>
The	O
first	O
tool	O
under	O
the	O
CINEMA	O
banner	O
developed	O
at	O
The	O
University	O
of	O
Manchester	O
was	O
a	O
Java-based	O
applet	O
launched	O
via	O
web	O
pages	O
,	O
which	O
is	O
but	O
is	O
no	O
longer	O
maintained	O
.	O
</s>
<s>
A	O
standalone	O
Java	B-Language
version	O
,	O
called	O
CINEMA-MX	O
,	O
was	O
also	O
released	O
but	O
is	O
no	O
longer	O
readily	O
available	O
.	O
</s>
<s>
A	O
C++	B-Language
version	O
of	O
CINEMA	O
,	O
called	O
CINEMA5	O
was	O
developed	O
early	O
on	O
as	O
part	O
of	O
the	O
UTOPIA	B-Application
project	O
,	O
and	O
was	O
released	O
as	O
a	O
stand-alone	O
sequence	B-Algorithm
alignment	I-Algorithm
application	O
.	O
</s>
<s>
It	O
has	O
now	O
been	O
replaced	O
by	O
a	O
version	O
of	O
the	O
tool	O
integrated	O
with	O
UTOPIA	B-Application
's	O
other	O
visualisation	O
applications	O
,	O
and	O
its	O
name	O
has	O
reverted	O
simply	O
to	O
CINEMA	O
.	O
</s>
