<s>
Galaxy	B-Application
is	O
a	O
scientific	B-Application
workflow	I-Application
,	O
data	B-General_Concept
integration	I-General_Concept
,	O
and	O
data	O
and	O
analysis	O
persistence	O
and	O
publishing	O
platform	O
that	O
aims	O
to	O
make	O
computational	O
biology	O
accessible	O
to	O
research	O
scientists	O
that	O
do	O
not	O
have	O
computer	B-General_Concept
programming	I-General_Concept
or	O
systems	B-Application
administration	I-Application
experience	O
.	O
</s>
<s>
Although	O
it	O
was	O
initially	O
developed	O
for	O
genomics	O
research	O
,	O
it	O
is	O
largely	O
domain	O
agnostic	O
and	O
is	O
now	O
used	O
as	O
a	O
general	O
bioinformatics	B-Application
workflow	I-Application
management	I-Application
system	I-Application
.	O
</s>
<s>
Galaxy	B-Application
is	O
a	O
scientific	B-Application
workflow	I-Application
system	I-Application
.	O
</s>
<s>
They	O
typically	O
provide	O
a	O
graphical	B-Application
user	I-Application
interface	I-Application
for	O
specifying	O
what	O
data	O
to	O
operate	O
on	O
,	O
what	O
steps	O
to	O
take	O
,	O
and	O
what	O
order	O
to	O
do	O
them	O
in	O
.	O
</s>
<s>
Galaxy	B-Application
is	O
also	O
a	O
data	B-General_Concept
integration	I-General_Concept
platform	O
for	O
biological	O
data	O
.	O
</s>
<s>
It	O
supports	O
data	O
uploads	O
from	O
the	O
user	O
's	O
computer	O
,	O
by	O
URL	O
,	O
and	O
directly	O
from	O
many	O
online	O
resources	O
(	O
such	O
as	O
the	O
UCSC	O
Genome	O
Browser	O
,	O
BioMart	B-Application
and	O
InterMine	O
)	O
.	O
</s>
<s>
Galaxy	B-Application
supports	O
a	O
range	O
of	O
widely	O
used	O
biological	O
data	O
formats	O
,	O
and	O
translation	O
between	O
those	O
formats	O
.	O
</s>
<s>
Galaxy	B-Application
provides	O
a	O
web	O
interface	O
to	O
many	O
text	O
manipulation	O
utilities	O
,	O
enabling	O
researchers	O
to	O
do	O
their	O
own	O
custom	O
reformatting	O
and	O
manipulation	O
without	O
having	O
to	O
do	O
any	O
programming	B-Language
.	O
</s>
<s>
Galaxy	B-Application
includes	O
interval	O
manipulation	O
utilities	O
for	O
doing	O
set	O
theoretic	O
operations	O
(	O
e.g.	O
</s>
<s>
Many	O
biological	O
file	O
formats	O
include	O
genomic	O
interval	O
data	O
(	O
a	O
frame	O
of	O
reference	O
,	O
e.g.	O
,	O
chromosome	O
or	O
contig	B-Application
name	O
,	O
and	O
start	O
and	O
stop	O
positions	O
)	O
,	O
allowing	O
these	O
data	O
to	O
be	O
integrated	O
.	O
</s>
<s>
Galaxy	B-Application
was	O
originally	O
written	O
for	O
biological	O
data	O
analysis	O
,	O
particularly	O
genomics	O
.	O
</s>
<s>
The	O
set	O
of	O
available	O
tools	O
has	O
been	O
greatly	O
expanded	O
over	O
the	O
years	O
and	O
Galaxy	B-Application
is	O
now	O
also	O
used	O
for	O
gene	O
expression	O
,	O
genome	O
assembly	O
,	O
proteomics	O
,	O
epigenomics	O
,	O
transcriptomics	O
and	O
host	O
of	O
other	O
disciplines	O
in	O
the	O
life	O
sciences	O
.	O
</s>
<s>
For	O
example	O
,	O
Galaxy	B-Application
servers	O
exist	O
for	O
image	O
analysis	O
,	O
computational	O
chemistry	O
and	O
drug	O
design	O
,	O
cosmology	O
,	O
climate	O
modeling	O
,	O
social	O
science	O
,	O
and	O
linguistics	O
.	O
</s>
<s>
Finally	O
,	O
Galaxy	B-Application
also	O
supports	O
data	O
and	O
analysis	O
persistence	O
and	O
publishing	O
.	O
</s>
<s>
Galaxy	B-Application
is	O
"	O
an	O
open	O
,	O
web-based	O
platform	O
for	O
performing	O
accessible	O
,	O
reproducible	O
,	O
and	O
transparent	O
genomic	O
science.	O
"	O
</s>
<s>
Computational	O
biology	O
is	O
a	O
specialized	O
domain	O
that	O
often	O
requires	O
knowledge	O
of	O
computer	B-General_Concept
programming	I-General_Concept
.	O
</s>
<s>
Galaxy	B-Application
aims	O
to	O
give	O
biomedical	O
researchers	O
access	O
to	O
computational	O
biology	O
without	O
also	O
requiring	O
them	O
to	O
understand	O
computer	B-General_Concept
programming	I-General_Concept
.	O
</s>
<s>
Galaxy	B-Application
does	O
this	O
by	O
stressing	O
a	O
simple	O
user	O
interface	O
over	O
the	O
ability	O
to	O
build	O
complex	O
workflows	O
.	O
</s>
<s>
(	O
See	O
Apache	B-Application
Taverna	I-Application
for	O
an	O
example	O
of	O
a	O
data-driven	O
workflow	O
system	O
that	O
supports	O
looping	O
.	O
)	O
</s>
<s>
Galaxy	B-Application
supports	O
reproducibility	O
by	O
capturing	O
sufficient	O
information	O
about	O
every	O
step	O
in	O
a	O
computational	O
analysis	O
,	O
so	O
that	O
the	O
analysis	O
can	O
be	O
repeated	O
,	O
exactly	O
,	O
at	O
any	O
point	O
in	O
the	O
future	O
.	O
</s>
<s>
Galaxy	B-Application
supports	O
transparency	O
in	O
scientific	O
research	O
by	O
enabling	O
researchers	O
to	O
share	O
any	O
of	O
their	O
Galaxy	B-Application
Objects	O
either	O
publicly	O
,	O
or	O
with	O
specific	O
individuals	O
.	O
</s>
<s>
Galaxy	B-Application
objects	O
are	O
anything	O
that	O
can	O
be	O
saved	O
,	O
persisted	O
,	O
and	O
shared	O
in	O
Galaxy	B-Application
:	O
</s>
<s>
Galaxy	B-Application
Pages	O
enables	O
the	O
creation	O
of	O
a	O
virtual	O
paper	O
that	O
describes	O
the	O
how	O
and	O
why	O
of	O
the	O
overall	O
experiment	O
.	O
</s>
<s>
Galaxy	B-Application
is	O
available	O
:	O
</s>
<s>
As	O
a	O
free	O
public	O
web	O
server	O
,	O
supported	O
by	O
the	O
Galaxy	B-Application
Project	O
.	O
</s>
<s>
As	O
open-source	B-Application
software	I-Application
that	O
can	O
be	O
downloaded	O
,	O
installed	O
and	O
customized	O
to	O
address	O
specific	O
needs	O
.	O
</s>
<s>
Galaxy	B-Application
can	O
be	O
installed	O
locally	O
or	O
using	O
a	O
computing	B-Architecture
cloud	I-Architecture
.	O
</s>
<s>
Several	O
organizations	O
with	O
their	O
own	O
Galaxy	B-Application
installation	O
have	O
also	O
opted	O
to	O
make	O
those	O
servers	O
available	O
to	O
others	O
.	O
</s>
<s>
Galaxy	B-Application
is	O
open-source	B-Application
software	I-Application
implemented	O
using	O
the	O
Python	B-Language
programming	I-Language
language	I-Language
.	O
</s>
<s>
It	O
is	O
developed	O
by	O
the	O
Galaxy	B-Application
team	O
at	O
Penn	O
State	O
,	O
Johns	O
Hopkins	O
University	O
,	O
Oregon	O
Health	O
&	O
Science	O
University	O
,	O
and	O
the	O
Galaxy	B-Application
Community	O
.	O
</s>
<s>
Galaxy	B-Application
is	O
extensible	O
,	O
as	O
new	O
command	O
line	O
tools	O
can	O
be	O
integrated	O
and	O
shared	O
within	O
the	O
.	O
</s>
<s>
An	O
example	O
of	O
extending	O
Galaxy	B-Application
is	O
from	O
the	O
University	O
of	O
Minnesota	O
Supercomputing	O
Institute	O
,	O
which	O
is	O
customized	O
as	O
a	O
data	O
analysis	O
platform	O
for	O
mass	O
spectrometry-based	O
proteomics	O
.	O
</s>
<s>
Galaxy	B-Application
is	O
an	O
open	O
source	O
project	O
and	O
the	O
community	O
includes	O
users	O
,	O
organizations	O
that	O
install	O
their	O
own	O
instance	O
,	O
Galaxy	B-Application
developers	O
,	O
and	O
bioinformatics	O
tool	O
developers	O
.	O
</s>
<s>
The	O
Galaxy	B-Application
project	O
has	O
mailing	O
lists	O
,	O
a	O
community	O
hub	O
,	O
and	O
annual	O
meetings	O
.	O
</s>
