<s>
Bioconductor	B-Application
is	O
a	O
free	B-Application
,	O
open	B-Application
source	I-Application
and	O
open	B-Application
development	I-Application
software	O
project	O
for	O
the	O
analysis	O
and	O
comprehension	O
of	O
genomic	O
data	O
generated	O
by	O
wet	O
lab	O
experiments	O
in	O
molecular	O
biology	O
.	O
</s>
<s>
Bioconductor	B-Application
is	O
based	O
primarily	O
on	O
the	O
statistical	O
R	B-Language
programming	I-Language
language	I-Language
,	O
but	O
does	O
contain	O
contributions	O
in	O
other	O
programming	O
languages	O
.	O
</s>
<s>
It	O
has	O
two	O
releases	O
each	O
year	O
that	O
follow	O
the	O
semiannual	O
releases	O
of	O
R	B-Language
.	O
At	O
any	O
one	O
time	O
there	O
is	O
a	O
release	O
version	O
,	O
which	O
corresponds	O
to	O
the	O
released	O
version	O
of	O
R	B-Language
,	O
and	O
a	O
development	O
version	O
,	O
which	O
corresponds	O
to	O
the	O
development	O
version	O
of	O
R	B-Language
.	O
Most	O
users	O
will	O
find	O
the	O
release	O
version	O
appropriate	O
for	O
their	O
needs	O
.	O
</s>
<s>
While	O
computational	O
methods	O
continue	O
to	O
be	O
developed	O
to	O
interpret	O
biological	O
data	O
,	O
the	O
Bioconductor	B-Application
project	O
is	O
an	O
open	B-Application
source	I-Application
software	I-Application
repository	O
that	O
hosts	O
a	O
wide	O
range	O
of	O
statistical	O
tools	O
developed	O
in	O
the	O
R	B-Language
programming	I-Language
environment	O
.	O
</s>
<s>
Utilizing	O
a	O
rich	O
array	O
of	O
statistical	O
and	O
graphical	B-Application
features	O
in	O
R	B-Language
,	O
many	O
Bioconductor	B-Application
packages	O
have	O
been	O
developed	O
to	O
meet	O
various	O
data	O
analysis	O
needs	O
.	O
</s>
<s>
The	O
use	O
of	O
these	O
packages	O
provides	O
a	O
basic	O
understanding	O
of	O
the	O
R	B-Language
programming	I-Language
/	O
command	O
language	O
.	O
</s>
<s>
As	O
a	O
result	O
,	O
R	B-Language
and	O
Bioconductor	B-Application
packages	O
,	O
which	O
have	O
a	O
strong	O
computing	O
background	O
,	O
are	O
used	O
by	O
most	O
biologists	O
who	O
will	O
benefit	O
significantly	O
from	O
their	O
ability	O
to	O
analyze	O
datasets	O
.	O
</s>
<s>
The	O
project	O
was	O
started	O
in	O
the	O
Fall	O
of	O
2001	O
and	O
is	O
overseen	O
by	O
the	O
Bioconductor	B-Application
core	O
team	O
,	O
based	O
primarily	O
at	O
the	O
Fred	O
Hutchinson	O
Cancer	O
Research	O
Center	O
,	O
with	O
other	O
members	O
coming	O
from	O
international	O
institutions	O
.	O
</s>
<s>
Most	O
Bioconductor	B-Application
components	O
are	O
distributed	O
as	O
R	B-Language
packages	I-Language
,	O
which	O
are	O
add-on	O
modules	O
for	O
R	B-Language
.	O
Initially	O
most	O
of	O
the	O
Bioconductor	B-Application
software	O
packages	O
focused	O
on	O
the	O
analysis	O
of	O
single	O
channel	O
Affymetrix	O
and	O
two	O
or	O
more	O
channel	O
cDNA/Oligo	O
microarrays	O
.	O
</s>
<s>
Provide	O
widespread	O
access	O
to	O
a	O
broad	O
range	O
of	O
powerful	O
statistical	O
and	O
graphical	B-Application
methods	O
for	O
the	O
analysis	O
of	O
genomic	O
data	O
.	O
</s>
<s>
literature	O
data	O
from	O
PubMed	B-Library
,	O
annotation	O
data	O
from	O
LocusLink/Entrez	O
.	O
</s>
<s>
Provide	O
a	O
common	O
software	B-Device
platform	I-Device
that	O
enables	O
the	O
rapid	O
development	O
and	O
deployment	B-Application
of	O
plug-able	B-Application
,	O
scalable	B-Architecture
,	O
and	O
interoperable	O
software	O
.	O
</s>
<s>
Each	O
Bioconductor	B-Application
package	O
contains	O
at	O
least	O
one	O
vignette	O
,	O
which	O
is	O
a	O
document	O
that	O
provides	O
a	O
textual	O
,	O
task-oriented	O
description	O
of	O
the	O
package	O
's	O
functionality	O
.	O
</s>
<s>
In	O
the	O
future	O
,	O
the	O
Bioconductor	B-Application
project	O
is	O
looking	O
towards	O
providing	O
vignettes	O
that	O
are	O
not	O
specifically	O
tied	O
to	O
a	O
package	O
,	O
but	O
rather	O
are	O
demonstrating	O
more	O
complex	O
concepts	O
.	O
</s>
<s>
As	O
with	O
all	O
aspects	O
of	O
the	O
Bioconductor	B-Application
project	O
,	O
users	O
are	O
encouraged	O
to	O
participate	O
in	O
this	O
effort	O
.	O
</s>
<s>
Statistical	O
and	O
graphical	B-Application
methods	O
.	O
</s>
<s>
The	O
Bioconductor	B-Application
project	O
aims	O
to	O
provide	O
access	O
to	O
a	O
wide	O
range	O
of	O
powerful	O
statistical	O
and	O
graphical	B-Application
methods	O
for	O
the	O
analysis	O
of	O
genomic	O
data	O
.	O
</s>
<s>
In	O
addition	O
,	O
the	O
R	B-Language
package	I-Language
system	O
itself	O
provides	O
implementations	O
for	O
a	O
broad	O
range	O
of	O
state-of-the-art	O
statistical	O
and	O
graphical	B-Application
techniques	I-Application
,	O
including	O
linear	B-General_Concept
and	O
non-linear	O
modeling	O
,	O
cluster	B-Algorithm
analysis	I-Algorithm
,	O
prediction	O
,	O
resampling	B-General_Concept
,	O
survival	O
analysis	O
,	O
and	O
time	O
series	O
analysis	O
.	O
</s>
<s>
The	O
Bioconductor	B-Application
project	O
provides	O
software	O
for	O
associating	O
microarray	O
and	O
other	O
genomic	O
data	O
in	O
real	O
time	O
to	O
biological	O
metadata	O
from	O
web	O
databases	O
such	O
as	O
GenBank	O
,	O
LocusLink	O
and	O
PubMed	B-Library
(	O
annotate	O
package	O
)	O
.	O
</s>
<s>
Software	B-Application
tools	I-Application
are	O
available	O
for	O
assembling	O
and	O
processing	O
genomic	O
annotation	O
data	O
,	O
from	O
databases	O
such	O
as	O
GenBank	O
,	O
the	O
Gene	O
Ontology	O
Consortium	O
,	O
LocusLink	O
,	O
UniGene	O
,	O
the	O
UCSC	O
Human	O
Genome	O
Project	O
and	O
others	O
with	O
the	O
AnnotationDbi	O
package	O
.	O
</s>
<s>
Affy	O
IDs	O
,	O
LocusLink	O
,	O
PubMed	B-Library
)	O
.	O
</s>
<s>
Open	B-Application
source	I-Application
.	O
</s>
<s>
The	O
Bioconductor	B-Application
project	O
has	O
a	O
commitment	O
to	O
full	O
open	B-Application
source	I-Application
discipline	O
,	O
with	O
distribution	O
via	O
a	O
SourceForge.net-like	O
platform	O
.	O
</s>
<s>
All	O
contributions	O
are	O
expected	O
to	O
exist	O
under	O
an	O
open	B-Application
source	I-Application
license	O
such	O
as	O
Artistic	B-License
2.0	I-License
,	O
GPL2	B-License
,	O
or	O
BSD	B-Operating_System
.	O
</s>
<s>
There	O
are	O
many	O
different	O
reasons	O
why	O
open-source	B-Application
software	I-Application
is	O
beneficial	O
to	O
the	O
analysis	O
of	O
microarray	O
data	O
and	O
to	O
computational	O
biology	O
in	O
general	O
.	O
</s>
<s>
Open	B-Application
development	I-Application
.	O
</s>
<s>
Users	O
are	O
encouraged	O
to	O
become	O
developers	B-Application
,	O
either	O
by	O
contributing	O
Bioconductor	B-Application
compliant	O
packages	O
or	O
documentation	O
.	O
</s>
<s>
Additionally	O
Bioconductor	B-Application
provides	O
a	O
mechanism	O
for	O
linking	O
together	O
different	O
groups	O
with	O
common	O
goals	O
to	O
foster	O
collaboration	O
on	O
software	O
,	O
possibly	O
at	O
the	O
level	O
of	O
shared	O
development	O
.	O
</s>
<s>
Each	O
release	O
of	O
Bioconductor	B-Application
is	O
developed	O
to	O
work	O
best	O
with	O
a	O
chosen	O
version	O
of	O
R	B-Language
.	O
In	O
addition	O
to	O
bugfixes	O
and	O
updates	O
,	O
a	O
new	O
release	O
typically	O
adds	O
packages	O
.	O
</s>
<s>
The	O
table	O
below	O
maps	O
a	O
Bioconductor	B-Application
release	O
to	O
a	O
R	B-Language
version	O
and	O
shows	O
the	O
number	O
of	O
available	O
Bioconductor	B-Application
software	O
packages	O
for	O
that	O
release	O
.	O
</s>
