<s>
BioPerl	B-Application
is	O
a	O
collection	O
of	O
Perl	B-Language
modules	O
that	O
facilitate	O
the	O
development	O
of	O
Perl	B-Language
scripts	O
for	O
bioinformatics	O
applications	O
.	O
</s>
<s>
BioPerl	B-Application
is	O
an	O
active	O
open	B-Application
source	I-Application
software	I-Application
project	O
supported	O
by	O
the	O
Open	B-Application
Bioinformatics	I-Application
Foundation	I-Application
.	O
</s>
<s>
The	O
first	O
set	O
of	O
Perl	B-Language
codes	O
of	O
BioPerl	B-Application
was	O
created	O
by	O
Tim	O
Hubbard	O
and	O
Jong	O
Bhak	O
at	O
MRC	O
Centre	O
Cambridge	O
,	O
where	O
the	O
first	O
genome	O
sequencing	O
was	O
carried	O
out	O
by	O
Fred	O
Sanger	O
.	O
</s>
<s>
Hubbard	O
was	O
using	O
the	O
th_lib.pl	O
Perl	B-Language
library	O
,	O
which	O
contained	O
many	O
useful	O
Perl	B-Language
subroutines	O
for	O
bioinformatics	O
.	O
</s>
<s>
Bhak	O
merged	O
the	O
two	O
Perl	B-Language
subroutine	O
libraries	O
into	O
Bio.pl	O
.	O
</s>
<s>
The	O
name	O
BioPerl	B-Application
was	O
coined	O
jointly	O
by	O
Bhak	O
and	O
Steven	O
Brenner	O
at	O
the	O
Centre	O
for	O
Protein	O
Engineering	O
(	O
CPE	O
)	O
.	O
</s>
<s>
In	O
1995	O
,	O
Brenner	O
organized	O
a	O
BioPerl	B-Application
session	O
at	O
the	O
Intelligent	O
Systems	O
for	O
Molecular	O
Biology	O
conference	O
,	O
held	O
in	O
Cambridge	O
.	O
</s>
<s>
BioPerl	B-Application
had	O
some	O
users	O
in	O
coming	O
months	O
including	O
Georg	O
Fuellen	O
who	O
organized	O
a	O
training	O
course	O
in	O
Germany	O
.	O
</s>
<s>
Fuellen	O
's	O
colleagues	O
and	O
students	O
greatly	O
extended	O
BioPerl	B-Application
;	O
this	O
was	O
further	O
expanded	O
by	O
others	O
,	O
including	O
Steve	O
Chervitz	O
who	O
was	O
actively	O
developing	O
Perl	B-Language
codes	O
for	O
his	O
yeast	O
genome	O
database	O
.	O
</s>
<s>
Version	O
series	O
1.7.x	O
is	O
considered	O
to	O
be	O
the	O
most	O
stable	O
(	O
in	O
terms	O
of	O
bugs	O
)	O
version	O
of	O
BioPerl	B-Application
and	O
is	O
recommended	O
for	O
everyday	O
use	O
.	O
</s>
<s>
In	O
order	O
to	O
take	O
advantage	O
of	O
BioPerl	B-Application
,	O
the	O
user	O
needs	O
a	O
basic	O
understanding	O
of	O
the	O
Perl	B-Language
programming	I-Language
language	I-Language
including	O
an	O
understanding	O
of	O
how	O
to	O
use	O
Perl	B-Language
references	O
,	O
modules	O
,	O
objects	O
and	O
methods	O
.	O
</s>
<s>
A	O
few	O
of	O
these	O
problems	O
were	O
solved	O
when	O
many	O
of	O
the	O
genomics	O
labs	O
started	O
to	O
use	O
Perl	B-Language
.	O
</s>
<s>
It	O
was	O
eventually	O
discovered	O
that	O
many	O
of	O
the	O
steps	O
could	O
be	O
implemented	O
as	O
loosely	O
coupled	O
programs	O
that	O
were	O
run	O
with	O
a	O
Perl	B-Language
shell	O
script	O
.	O
</s>
<s>
This	O
minimized	O
the	O
number	O
of	O
scripts	O
needed	O
and	O
data	O
exchange	O
became	O
simplified	O
with	O
Perl	B-Language
.	O
</s>
<s>
BioPerl	B-Application
provides	O
software	O
modules	O
for	O
many	O
of	O
the	O
typical	O
tasks	O
of	O
bioinformatics	O
programming	O
.	O
</s>
<s>
In	O
addition	O
to	O
being	O
used	O
directly	O
by	O
end-users	O
,	O
BioPerl	B-Application
has	O
also	O
provided	O
the	O
base	O
for	O
a	O
wide	O
variety	O
of	O
bioinformatic	O
tools	O
,	O
including	O
:	O
</s>
<s>
New	O
tools	O
and	O
algorithms	O
from	O
external	O
developers	O
are	O
often	O
integrated	O
directly	O
into	O
BioPerl	B-Application
itself	O
:	O
</s>
<s>
BioPerl	B-Application
was	O
one	O
of	O
the	O
first	O
biological	O
module	O
repositories	O
that	O
increased	O
its	O
usability	O
.	O
</s>
<s>
BioPerl	B-Application
uses	O
good	O
test	O
modules	O
for	O
a	O
large	O
variety	O
of	O
processes	O
.	O
</s>
<s>
There	O
are	O
many	O
ways	O
to	O
use	O
BioPerl	B-Application
,	O
from	O
simple	O
scripting	O
to	O
very	O
complex	O
object	O
programming	O
.	O
</s>
<s>
For	O
as	O
many	O
modules	O
that	O
BioPerl	B-Application
has	O
,	O
some	O
do	O
not	O
always	O
work	O
the	O
way	O
they	O
are	O
intended	O
.	O
</s>
<s>
Several	O
related	O
bioinformatics	O
libraries	O
implemented	O
in	O
other	O
programming	O
languages	O
exist	O
as	O
part	O
of	O
the	O
Open	B-Application
Bioinformatics	I-Application
Foundation	I-Application
,	O
including	O
:	O
</s>
