<s>
BioRuby	B-Application
is	O
a	O
collection	O
of	O
open-source	B-Application
Ruby	B-Language
code	O
,	O
comprising	O
classes	O
for	O
computational	O
molecular	O
biology	O
and	O
bioinformatics	O
.	O
</s>
<s>
It	O
contains	O
classes	O
for	O
DNA	O
and	O
protein	O
sequence	O
analysis	O
,	O
sequence	B-Algorithm
alignment	I-Algorithm
,	O
biological	O
database	O
parsing	O
,	O
structural	O
biology	O
and	O
other	O
bioinformatics	O
tasks	O
.	O
</s>
<s>
BioRuby	B-Application
is	O
released	O
under	O
the	O
GNU	B-License
GPL	I-License
version	O
2	O
or	O
Ruby	B-License
licence	I-License
and	O
is	O
one	O
of	O
a	O
number	O
of	O
Bio*	O
projects	O
,	O
designed	O
to	O
reduce	O
code	O
duplication	O
.	O
</s>
<s>
In	O
2011	O
,	O
the	O
BioRuby	B-Application
project	O
introduced	O
the	O
Biogem	O
software	O
plugin	O
system	O
,	O
with	O
two	O
or	O
three	O
new	O
plugins	O
added	O
every	O
month	O
.	O
</s>
<s>
BioRuby	B-Application
is	O
managed	O
via	O
the	O
BioRuby	B-Application
website	O
and	O
GitHub	B-Application
repository	O
.	O
</s>
<s>
The	O
BioRuby	B-Application
project	O
was	O
first	O
started	O
in	O
2000	O
by	O
Toshiaki	O
Katayama	O
as	O
a	O
Ruby	B-Language
implementation	O
of	O
similar	O
bioinformatics	O
packages	O
such	O
as	O
BioPerl	B-Application
and	O
BioPython	B-Library
.	O
</s>
<s>
The	O
initial	O
release	O
of	O
version	O
0.1	O
was	O
frequently	O
updated	O
by	O
contributors	O
both	O
informally	O
and	O
at	O
organised	O
“	O
hackathon	O
”	O
events	O
;	O
in	O
June	O
2005	O
,	O
BioRuby	B-Application
was	O
funded	O
by	O
IPA	O
as	O
an	O
Exploratory	O
Software	O
Project	O
,	O
culminating	O
with	O
the	O
release	O
of	O
version	O
1.0.0	O
in	O
February	O
2006	O
.	O
</s>
<s>
Between	O
2009	O
and	O
2012	O
,	O
BioRuby	B-Application
was	O
the	O
focus	O
of	O
a	O
number	O
of	O
Google	B-Application
Summer	I-Application
of	I-Application
Code	I-Application
projects	O
to	O
improve	O
the	O
codebase	O
.	O
</s>
<s>
BioRuby	B-Application
Version	O
2.0.0	O
was	O
released	O
in	O
2019	O
.	O
</s>
<s>
Biogem	O
provides	O
a	O
set	O
of	O
tools	O
for	O
bioinformaticians	O
who	O
want	O
to	O
code	O
an	O
application	O
or	O
library	O
that	O
uses	O
or	O
extends	O
BioRuby	B-Application
's	O
core	O
library	O
,	O
as	O
well	O
as	O
share	O
the	O
code	O
as	O
a	O
gem	O
on	O
rubygems.org	O
.	O
</s>
<s>
The	O
aim	O
of	O
Biogem	O
is	O
to	O
promote	O
a	O
modular	O
approach	O
to	O
the	O
BioRuby	B-Application
package	O
and	O
simplify	O
the	O
creation	O
of	O
modules	O
by	O
automating	O
process	O
of	O
setting	O
up	O
directory/file	O
scaffolding	O
,	O
a	O
git	O
repository	O
and	O
releasing	O
online	O
package	O
databases	O
.	O
</s>
<s>
#	O
Biogem	O
Description	O
Version	O
1	O
bio	O
Bioinformatics	O
Library	O
1.4.3.0001	O
2	O
biodiversity	O
Parser	O
of	O
scientific	O
names	O
3.1.5	O
3	O
Simple	O
Spreadsheet	O
extractor	O
Basic	O
spreadsheet	O
content	O
extraction	O
using	O
Apache	O
poi	O
0.13.3	O
4	O
Bio	O
gem	O
Software	O
generator	O
for	O
Ruby	B-Language
1.36	O
5	O
Bio	O
samtools	O
Binder	O
of	O
samtools	O
for	O
Ruby	B-Language
2.1.0	O
6	O
t2	O
server	O
Support	O
for	O
interacting	O
with	O
the	O
taverna	O
2	O
server	O
1.1.0	O
7	O
bio	O
ucsc	O
api	O
The	O
Ruby	B-Language
ucsc	O
api	O
0.6.2	O
8	O
entrez	O
http	O
request	O
to	O
entrez	O
e-utilities	O
0.5.8.1	O
9	O
bio	O
gadget	O
Gadget	O
for	O
bioinformatics	O
0.4.8	O
10	O
sequenceserver	O
Blast	O
search	O
made	O
easy	O
!	O
</s>
