This document describes Bio-NGS, a BioRuby plugin for conducting programmable workflows for Next Generation Sequencing (NGS) data. Bio-NGS provides a software development framework, application, and project environment for analyzing NGS data. It integrates third-party bioinformatics tools as wrappers or bindings and allows for modular, reusable plugins. The document outlines features of the Bio-NGS application, software development framework, and project environment.

1. Bio-­‐NGS:
BioRuby
plugin
to
conduct
programmable
workflows
for
Next
Genera?on
Sequencing
data
Raoul
J.P.
Bonnal
co-­‐authors
bonnal@ingm.org
Francesco
Strozzi
Valeria
Ranzani
Integra(ve
Biology
Program
Toshiaki
Katayama
Is(tuto
Nazionale
di
Gene(ca
Molecolare
Italy
July
15,
2011
BOSC,
Vienna,
Austria

2. Bio-­‐Gem
authors:
Raoul
J.P.
Bonnal,
Pjotr
Prins,
Toshiaki
Katayama
• a
soOware
generator
for
crea(ng
BioRuby
plugins
• last
year
(@BOSC
2010)
was
an
idea
and
a
prototype
• Features:
• bio-­‐assembly
(0.1.0)
• bio-­‐isoelectric_point
(0.1.1)
• bio-­‐blastxmlparser
(0.6.1)
• bio-­‐kb-­‐illumina
(0.1.0)
• bio-­‐bwa
(0.2.2)
• bio-­‐lazyblastxml
(0.4.0)
– Extend
BioRuby
• bio-­‐cnls_screenscraper
(0.1.0)
• bio-­‐
• bio-­‐logger
(0.9.0)
• bio-­‐nexml
(0.0.1)
• bio-­‐ngs
(0.2.1)
– Modularity
emboss_six_frame_nucleo(de • bio-­‐octopus
(0.1.1)
_sequences
(0.1.0)
• bio-­‐gem
(0.2.2)
• bio-­‐samtools
(0.2.4)
• bio-­‐sge
(0.0.0)
– Easy
• bio-­‐genomic-­‐interval
(0.1.2)
• bio-­‐tm_hmm
(0.2.0)
• bio-­‐gff3
(0.8.6)
• bio-­‐graphics
(1.4)
• bio-­‐ucsc-­‐api
(0.1.0)
• sharing:packaging:publishing
• bio-­‐hello
(0.0.0)
– Just
Code
!
Dev:
hcps://github.com/helios/bioruby-­‐gem
Install:
gems
install
bio-­‐gem
July
15,
2011
BOSC,
Vienna,
Austria

3. Bio-­‐NGS
An
Applica(on
A
SoOware
Development
Framework
A
Project
Environment
July
15,
2011
BOSC,
Vienna,
Austria

4. Applica(on
• Stand
alone
– Auto
install
everything
it
needs
–
sandbox/isola*on-­‐
– System-­‐wide
or
User
(RVM
–Ruby
Version
Manager-­‐)
• Mul(
plagorms
– Linux,
OS
X
– MRI,
JRuby
• Command
line
– Thor:
a
simple
and
efficient
tool
for
building
self-­‐documen(ng
command
line
u(li(es
• Common
syntax
to
different
applica(ons
• Collec(on
of
Tasks
– Basic,
Advanced
RVM
hcps://rvm.beginrescueend.com/
Thor
hcps://github.com/wycats/thor
July
15,
2011
BOSC,
Vienna,
Austria

5. SoOware
Development
Framework
• Expand
BioRuby’s
func(onali(es
to
NGS
• API
+
Consistent
Namespace
• Integrate
third-­‐party
tools
• Wrapping
:
quick,
easy
support,
increase
produc(vity
• Binding
:
low-­‐level
func(onali(es
• Modular,
reuse
other
plug-­‐ins
• BioBwa
(binding)
• BioSamtools
(binding)
July
15,
2011
BOSC,
Vienna,
Austria

6. Project
Environment
• Directory
scaffold
• Customize
– Tasks
:
Thor
or
Rake
(Ruby
DSL)
– Configura(ons:
YAML
• History
• Embedded
DB
– SQLite3
July
15,
2011
BOSC,
Vienna,
Austria

7. Tools
e/
Bow(
BWA
?
?
More…
Quant
FASTX-­‐
Toolkit
July
15,
2011
BOSC,
Vienna,
Austria

8. Tools
Bio-­‐NGS
Primary:
Secondary:
Ter(ary:
Pre-­‐Processing
Alignment
Knowledge
Conversion,
Filter,
Bow(e/
TopHat
Samtools
Cufflinks
Ontology
FASTX-­‐Toolkit
BWA
More…
BAM
More…
Differen(al
More…
Illumina
bcl
FASTQ
Quant
Expression
Local
Execu(on
Distributed/Parallel
July
15,
2011
BOSC,
Vienna,
Austria

9. Wrapper
module Bio
module Ngs
module Cufflinks
class Compare
include Bio::Command::Wrapper
set_program Bio::Ngs::Utils.binary("cufflinks/cuffcompare")
use_aliases
add_option "outprefix", :type => :string, :aliases => '-o', :default =>
"Comparison"
add_option "gtf_combine_file", :type => :string, :aliases => '-i'
add_option "gtf_reference", :type => :string, :aliases => '-r'
add_option "only_overlap", :type => :boolean, :aliases => '-R'
add_option "discard_transfrags", :type => :boolean, :aliases => '-M’
end
end
end
end
July
15,
2011
BOSC,
Vienna,
Austria

10. Wrapper
module Bio
module Ngs
module Cufflinks
class Compare
include Bio::Command::Wrapper
set_program Bio::Ngs::Utils.binary("cufflinks/cuffcompare")
use_aliases
add_option "outprefix", :type => :string, :aliases => '-o', :default =>
"Comparison"
add_option "gtf_combine_file", :type => :string, :aliases => '-i'
add_option "gtf_reference", :type => :string, :aliases => '-r'
irb(main):001:0> require:type => :boolean, :aliases => '-R'
add_option "only_overlap", ‘bio-ngs’
add_option "discard_transfrags", :type => :boolean, :aliases => '-M’
irb(main):001:1> cuffcompare = Bio::Ngs::Cufflinks::Compare.new
irb(main):001:2> cuffcompare.params = {….}
irb(main):001:3> cuffcompare.run(:arguments=>[…])
end
end
=> #<Bio::Ngs::Cufflinks::Compare:0x0000000c1630f8 @program="/
end
end usr/local/lib/ruby/gems/1.9.1/gems/bio-ngs-0.2.1/lib/bio/ngs/
ext/bin/linux/cufflinks/cuffcompare", @options={}, @params={}>
July
15,
2011
BOSC,
Vienna,
Austria

11. Tasks
No
binary
found
with
this
name:
setupBclToQseq.py
biongs
convert:qseq:fastq:samples_by_lane
SAMPLES
LANE
project
No
binary
found
with
this
name:
fastq_quality_boxplot_graph.sh
OUTPUT
-­‐-­‐-­‐-­‐-­‐-­‐-­‐
No
binary
found
with
this
name:
blastn
biongs
project:new
[NAME]
No
binary
found
with
this
name:
blastx
history
biongs
project:update
[TYPE]
WARNING:
no
program
is
associated
with
BCLQSEQ
task,
does
-­‐-­‐-­‐-­‐-­‐-­‐-­‐
not
make
sense
to
create
a
thor
task.
biongs
history:8
#
Task
convert:illumina:de:isoform
quality
WARNING:
no
program
is
associated
with
BLASTN
task,
does
not
PARAMETERS:
/Users/bonnalraoul/Desktop/
make
sense
to
create
a
thor
task.
RRep16giugno/DE_lane1-­‐2-­‐3-­‐4-­‐6-­‐8/DE_lane1-­‐2-­‐3-­‐4-­‐6-­‐8/ -­‐-­‐-­‐-­‐-­‐-­‐-­‐
isoform_exp.diff
/Users/bonnalraoul/Desktop/ biongs
quality:boxplot
FASTQ_QUALITY_STATS
WARNING:
no
program
is
associated
with
BLASTX
task,
does
not
RRep16giugno/COMPARE_lane1-­‐2-­‐3-­‐4-­‐6-­‐8/COMPA...
biongs
quality:fastq_stats
FASTQ
make
sense
to
create
a
thor
task.
biongs
quality:illumina_b_profile_raw
FASTQ
-­‐-­‐read-­‐length=N
bwa
homology
biongs
quality:illumina_b_profile_svg
FASTQ
-­‐-­‐read-­‐length=N
-­‐-­‐-­‐
-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐
biongs
quality:reads
FASTQ
biongs
bwa:aln:long
[FASTQ]
-­‐-­‐file-­‐out=FILE_OUT
-­‐-­‐prefix=PREFIX
biongs
homology:convert:blast2text
[XML
FILE]
-­‐-­‐file-­‐ biongs
quality:reads_coverage
FASTQ_QUALITY_STATS
biongs
bwa:aln:short
[FASTQ]
-­‐-­‐file-­‐out=FILE_OUT
-­‐-­‐ out=FILE_OUT
biongs
quality:scacerplot
EXPR1
EXPR2
OUTPUT
prefix=PREFIX
biongs
homology:convert:go2json
biongs
quality:trim
FASTQ
biongs
bwa:index:long
[FASTA]
biongs
bwa:index:short
[FASTA]
biongs
homology:db:export
[TABLE]
-­‐-­‐fileout=FILEOUT
rna
biongs
bwa:sam:paired
-­‐-­‐fastq=one
two
three
-­‐-­‐file-­‐ biongs
homology:db:init
out=FILE_OUT
-­‐-­‐prefix=PREFIX
-­‐-­‐sai=one
two
three
-­‐-­‐-­‐
biongs
bwa:sam:single
[SAI]
-­‐-­‐fastq=FASTQ
-­‐-­‐file-­‐ biongs
homology:download:all
biongs
rna:compare
GTF_REF
OUTPUTDIR
out=FILE_OUT
-­‐-­‐prefix=PREFIX
biongs
homology:download:goannota(on
GTFS_QUANTIFICATION
biongs
homology:download:uniprot
biongs
rna:idx2fasta
INDEX
FASTA
convert
biongs
homology:load:blast
[FILE]
biongs
rna:mapquant
DIST
INDEX
OUTPUTDIR
FASTQS
-­‐-­‐-­‐-­‐-­‐-­‐-­‐
biongs
homology:load:goa
biongs
rna:quant
GTF
OUTPUTDIR
BAM
biongs
convert:bam:extract_genes
BAM
GENES
-­‐-­‐ensembl-­‐ biongs
homology:report:blast
biongs
rna:tophat
DIST
INDEX
OUTPUTDIR
FASTQS
release=N
-­‐o,
-­‐-­‐output=OUTPUT
biongs
convert:bam:merge
-­‐i,
-­‐-­‐input-­‐bams=one
two
three
ontology
sff
biongs
convert:bam:sort
BAM
[PREFIX]
-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐
-­‐-­‐-­‐
biongs
convert:bcl:qseq:convert
RUN
OUTPUT
[JOBS]
biongs
ontology:db:export
[TABLE]
-­‐-­‐fileout=FILEOUT
biongs
sff:extract
[FILE]
biongs
convert:illumina:de:gene
DIFF
GTF
biongs
ontology:db:init
biongs
convert:illumina:de:isoform
DIFF
GTF
biongs
ontology:download:all
biongs
convert:illumina:de:rename_qs
DIFF_FILE
NAMES
biongs
ontology:download:go
biongs
convert:illumina:fastq:trim_b
FASTQ
biongs
ontology:download:goslim
biongs
convert:illumina:humanize:build_compare_kb
GTF
biongs
ontology:load:genego
[FILE]
biongs
convert:illumina:humanize:isoform_exp
GTF
ISOFORM
biongs
ontology:load:go
[FILE]
biongs
convert:qseq:fastq:by_file
FIRST
OUTPUT
biongs
ontology:report:go
biongs
convert:qseq:fastq:by_lane
LANE
OUTPUT
biongs
convert:qseq:fastq:by_lane_index
LANE
INDEX
OUTPUT
July
15,
2011
BOSC,
Vienna,
Austria

12. N o
B i n a r y
Tasks
Task
disabled
No
binary
found
with
this
name:
setupBclToQseq.py
biongs
convert:qseq:fastq:samples_by_lane
SAMPLES
LANE
project
Keep
OUTPUT
No
binary
found
with
this
name:
fastq_quality_boxplot_graph.sh
No
binary
found
with
this
name:
blastn
-­‐-­‐-­‐-­‐-­‐-­‐-­‐
biongs
project:new
[NAME]
everything
No
binary
found
with
this
name:
blastx
history
biongs
project:update
[TYPE]
WARNING:
no
program
is
associated
with
BCLQSEQ
task,
does
-­‐-­‐-­‐-­‐-­‐-­‐-­‐
not
make
sense
to
create
a
thor
task.
biongs
history:8
#
Task
convert:illumina:de:isoform
organized
quality
WARNING:
no
program
is
associated
with
BLASTN
task,
does
not
PARAMETERS:
/Users/bonnalraoul/Desktop/
make
sense
to
create
a
thor
task.
RRep16giugno/DE_lane1-­‐2-­‐3-­‐4-­‐6-­‐8/DE_lane1-­‐2-­‐3-­‐4-­‐6-­‐8/ -­‐-­‐-­‐-­‐-­‐-­‐-­‐
isoform_exp.diff
/Users/bonnalraoul/Desktop/ biongs
quality:boxplot
FASTQ_QUALITY_STATS
WARNING:
no
program
is
associated
with
BLASTX
task,
does
not
RRep16giugno/COMPARE_lane1-­‐2-­‐3-­‐4-­‐6-­‐8/COMPA...
biongs
quality:fastq_stats
FASTQ
make
sense
to
create
a
thor
task.
biongs
quality:illumina_b_profile_raw
FASTQ
-­‐-­‐read-­‐length=N
bwa
homology
biongs
quality:illumina_b_profile_svg
FASTQ
-­‐-­‐read-­‐length=N
-­‐-­‐-­‐
-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐
biongs
quality:reads
FASTQ
biongs
bwa:aln:long
[FASTQ]
-­‐-­‐file-­‐out=FILE_OUT
-­‐-­‐prefix=PREFIX
biongs
homology:convert:blast2text
[XML
FILE]
-­‐-­‐file-­‐ biongs
quality:reads_coverage
FASTQ_QUALITY_STATS
biongs
bwa:aln:short
[FASTQ]
-­‐-­‐file-­‐out=FILE_OUT
-­‐-­‐ out=FILE_OUT
biongs
quality:scacerplot
EXPR1
EXPR2
OUTPUT
prefix=PREFIX
biongs
bwa:index:long
[FASTA]
biongs
homology:convert:go2json
Repor(ng
biongs
quality:trim
FASTQ
biongs
bwa:index:short
[FASTA]
biongs
bwa:sam:paired
-­‐-­‐fastq=one
two
three
-­‐-­‐file-­‐
Recall
an
biongs
homology:db:export
[TABLE]
-­‐-­‐fileout=FILEOUT
rna
biongs
homology:db:init
-­‐-­‐-­‐
old
out=FILE_OUT
-­‐-­‐prefix=PREFIX
-­‐-­‐sai=one
two
three
biongs
bwa:sam:single
[SAI]
-­‐-­‐fastq=FASTQ
-­‐-­‐file-­‐
out=FILE_OUT
-­‐-­‐prefix=PREFIX
biongs
homology:download:all
biongs
homology:download:goannota(on
biongs
rna:compare
GTF_REF
OUTPUTDIR
GTFS_QUANTIFICATION
convert
analysis
biongs
homology:download:uniprot
biongs
homology:load:blast
[FILE]
biongs
rna:idx2fasta
INDEX
FASTA
biongs
rna:mapquant
DIST
INDEX
OUTPUTDIR
FASTQS
-­‐-­‐-­‐-­‐-­‐-­‐-­‐
biongs
homology:load:goa
biongs
rna:quant
GTF
OUTPUTDIR
BAM
biongs
convert:bam:extract_genes
BAM
GENES
-­‐-­‐ensembl-­‐ biongs
homology:report:blast
biongs
rna:tophat
DIST
INDEX
OUTPUTDIR
FASTQS
release=N
-­‐o,
-­‐-­‐output=OUTPUT
biongs
convert:bam:merge
-­‐i,
-­‐-­‐input-­‐bams=one
two
three
ontology
sff
biongs
convert:bam:sort
BAM
[PREFIX]
-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐
-­‐-­‐-­‐
biongs
convert:bcl:qseq:convert
RUN
OUTPUT
[JOBS]
biongs
ontology:db:export
[TABLE]
-­‐-­‐fileout=FILEOUT
biongs
sff:extract
[FILE]
biongs
convert:illumina:de:gene
DIFF
GTF
biongs
ontology:db:init
biongs
convert:illumina:de:isoform
DIFF
GTF
biongs
ontology:download:all
biongs
convert:illumina:de:rename_qs
DIFF_FILE
NAMES
biongs
ontology:download:go
biongs
convert:illumina:fastq:trim_b
FASTQ
biongs
ontology:download:goslim
biongs
convert:illumina:humanize:build_compare_kb
GTF
biongs
ontology:load:genego
[FILE]
biongs
convert:illumina:humanize:isoform_exp
GTF
ISOFORM
biongs
ontology:load:go
[FILE]
biongs
convert:qseq:fastq:by_file
FIRST
OUTPUT
biongs
convert:qseq:fastq:by_lane
LANE
OUTPUT
biongs
ontology:report:go
Basic
Advanced
biongs
convert:qseq:fastq:by_lane_index
LANE
INDEX
OUTPUT
July
15,
2011
BOSC,
Vienna,
Austria

13. Tasks
class Rna < Thor
desc "mapquant DIST INDEX OUTPUTDIR FASTQS", "map and quantify"
method_option :paired, :type => :boolean, :default => false, :desc => 'Are reads paired? If you chose
this option pass just the basename
of the file without forward/reverse
and .fastq'
def mapquant(dist, index, outputdir, fastqs)
#tophat
invoke :tophat, [dist, index, outputdir, fastqs], :paired=>options.paired
#cufflinks quantification on gtf
invoke :quant, ["#{index}.gtf", File.join(outputdir,"quantification"), File.join(outputdir,"accepted_hits_sort.bam")]
end
…
end
July
15,
2011
BOSC,
Vienna,
Austria

14. Tasks
class Rna < Thor
# you'll end up with 3 accept file, regular, sorted, sorted-indexed
desc "tophat DIST INDEX OUTPUTDIR FASTQS", "run tophat as from command line, default 6 processors and then create a
sorted bam indexed."
method_option :paired, :type => :boolean, :default => false, :desc => 'Are reads paired? If you chose this option pass
just the…’
Bio::Ngs::Tophat.new.thor_task(self, :tophat) do |wrapper, task, dist, index, outputdir, fastqs|
wrapper.params = task.options #merge passed options to the wrapper.
wrapper.params = {"mate-inner-dist"=>dist, "output-dir"=>outputdir, "num-threads"=>6, "solexa1.3-quals"=>true}
fastq_files = task.options[:paired] ? ["#{fastqs}_forward.fastq","#{fastqs}_reverse.fastq"] : ["#{fastqs}"]
wrapper.run :arguments=>[index, fastq_files ].flatten, :separator=>"="
class Rna < Thor
accepted_hits_bam_fn = File.join(outputdir, "accepted_hits.bam")
desc "mapquant DIST INDEX OUTPUTDIR FASTQS", "map and quantify"
method_option :paired, "convert:bam:sort", :default => false, :desc => 'Are reads paired? If you chose
task.invoke :type => :boolean, [accepted_hits_bam_fn] # call the sorting procedure.
end this option pass just the basename
end of the file without forward/reverse
and .fastq'
def mapquant(dist, index, outputdir, fastqs)
#tophat
invoke :tophat, [dist, index, outputdir, fastqs], :paired=>options.paired
#cufflinks quantification on gtf
invoke :quant, ["#{index}.gtf", File.join(outputdir,"quantification"), File.join(outputdir,"accepted_hits_sort.bam")]
end
…
end
July
15,
2011
BOSC,
Vienna,
Austria

15. Tasks
class Rna < Thor
# you'll end up with 3 accept file, regular, sorted, sorted-indexed
desc "tophat DIST INDEX OUTPUTDIR FASTQS", "run tophat as from command line, default 6 processors and then create a
sorted bam indexed."
method_option :paired, :type => :boolean, :default => false, :desc => 'Are reads paired? If you chose this option pass
just the…’
Bio::Ngs::Tophat.new.thor_task(self, :tophat) do |wrapper, task, dist, index, outputdir, fastqs|
wrapper.params = task.options #merge passed options to the wrapper.
wrapper.params = {"mate-inner-dist"=>dist, "output-dir"=>outputdir, "num-threads"=>6, "solexa1.3-quals"=>true}
fastq_files = task.options[:paired] ? ["#{fastqs}_forward.fastq","#{fastqs}_reverse.fastq"] : ["#{fastqs}"]
wrapper.run :arguments=>[index, fastq_files ].flatten, :separator=>"="
class Rna < Thor
accepted_hits_bam_fn = File.join(outputdir, "accepted_hits.bam")
desc "mapquant DIST INDEX OUTPUTDIR FASTQS", "map and quantify"
method_option :paired, "convert:bam:sort", :default => false, :desc => 'Are reads paired? If you chose
task.invoke :type => :boolean, [accepted_hits_bam_fn] # call the sorting procedure.
end this option pass just the basename
end of the file without forward/reverse
and .fastq'
def mapquant(dist, index, outputdir, fastqs)
#tophat
invoke :tophat, [dist, index, outputdir, fastqs], :paired=>options.paired
#cufflinks quantification on gtf
invoke :quant, ["#{index}.gtf", File.join(outputdir,"quantification"), File.join(outputdir,"accepted_hits_sort.bam")]
end
…
end
class Rna < Thor
desc "quant GTF OUTPUTDIR BAM ", "Genes and transcripts quantification"
Bio::Ngs::Cufflinks::Quantification.new.thor_task(self, :quant) do |wrapper, task, gtf, outputdir, bam|
wrapper.params = task.options
wrapper.params = {"num-threads" => 6, "output-dir" => outputdir, "GTF" => gtf }
wrapper.run :arguments=>[bam], :separator => "="
end
end
July
15,
2011
BOSC,
Vienna,
Austria

16. Next?
• Support
more
soOware,
not
only
NGS
• Wrap
EMBOSS
on
the
fly
reading
acd
files
• Tune
according
to
hardware
• Share
tasks
– Thor
&
Rake
• Improve
JRuby
compa(bility
• Contributes
• Scalability
– Cloud
?
BioLinux
– BioHub:
distribute
tasks
using
messaging
• Ac(veMQ
• Stomp
• Ac(veMessaging
• Adapters
for
Queuing
Systems
July
15,
2011
BOSC,
Vienna,
Austria

17. Next?
• Support
more
soOware,
not
only
NGS
• Wrap
EMBOSS
on
the
fly
reading
acd
files
• Tune
according
to
hardware
• Share
tasks
– Thor
&
Rake
• Improve
JRuby
compa(bility
• Contributes
• Scalability
– Cloud
?
BioLinux
– BioHub:
distribute
tasks
using
messaging
• Ac(veMQ
• Stomp
• Ac(veMessaging
• Adapters
for
Queuing
Systems
July
15,
2011
BOSC,
Vienna,
Austria

18. Acknowledgments
Serena
Cur(
Francesco
Strozzi1,3
Groningen
Bioinforma(cs
Centre
Debora
Mascheroni
Pjotr
Prins2
Alessandra
Stella
Valeria
Parente
Valeria
Ranzani1
Anna
Ripamon(
Grazisa
Rossez
Riccardo
L.
Rossi
Laboratory
of
Genome
Database
Dan
MacLean
4
Roberto
Sciarreca
Toshiaki
Katayama1,2
The
Genome
Analysis
Centre
Ricardo
Ramirez-­‐Gonzalez
4
Massimiliano
Pagani
1
bio-­‐ngs,
2
bio-­‐gem,
3
bio-­‐bwa,
4
bio-­‐samtools
July
15,
2011
BOSC,
Vienna,
Austria

19. Ques(ons
?
INFO
E-­‐mail:
bonnal@ingm.org
/
r@bioruby.org
Dev
:
hcp://github/helios/bioruby-­‐ngs
Docs
:
hcps://github.com/helios/bioruby-­‐ngs/blob/master/README.rdoc
Wiki
:
hcp://bioruby.open-­‐bio.org/wiki/Next_Genera(on_Sequencing
BioRuby-­‐ML:
hcp://lists.open-­‐bio.org/mailman/lis(nfo/bioruby
Irc:
#bioruby
(
irc.freenode.org
)
July
15,
2011
BOSC,
Vienna,
Austria