<s>
A	O
scientific	B-Application
workflow	I-Application
system	I-Application
is	O
a	O
specialized	O
form	O
of	O
a	O
workflow	B-Operating_System
management	O
system	O
designed	O
specifically	O
to	O
compose	O
and	O
execute	O
a	O
series	O
of	O
computational	O
or	O
data	O
manipulation	O
steps	O
,	O
or	O
workflow	B-Operating_System
,	O
in	O
a	O
scientific	O
application	O
.	O
</s>
<s>
Scientific	B-Application
workflow	I-Application
systems	I-Application
play	O
an	O
important	O
role	O
in	O
enabling	O
this	O
vision	O
.	O
</s>
<s>
More	O
specialized	O
scientific	B-Application
workflow	I-Application
systems	I-Application
provide	O
a	O
visual	O
programming	O
front	O
end	O
enabling	O
users	O
to	O
easily	O
construct	O
their	O
applications	O
as	O
a	O
visual	O
graph	O
by	O
connecting	O
nodes	O
together	O
,	O
and	O
tools	O
have	O
also	O
been	O
developed	O
to	O
build	O
such	O
applications	O
in	O
a	O
platform-independent	O
manner	O
.	O
</s>
<s>
Each	O
directed	O
edge	O
in	O
the	O
graph	O
of	O
a	O
workflow	B-Operating_System
typically	O
represents	O
a	O
connection	O
from	O
the	O
output	O
of	O
one	O
application	O
to	O
the	O
input	O
of	O
the	O
next	O
.	O
</s>
<s>
A	O
sequence	O
of	O
such	O
edges	O
may	O
be	O
called	O
a	O
pipeline	B-General_Concept
.	O
</s>
<s>
A	O
bioinformatics	B-Application
workflow	I-Application
management	I-Application
system	I-Application
is	O
a	O
specialized	O
scientific	B-Application
workflow	I-Application
system	I-Application
focused	O
on	O
bioinformatics	O
.	O
</s>
<s>
The	O
simplest	O
computerized	O
scientific	O
workflows	B-Operating_System
are	O
scripts	O
that	O
call	O
in	O
data	O
,	O
programs	O
,	O
and	O
other	O
inputs	O
and	O
produce	O
outputs	O
that	O
might	O
include	O
visualizations	O
and	O
analytical	O
results	O
.	O
</s>
<s>
These	O
may	O
be	O
implemented	O
in	O
programs	O
such	O
as	O
R	B-Language
or	O
MATLAB	B-Language
,	O
using	O
a	O
scripting	O
language	O
such	O
as	O
Python	B-Language
with	O
a	O
command-line	B-Application
interface	I-Application
,	O
or	O
more	O
recently	O
using	O
open-source	O
web	O
applications	O
such	O
as	O
Jupyter	O
Notebook	O
.	O
</s>
<s>
There	O
are	O
many	O
motives	O
for	O
differentiating	O
scientific	O
workflows	B-Operating_System
from	O
traditional	O
business	O
process	O
workflows	B-Operating_System
.	O
</s>
<s>
providing	O
an	O
easy-to-use	O
environment	O
for	O
individual	O
application	O
scientists	O
themselves	O
to	O
create	O
their	O
own	O
workflows	B-Operating_System
.	O
</s>
<s>
providing	O
interactive	O
tools	O
for	O
the	O
scientists	O
enabling	O
them	O
to	O
execute	O
their	O
workflows	B-Operating_System
and	O
view	O
their	O
results	O
in	O
real-time	O
.	O
</s>
<s>
simplifying	O
the	O
process	O
of	O
sharing	O
and	O
reusing	O
workflows	B-Operating_System
between	O
the	O
scientists	O
.	O
</s>
<s>
enabling	O
scientists	O
to	O
track	O
the	O
provenance	O
of	O
the	O
workflow	B-Operating_System
execution	O
results	O
and	O
the	O
workflow	B-Operating_System
creation	O
steps	O
.	O
</s>
<s>
Scientific	O
workflows	B-Operating_System
are	O
now	O
recognized	O
as	O
a	O
crucial	O
element	O
of	O
the	O
cyberinfrastructure	O
,	O
facilitating	O
e-Science	O
.	O
</s>
<s>
Typically	O
sitting	O
on	O
top	O
of	O
a	O
middleware	B-General_Concept
layer	O
,	O
scientific	O
workflows	B-Operating_System
are	O
a	O
means	O
by	O
which	O
scientists	O
can	O
model	O
,	O
design	O
,	O
execute	O
,	O
debug	O
,	O
re-configure	O
,	O
and	O
re-run	O
their	O
analysis	O
and	O
visualization	O
pipelines	B-General_Concept
.	O
</s>
<s>
It	O
is	O
the	O
same	O
in	O
e-Science	O
,	O
except	O
provenance	O
data	O
are	O
a	O
record	O
of	O
the	O
workflow	B-Operating_System
activities	O
invoked	O
,	O
services	O
and	O
databases	O
accessed	O
,	O
data	O
sets	O
used	O
,	O
and	O
so	O
forth	O
.	O
</s>
<s>
Such	O
information	O
is	O
useful	O
for	O
a	O
scientist	O
to	O
interpret	O
their	O
workflow	B-Operating_System
results	O
and	O
for	O
other	O
scientists	O
to	O
establish	O
trust	O
in	O
the	O
experimental	O
result	O
.	O
</s>
<s>
Social	O
networking	O
communities	O
such	O
as	O
myExperiment	O
have	O
been	O
developed	O
to	O
facilitate	O
sharing	O
and	O
collaborative	O
development	O
of	O
scientific	O
workflows	B-Operating_System
.	O
</s>
<s>
Galaxy	B-Application
provide	O
collaborative	O
mechanisms	O
for	O
editing	O
and	O
publication	O
of	O
workflow	B-Operating_System
definitions	O
and	O
workflow	B-Operating_System
results	O
directly	O
on	O
the	O
Galaxy	B-Application
installation	O
.	O
</s>
<s>
A	O
key	O
assumption	O
underlying	O
all	O
scientific	B-Application
workflow	I-Application
systems	I-Application
is	O
that	O
the	O
scientists	O
themselves	O
will	O
be	O
able	O
to	O
use	O
a	O
workflow	B-Operating_System
system	O
to	O
develop	O
their	O
applications	O
based	O
on	O
visual	O
flowcharting	O
,	O
logic	O
diagramming	O
,	O
or	O
,	O
as	O
a	O
last	O
resort	O
,	O
writing	O
code	O
to	O
describe	O
the	O
workflow	B-Operating_System
logic	O
.	O
</s>
<s>
Powerful	O
workflow	B-Operating_System
systems	O
make	O
it	O
easy	O
for	O
non-programmers	O
to	O
first	O
sketch	O
out	O
workflow	B-Operating_System
steps	O
using	O
simple	O
flowcharting	O
tools	O
,	O
and	O
then	O
hook	O
in	O
various	O
data	O
acquisition	O
,	O
analysis	O
,	O
and	O
reporting	O
tools	O
.	O
</s>
<s>
Workflow	B-Operating_System
analysis	O
techniques	O
can	O
be	O
used	O
to	O
analyze	O
the	O
properties	O
of	O
such	O
workflows	B-Operating_System
to	O
verify	O
certain	O
properties	O
before	O
executing	O
them	O
.	O
</s>
<s>
An	O
example	O
of	O
a	O
theoretical	O
formal	O
analysis	O
framework	O
for	O
the	O
verification	O
and	O
profiling	O
of	O
the	O
control-flow	O
aspects	O
of	O
scientific	O
workflows	B-Operating_System
and	O
their	O
data	O
flow	O
aspects	O
for	O
the	O
Discovery	O
Net	O
system	O
is	O
described	O
in	O
the	O
paper	O
,	O
"	O
The	O
design	O
and	O
implementation	O
of	O
a	O
workflow	B-Operating_System
analysis	O
tool	O
"	O
by	O
Curcin	O
et	O
al	O
.	O
</s>
<s>
The	O
authors	O
note	O
that	O
introducing	O
program	O
analysis	O
and	O
verification	O
into	O
the	O
workflow	B-Operating_System
world	O
requires	O
detailed	O
understanding	O
of	O
execution	O
semantics	O
of	O
workflow	B-Operating_System
language	O
,	O
including	O
execution	O
properties	O
of	O
nodes	O
and	O
arcs	O
in	O
the	O
workflow	B-Operating_System
graph	O
,	O
understanding	O
functional	B-Language
equivalencies	O
between	O
workflow	B-Operating_System
patterns	O
,	O
and	O
many	O
other	O
issues	O
.	O
</s>
<s>
Petri	B-Operating_System
nets	I-Operating_System
)	O
and	O
building	O
on	O
these	O
formal	O
methods	O
to	O
develop	O
user-level	O
tools	O
to	O
reason	O
about	O
the	O
properties	O
of	O
both	O
workflows	B-Operating_System
and	O
workflow	B-Operating_System
systems	O
.	O
</s>
<s>
The	O
lack	O
of	O
such	O
tools	O
in	O
the	O
past	O
stopped	O
automated	O
workflow	B-Operating_System
management	O
solutions	O
from	O
maturing	O
from	O
nice-to-have	O
academic	O
toys	O
to	O
production-level	O
tools	O
used	O
outside	O
the	O
narrow	O
circle	O
of	O
early	O
adopters	O
and	O
workflow	B-Operating_System
enthusiasts	O
.	O
</s>
<s>
Notable	O
scientific	B-Application
workflow	I-Application
systems	I-Application
include	O
:	O
</s>
<s>
Bioclipse	B-Language
,	O
a	O
graphical	O
workbench	O
,	O
with	O
a	O
scripting	O
environment	O
that	O
lets	O
you	O
perform	O
complex	O
actions	O
as	O
a	O
kind	O
of	O
workflow	B-Operating_System
.	O
</s>
<s>
Common	O
Workflow	B-Operating_System
Language	O
,	O
a	O
community-developed	O
YAML-based	O
workflow	B-Operating_System
language	O
,	O
supported	O
by	O
multiple	O
engine	O
implementations	O
.	O
</s>
<s>
Cuneiform	B-Language
,	O
a	O
functional	B-Language
workflow	B-Operating_System
language	O
.	O
</s>
<s>
GenePattern	O
,	O
a	O
powerful	O
scientific	B-Application
workflow	I-Application
system	I-Application
that	O
provides	O
access	O
to	O
hundreds	O
of	O
genomic	O
analysis	O
tools	O
.	O
</s>
<s>
Swift	B-Language
parallel	I-Language
scripting	I-Language
language	I-Language
,	O
a	O
scripting	O
language	O
with	O
many	O
of	O
the	O
capabilities	O
of	O
scientific	B-Application
workflow	I-Application
systems	I-Application
built-in	O
.	O
</s>
<s>
More	O
than	O
280	O
computational	O
data	O
analysis	O
workflow	B-Operating_System
systems	O
have	O
been	O
identified	O
,	O
although	O
the	O
distinction	O
between	O
data	O
analysis	O
workflows	B-Operating_System
and	O
scientific	O
workflows	B-Operating_System
is	O
fluid	O
,	O
as	O
not	O
all	O
analysis	O
workflow	B-Operating_System
systems	O
are	O
used	O
for	O
scientific	O
purposes	O
.	O
</s>
