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Col
labo
rati
ng w
ith
com
pute
r sc
ient
ists
, inf
orm
atic
ists
*, a
nd
soft
war
e de
velo
pers
for
Int
egra
ted
Eco
syst
em A
sses
smen
tsP
eter
Fox
1 ; H
eidi
Sos
ik, S
tace
Bea
ulie
u (s
tace
@w
hoi.e
du),
and
Jose
ph F
utre
lle 2 ;
Dav
id M
ark
Wel
ch 3 ;
Jon
Har
e an
d M
icha
el F
ogar
ty 4
1 Te
ther
less
Wor
ld C
onst
ella
tion
(TW
C),
Ren
ssel
aer P
olyt
echn
ic In
stitu
te; 2
Woo
ds H
ole
Oce
anog
raph
ic In
stitu
tion;
3 M
arin
e B
iolo
gica
l Lab
orat
ory;
4 N
orth
east
Fis
herie
s S
cien
ce C
ente
r
EC
O-O
P U
se C
ase:
Eco
syst
em S
tatu
s R
epor
t
Out
com
es
EC
O-O
P U
se C
ase:
Link
ed D
ata
Pro
vena
nce
Out
com
es•
Ext
ende
d th
e P
RO
V O
ntol
ogy
for c
aptu
ring
prov
enan
ce in
the
IPyt
hon
Not
eboo
k, a
sof
twar
e pl
atfo
rm th
at e
nabl
es tr
ansp
aren
t wor
kflo
ws
http
s://g
ithub
.com
/teth
erle
ss-w
orld
/eco
op/tr
ee/m
aste
r/pro
v•
App
lied
the
prov
-eco
op o
ntol
ogy
to c
ase
stud
ies
that
incl
uded
the
Clim
ate
Forc
ing
Cha
pter
, a re
gion
al m
ap o
f prim
ary
prod
uctio
n, a
nd a
fish
erie
s in
dica
tor i
n th
e E
cosy
stem
Sta
tus
Rep
ort
•B
ook
chap
ter i
n pr
ess
for O
cean
ogra
phic
and
Mar
ine
Cro
ss-D
omai
n D
ata
Man
agem
ent f
or S
usta
inab
le D
evel
opm
ent:
Doc
umen
ting
prov
enan
ce fo
r rep
rodu
cibl
e m
arin
e ec
osys
tem
ass
essm
ent
in o
pen
scie
nce
Mar
ine
Bio
dive
rsit
y V
irtu
al
Labo
rato
ry (
MB
VL)
Wor
k in
Pro
gres
s•
Pro
ject
web
site
: http
s://t
w.rp
i.edu
//web
/pro
ject
/MB
VL/
•Fo
cusi
ng o
n O
bjec
tives
1, 2
, and
4 in
this
firs
t yea
r:1)
dev
elop
ing
data
acc
ess
and
com
puta
tiona
l inf
rast
ruct
ure
for t
he M
BV
L;2)
gen
erat
ing
deriv
ed d
ata
prod
ucts
;4)
pro
duci
ng tr
acea
ble
prod
uct w
orkf
low
s.
•W
e w
ill w
ork
this
sum
mer
with
Mat
thew
Bal
l, un
derg
radu
ate
stud
ent i
n co
mpu
ter s
cien
ces
from
Bow
ie S
tate
Uni
vers
ity, i
n th
e P
EP
prog
ram
.
Mor
e te
am m
embe
rs: X
. Ma,
L. F
u 1
Mor
e te
am m
embe
rs: B
. Lee
, S. Z
edni
k 1 ;
A. S
hipu
nova
, A. V
oorh
is 3
Mor
e te
am m
embe
rs: M
. Di S
tefa
no, P
. Wes
t 1;A
. Maf
fei 2
; G. D
ePip
er,
K. F
riedl
and,
S. G
aich
as, K
. Hyd
e, R
. Gam
ble,
M. J
ones
, S. L
ucey
4
The
EC
O-O
P an
d M
BV
L pr
ojec
ts w
ere
fund
ed b
y th
e U
.S. N
atio
nal S
cien
ce F
ound
atio
n, g
rant
num
bers
095
5649
and
153
9256
, res
pect
ivel
y.
•A
pilo
t tow
ard
end-
to-e
nd tr
ansp
aren
cy fr
om s
cien
tists
’ des
ks to
a re
port
prov
ided
to p
olic
y m
aker
s an
d th
e pu
blic
, im
porta
nt fo
r sci
ence
-bas
ed
deci
sion
mak
ing.
•P
roto
type
ena
bled
an
exec
utab
le w
orkf
low
for t
he p
rodu
ctio
n of
a
colla
bora
tive,
mul
tidis
cipl
inar
y re
port
with
ver
y he
tero
gene
ous
data
type
s ht
tps:
//gith
ub.c
om/te
ther
less
-wor
ld/e
coop
/tree
/mas
ter/p
yeco
op•
Sm
all t
eam
with
com
pute
r sci
entis
ts a
nd IT
spe
cial
ists
wor
king
dire
ctly
with
fis
herie
s sc
ient
ists
led
to ra
pid
resu
lts, w
ith a
lim
iting
fact
or b
eing
suf
ficie
nt
train
ing
for a
dopt
ion
of te
chno
logi
es b
y th
e la
rger
gro
up o
f dom
ain
scie
ntis
ts.
•M
anus
crip
t und
er re
view
in E
arth
Sci
ence
Info
rmat
ics:
Tow
ard
cybe
rinfr
astr
uctu
re to
faci
litat
e co
llabo
ratio
n an
d re
prod
ucib
ility
fo
r mar
ine
Inte
grat
ed E
cosy
stem
Ass
essm
ents
Our
sol
utio
n fo
r sh
arin
g w
orkf
low
s an
d de
liver
ing
repr
oduc
ible
do
cum
ents
:
ECO
-OP:
An
abbr
evia
tion
of E
CO
syst
em a
nd in
terO
Pera
bilit
yG
oal:
to d
evel
op a
nd d
eplo
y a
softw
are
envi
ronm
ent t
o ge
nera
te a
po
rtion
of t
he E
cosy
stem
Sta
tus
Rep
ort f
or th
e N
orth
east
U.S
. Con
tinen
tal
She
lf La
rge
Mar
ine
Eco
syst
em, r
etai
ning
trac
eabi
lity
of d
eriv
ed d
atas
ets
incl
udin
g in
dica
tors
of p
hysi
cal p
ress
ures
and
eco
syst
em s
tate
s.
How
can
we
gene
raliz
e ou
r wor
kflo
ws
for b
iodi
vers
ity?
* Wha
t is
an in
form
atic
ist?
One
can
thin
k of
info
rmat
ics
as th
e st
eps
and
skill
s in
volv
ed to
mak
e se
nse
out o
f dat
a –
som
e of
this
is d
omai
n-sp
ecifi
c (s
cien
tists
ar
e in
form
atic
ists
in th
eir d
omai
ns),
and
som
e of
this
is g
ener
al to
info
rmat
ion
proc
essi
ng o
r to
the
engi
neer
ing
of in
form
atio
n sy
stem
s.
Take
sam
ple
from
en
viro
nmen
t
Ext
ract
sub
set o
f or
gani
sms
from
sam
ple
Mea
sure
attr
ibut
es fo
r th
e sa
mpl
ed o
rgan
ism
s
Cla
ssify
the
orga
nism
s in
to c
ateg
orie
s
Det
erm
ine
the
num
ber
of c
lass
ified
org
anis
ms
in e
ach
cate
gory
VAM
PS: V
isua
lizat
ion
and
Ana
lysi
s of
Mic
robi
al
Pop
ulat
ion
Stru
ctur
esht
tps:
//vam
ps.m
bl.e
du/
IFC
B:
Imag
ing
Flow
Cyt
oBot
http
://ifc
b-da
ta.w
hoi.e
du/
Goa
l: Th
is re
sear
ch e
ffort
brin
gs to
geth
er c
ompu
tatio
nal a
nd in
form
atio
n sc
ient
ists
, oce
anog
raph
ers
and
mic
robi
olog
ists
to d
evel
op a
Mar
ine
Bio
dive
rsity
Virt
ual L
abor
ator
y (M
BV
L) to
add
ress
mul
ti-sc
ale,
he
tero
gene
ous
data
cha
lleng
es w
ith in
form
atic
s so
lutio
ns th
at e
nabl
e th
e cy
ber-
gene
ratio
n an
d do
cum
enta
tion
of b
iodi
vers
ity in
dica
tors
, pro
vidi
ng th
e tra
ceab
ility
bet
wee
n da
ta a
nd in
form
atio
n to
be
used
as
a ba
sis
for
sust
aina
ble
ecos
yste
m-b
ased
man
agem
ent a
nd n
eede
d po
licy
deci
sion
s.
Cur
rent
em
phas
is o
n lo
wer
trop
hic
leve
ls
Goa
l: to
pro
vide
sta
ndar
dize
d pr
oven
ance
as
met
adat
a fo
r dat
a pr
oduc
ts,
so th
at a
hum
an (a
nd, u
ltim
atel
y, in
the
futu
re, a
mac
hine
) cou
ld tr
ace
back
to
the
sour
ce o
bser
vatio
nal d
ata
and
mod
els
used
to c
ompi
le a
n in
dica
tor.
For t
he c
omm
unity
sta
ndar
d, w
e ch
ose
the
PR
OV
Ont
olog
y fo
r rep
rese
ntin
g an
d ex
chan
ging
pro
vena
nce
info
rmat
ion
as L
inke
d D
ata
in th
e S
eman
tic W
eb.
Dia
gram
for t
he th
ree
top
clas
ses
in P
RO
V-O
and
the
prop
ertie
s th
at re
late
them
.
Pro
pose
d im
plem
enta
tion
of a
w
orkf
low
usi
ng IP
ytho
n N
oteb
ook
to g
ener
ate
a fis
herie
s in
dica
tor.
Ent
ities
: 1 IP
ytho
n N
oteb
ook;
2
Cel
l; 3
Dat
aset
s; 4
scr
ipt
writ
ten
in o
ther
pro
gram
min
g la
ngua
ge (R
) tha
t was
spl
it in
to fi
ve C
ells
; 5 o
ther
so
ftwar
e en
viro
nmen
ts.
Four
diff
eren
t age
nts
are
iden
tifie
d as
con
tribu
ting
sour
ce d
atas
ets.
Act
iviti
es: 1
Cel
lRun
; 2 o
ther
ac
tiviti
es p
erfo
rmed
in o
ther
so
ftwar
e en
viro
nmen
ts.
Dia
gram
for T
WC
M
etho
dolo
gy.
The
use
case
def
ines
the
inte
ract
ions
bet
wee
n pe
ople
, ha
rdw
are,
sof
twar
e, a
nd
desi
red
prod
ucts
and
can
be
adju
sted
or r
efin
ed a
fter
each
iter
atio
n of
the
cycl
e.
PD
F of
Clim
ate
Forc
ing
Cha
pter
IPyt
hon
(now
Jup
yter
) N
oteb
ook
Recommended