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A presentation given by Dave Roberts and coauthored by David King, Simon Rycroft, David Morse, Lyubomir Penev, Donat Agosti & Vince Smith. This was given at the Fourth Metadata and Semantics Research Conference (MTSR 2010) at Acala de Henares, Madrid, in the premises of the Faculty of Law.
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The cost of sequencing a genome has been dramatically reduced by several orders of magnitude in the last decade, and the natural consequence is that more and more researchers are sequencing more and more new genomes, both within populations and across species. Because individual researchers can now readily sequence many genomes of interest, the need for a universally accessible genomic curation tool logically follows. Each new exome or genome sequenced requires visualization and curation to obtain biologically accurate genomic features sets, even for limited set of genes, because computational genome analysis remains an imperfect art. Additionally, unlike earlier genome projects, which had the advantage of more highly polished genomes, recent projects usually have lower coverage. Therefore researchers now face additional work correcting for more frequent assembly errors and annotating genes split across multiple contigs.
Genome annotation is an inherently collaborative task; researchers only very rarely work in isolation, turning to colleagues for second opinions and insights from those with with expertise in particular domains and gene families. The new JavaScript based Apollo, allows researchers real-time interactivity, breaking down large amounts of data into manageable portions to mobilize groups of researchers with shared interests. We are also focused on training the next generation of researchers by reaching out to educators to make these tools available as part of curricula via workshops and webinars, and through widely applied systems such as iPlant and DNA Subway. Here we offer details of our progress.
Presentation at Genome Informatics, Session (3) on Databases, Data Mining, Visualization, Ontologies and Curation.
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The cost of sequencing a genome has been dramatically reduced by several orders of magnitude in the last decade, and the natural consequence is that more and more researchers are sequencing more and more new genomes, both within populations and across species. Because individual researchers can now readily sequence many genomes of interest, the need for a universally accessible genomic curation tool logically follows. Each new exome or genome sequenced requires visualization and curation to obtain biologically accurate genomic features sets, even for limited set of genes, because computational genome analysis remains an imperfect art. Additionally, unlike earlier genome projects, which had the advantage of more highly polished genomes, recent projects usually have lower coverage. Therefore researchers now face additional work correcting for more frequent assembly errors and annotating genes split across multiple contigs.
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Telecommunication Networks and integrated Services (TNS) Living LabProf. P. Demestichas, Dr K. Tsagkaris, Dr G. Athanasiou, Dr Y. Kritikou, ENoLL 5th Wave, May 16th 2011.
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1. EVO:
Remote
Par.cipa.on
for
LIGO
and
the
LIGO
Scien.fic
Collabora.on
Kent
Blackburn
(LIGO/Caltech),
Nelson
Christensen
(LSC/Carlton
College),
Harvey
Newman
(EVO/Caltech),
Philippe
Galvez
(EVO/Caltech)
Na.onal
Science
Founda.on
STCI/SDCI
PI
Mee.ng
Arlington
Virginia,
January
28th
&
29th,
2010
LIGO
&
The
LIGO
Scien.fic
Collabora.on
Remote
Par.cipa.on
for
LIGO
and
the
LSC
EVO:
Enabling
Virtual
Organiza.ons
The
search
for
gravita.onal
waves
has
become
a
world-‐wide
effort,
with
scien-sts
in
LIGO’s
Scien-fic
Mission
is
to
directly
detect
constant
communica-on
with
each
other.
LIGO
and
Virgo
hold
four
joint
collabora-on
A
unique
global-‐scale
collabora-ve
system,
the
oscilla-ons
of
space-‐-me
as
predicted
by
mee-ngs
per
year:
two
in
the
United
States
and
two
in
Europe.
These
collabora-on
with
an
underlying
autonomous
infrastructure,
Einstein’s
General
Theory
of
Rela-vity
known
gatherings
have
a
number
of
satellite
sessions
before
and
aher,
such
as
the
face-‐to-‐face
integra-ng
across
the
full
range
of
working
as
gravita-onal
waves,
which
are
produced
by
mee-ngs
of
the
four
different
search
groups
(looking
for
signals
with
burst-‐like
environments,
from
the
desktop/laptop
to
some
of
the
most
energe-c
events
in
the
signatures,
those
due
to
binary
inspirals,
pulsars,
and
from
possible
sources
of
stochas-c
mee-ng
rooms,
control
rooms
&
auditoria;
universe,
and
in
the
same
frequency
range
as
backgrounds).
Recently
the
LSC
and
Virgo
have
made
a
concerted
effort
to
provide
the
supported
on
all
popular
opera-ng
systems
&
human
hearing,
but
they’re
not
sound
waves.
means
by
which
scien-sts
can
watch
and
par-cipate
in
mee-ngs
without
actually
having
protocols,
base
on
over
ten
year
of
experience.
to
travel
to
the
physical
loca-on.
The
LSC
and
Virgo
are
now
using
EVO
as
their
preferred
technology
for
high-‐quality
teleconferencing.
EVO
was
developed
ini-ally
for
use
in
high
EVO
Features:
energy
physics
collabora-ons.
Numerous
scien-fic
and
academic
organiza-ons
use
EVO;
• EVO
GUI
is
available
in
11
languages
the
LSC-‐Virgo
community
is
now
the
fourth
largest
on
EVO;
the
LSC's
use
of
EVO
will
• Deals
with
all
-me
zones
con-nue
to
grow.
Collabora-on
members
need
not
physically
travel
to
a
mee-ng
in
• Works
on
MS
Windows,
Mac
OS
X,
Linux
order
to
join
in;
the
goal
of
the
technology
is
to
allow
the
full
par-cipa-on
in
the
• Connects
to
H.323
client,
H.323
MCU,
SIP
sessions
from
afar.
In
the
near
future
EVO
will
be
obligated
to
require
a
contribu-on
client,
SIP
MCU,
IP
telephone,
standard
from
LIGO
and
the
LSC.
The
aim
of
this
NSF
Award
is
to
fund
contribu-on
to
EVO's
telephone
Compact
Binary
(Black
Holes,
Neutron
Stars)
Coalescence
Periodic
(Pulsar)
Sources
support
and
con-nuing
development
of
remote
par-cipa-on
technology,
and
pave
the
• Works
on
Unicast
and
Mul-cast
way
for
our
collabora-on's
use
of
this
service.
• Accepts
4CIF,
CIF,
VGA,
4CIF,
720p,
1080i,
1080p
resolu-ons
• Deals
with
IPv4
and
IPv6
EVO
provides
unique
End-‐to-‐End,
self
Unmodeled
Bursts
(Supernovae)
Gravitational
Stochastic
(Big
Bang)
Background
managed
and
secure
infrastructure
for
collabora-on;
Integra-ng
with
all
LIGO
has
two
observatory
sites
located
work
environments,
protocols
and
in
Hanford,
Washington
and
Livingston,
conferencing
systems,
as
well
as
Louisiana,
approximately
3000
km
apart.
other
collabora-ve
tools.
Content
is
• L-‐shaped
arms
4
km
long
on
each
side
ranges
cover
audio,
video,
chat,
house
its
sensi-ve
interferometer.
desktop
sharing,
recording
and
• Beam
tubes
as
long
has
the
arms
playback.
provide
the
largest
high
vacuum
system
on
the
Earth’s
surface
to
reduce
scaOer.
• LIGO
is
able
to
measure
length
changes
of
one-‐thousandth
the
size
of
a
proton
over
these
4
km
distance.
• Operates
a
Data
and
Compu-ng
Grid
in
collabora-on
with
the
LSC.
• Instrumenta-on
records
roughly
one
LIGO
and
Virgo
see
the
extremely
posi.ve
broader
impacts
of
developing
and
using
and
a
quarter
Terabytes
per
day.
remote
par.cipa.on
technology.
Ul-mately
there
will
be
considerable
cost
savings
for
• Funded
by
Na-onal
Science
Founda-on
mul-ple
groups
within
our
collabora-on.
By
providing
remote
access
to
mee-ngs
the
collabora-on
becomes
more
inclusive;
small
groups,
students,
those
with
limited
The
LIGO
Scien-fic
Collabora-on
(LSC)
has
funding,
and
others
with
difficulty
traveling
are
able
to
fully
join
in
on
all
important
776
people
at
70
ins-tu-ons
and
13
discussions
and
presenta-ons.
It
is
quite
rare
for
undergraduates
or
new
graduate
countries
worldwide
as
of
December
2009.
students
to
travel
to
these
collabora-on
mee-ngs,
but
this
remote
par-cipa-on
will
The
LSC
establishes
overall
data
analysis
bring
the
collabora-ons
comprehensive
research
right
to
their
desk
top.
In
this
age
of
strategy,
goals,
-melines,
carries
out
data
concern
for
the
environment
and
carbon
footprints
it
is
clear
that
reducing
air
travel
is
a
analysis
program
iden-fies
priori-es
for
posi-ve
impact
of
remote
par-cipa-on
in
collabora-on
mee-ngs.
This
technology
also
R&D,
outreach
program
to
communicate
promotes
good
interna-onal
rela-onships
by
bringing
together
scien-sts
from
around
LIGO’s
ac-vi-es
and
goals
to
the
public,
the
world
and
their
work.
disseminates
the
results
of
the
data
analysis
program,
the
R&D
program
par-cipates
in
LHC
(CMS,
ATLAS,
LHCb
,
ALICE)
Usage
in
2009:
LIGO
Usage
in
2009:
Key
Architectural
Features:
• Users:
6000
• Users:
600
the
scien-fic
opera-ons
of
the
LIGO
and
• Dynamic
auto-‐registra-on
to
high
level
directory
services
to
provide
a
global
• Mee-ngs:
14,500
• Mee-ngs:
1030
evaluates
progress
of
R&D
and
analyses,
• Phone
Connec-ons:
10,100
• Phone
Connec-ons:
900
infrastructure
view.
making
necessary
adjustments.
• Total
Dura-on
for
all
par-cipants:
132,500
hours
• Total
Dura-on
for
all
par-cipants:
10,300
hours
• Automa-c
Alarm
no-fica-ons
when
monitored
parameters
(system
or
network)
go
outside
preset
bounds.
During
the
last
year
the
LSC
and
Virgo
made
a
concerted
effort
to
provide
the
means
• Automa-c
Re-‐ac-va-on
of
components
and
services.
LIGO-‐LHO
LIGO-‐LLO
by
which
scien.sts
can
watch,
listen,
and
ac.vely
par.cipate
in
mee.ngs
without
• Con-nuous
Monitoring
of
network
quality
(packet
loss,
jiOer,
latency)
between
its
having
to
travel
to
the
physical
loca.on.
There
are
a
number
of
reasons
why
the
peers
and
its
possible
peers
(short
list).
collabora-ons
are
doing
this.
The
cost
of
travel
to
an
increasing
frequency
of
mee-ngs
is
• Automa-c
Rerou-ng
for
the
best
performance/quality.
large;
there
is
a
strain
on
the
travel
budgets
of
all
groups.
Small
groups
within
the
LSC
• Dynamics
Services
(video,
audio,
screen
content,
data,
...)
VIRGO
GEO
have
had
chronic
difficulty
in
aOending
mee-ngs
as
their
budgets
are
par-cularly
that
matches
current
resources/capabili-es
of
the
end-‐client
machines
and
limited.
Mee-ngs
that
take
place
during
the
academic
year
can
be
impossible
to
aOend
applica-ons.
for
some
students
and
professors.
By
providing
the
means
to
remotely
par-cipate
the
• Encryp-on
among
the
core
nodes
(Pandas)
and
between
each
node
and
its
clients
en-re
collabora-on
can
ac-vely
contribute
to
the
mee-ngs.
The
remote
par-cipa-on
(Panda
⌠
Koalas)
TAMA
AIGA
opportuni-es
create
a
good
synergy,
and
make
the
work
of
the
collabora-on
both
more
• Access
to
real-‐-me
and
historical
monitoring
data;
effec-ve
and
economically
beneficial.
Developing
the
means
to
collaborate
successfully
extensive
drill-‐down
capability
while
reducing
the
resul-ng
pollu-on
footprint
is
a
priority.
In
2008,
a
remote
par-cipa-on
working
group
was
established
by
the
LSC
and
Virgo.
Aher
inves-ga-ng
a
Cost
Effec.ve
EVO
High
Defini.on
Setup
number
of
possible
internet
and
telephone
based
conferencing
op-ons,
the
choice
was
made
to
use
EVO.
The
EVO
client
uses
Java,
and
is
cross-‐plamorm
(Windows,
MacOS,
AEI
Hannover
Linux)
compa-ble.
EVO
was
developed
primarily
for
use
in
high
energy
physics
Example setup:
Cardiff
AEI
Berlin
Syracuse
collabora-ons,
especially
at
the
LHC.
Presently
there
are
dozens
of
collabora-ons,
• Quad Core Dell PC
LIGO
Hanford
UW
Milwaukee
LIGO
communi-es,
and
projects
using
EVO.
LIGO
and
Virgo
have
now
used
EVO
during
six
• Blackmagic Intensity HD video
MIT
collabora-on
mee-ngs,
plus
other
mee-ngs
throughout
the
year.
We
are
very
pleased
grabber card
LIGO
Caltech
LIGO
Livingston
with
the
remote
par-cipa-on
capabili-es
that
EVO
has
provided,
and
it
has
certainly
• Sony HD camcorder
allowed
numerous
LSC
and
Virgo
members
par-cipate
in
important
mee-ngs
that
would
• Panasonic HD Plasma Monitor
have
otherwise
been
inaccessible
to
them.
Scien-sts
located
around
the
world
are
able
• Phoenix Duet echo canceling
to
view
presenta-ons,
ask
ques-ons,
hold
conversa-ons,
show
data,
all
in
real
-me.
mic
The
LIGO
Scien-fic
Collabora-on
operates
9
clusters
know
as
the
LIGO
Data
Grid
While
we
s-ll
see
avenues
for
improvement
and
more
capability
in
EVO,
we
can
already
• Total: ~$3000
(LDG),
with
a
total
of
approximately
17,000
cores
worldwide.
The
Virtual
Data
hold
very
effec-ve
mee-ngs
that
include
remote
par-cipants.
It
is
an-cipated
that
an
Toolkit
is
a
source
of
much
of
the
grid
compu-ng
middleware
being
deployed.
addi-onal
2000
users
from
the
NSF
community
will
also
benefit
from
this
award.
To
learn
more
visit:
hOp://www.ligo.caltech.edu
&
hOp://www.ligo.org
NSF
Award
No.
PHY-‐0938825
To
learn
more
visit:
hOp://evo.caltech.edu/evoGate
LIGO-‐G1000004