This document discusses balancing usability and reusability in science gateways for life sciences. It notes that while sophisticated tools, methods, and distributed computing infrastructures exist, researchers do not widely use them due to issues like limited usability of tools, complex methods and workflows, lack of graphical user interfaces, and complexity of infrastructures. Science gateways aim to address these issues by abstracting complexity and providing intuitive interfaces to enable researchers to focus on their work rather than technology.

1. Science
Gateways
for
Life
Sciences
–
Balancing
Usability
and
Re-­‐Usability
Sandra
Gesing
Center
for
Research
Compu?ng
sandra.gesing@nd.edu
19
September
2013

2. Life
Sciences
“the
sciences
concerned
with
the
study
of
living
organisms,
including
biology,
botany,
zoology,
microbiology,
physiology,
biochemistry,
and
related
subjects”
hMp://www.thefreedic?onary.com
• Technologies
and
methods
for
crea?ng,
analyzing
and
predic?on
of
data
available
• Immense
amount
of
data,
e.g.,
• ZINC
database:
~20
Mio
molecular
structures
• Human
genome:
~
3
Bio
DNA
base
pairs
Sandra
Gesing
Science
Gateways
for
Life
Sciences
2

3. Life
Sciences
and
Computa?on
The
Genomics
Boom
February
16,
2001
biotech
company
Celera
Sandra
Gesing
February
15,
2001
The
Human
Genome
Project
Science
Gateways
for
Life
Sciences
3

4. Life
Sciences
and
Computa?on
The
Genomics
Boom
Craig
Venter
(le`)
and
Francis
Collins
(right)
Sandra
Gesing
Science
Gateways
for
Life
Sciences
4

5. Areas
in
the
Life
Sciences
•
A
lot
of
“omics”
sciences,
e.g.
•
Genomics
•
Proteomics
Black
Swallowtail
-­‐
larvae
and
buMerfly
Sandra
Gesing
Science
Gateways
for
Life
Sciences
5

6. Molecular
Simula?ons
and
Docking
•
Predic?on
and
analysis
of
molecular
structures
•
Numerous
applica?ons,
e.g.
•
Materials
science
•
Drug
design
ligands
docking
Sandra
Gesing
target
?
Science
Gateways
for
Life
Sciences
6

7. Molecular
Simula?ons
and
Docking
•
Predic?on
and
analysis
of
molecular
structure
•
Numerous
applica?ons,
e.g.
•
Materials
science
•
Drug
design
ligands
docking
Sandra
Gesing
binding
energy
scoring
func?ons
Science
Gateways
for
Life
Sciences
target
binding
pocket
7

8. Simula?ons
•
Basic
data
with
heterogeneous
provenance,
e.g.
Research
in
Malaria
•
Data
on
weather
•
Data
on
demography
•
Data
on
interven?ons
•
...
•
Mathema?cal
models
needing
a
baseline
•
Predic?on
of
interven?ons
Sandra
Gesing
Science
Gateways
for
Life
Sciences
8

9. State-­‐of-­‐the-­‐art
•
Data
intensive
and
compute
intensive
problems
•
Sophis?cated
tools
and
methods
available
•
Distributed
data
management
available
•
DCIs
(Distributed
Compu?ng
Infrastructures)
available
Why
do
researchers
not
use
the
tools
and
distributed
environments
on
a
large
scale?
Sandra
Gesing
Science
Gateways
for
Life
Sciences
9

10. Open
Issues
•
Usability
of
tools
o`en
limited
•
Complexity
of
methods
•
Lack
of
graphical
user
interfaces
Sandra
Gesing
Science
Gateways
for
Life
Sciences
10

11. Open
Issues
•
Usability
of
tools
o`en
limited
•
Complexity
of
methods
•
Lack
of
graphical
user
interfaces
Sandra
Gesing
Science
Gateways
for
Life
Sciences
11

12. Open
Issues
•
Usability
of
tools
o`en
limited
•
Complexity
of
methods
•
Lack
of
graphical
user
interfaces
•
Workflows
steps
in
a
defined
order
a
sequence
of
connected
based
on
their
control
nd
data
dependencies
a
Sandra
Gesing
Science
Gateways
for
Life
Sciences
12

13. Open
Issues
•
Usability
of
tools
o`en
limited
•
Complexity
of
methods
•
Lack
of
graphical
user
interfaces
•
Workflows
12181
12241
12301
12361
12421
12481
12541
12601
12661
12721
12781
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steps
in
a
defined
order
a
sequence
of
connected
based
on
their
control
nd
data
dependencies
a
Slide
copied
from:
Stuart
Owen
„Workflows
with
Taverna“
Sandra
Gesing
Science
Gateways
for
Life
Sciences
13

14. Open
Issues
•
Usability
of
tools
o`en
limited
•
Complexity
of
methods
•
Lack
of
graphical
user
interfaces
•
Workflows
•
Complexity
of
infrastructures
•
Users
are
generally
not
IT
specialists
Sandra
Gesing
Science
Gateways
for
Life
Sciences
14

15. Open
Issues
•
Usability
of
tools
o`en
limited
•
Complexity
of
methods
•
Lack
of
graphical
user
interfaces
•
Workflows
•
Complexity
of
infrastructures
•
Users
are
generally
not
IT
specialists
Sandra
Gesing
Science
Gateways
for
Life
Sciences
15

16. Open
Issues
•
Usability
of
tools
o`en
limited
•
Complexity
of
methods
•
Lack
of
graphical
user
interfaces
•
Workflows
•
Complexity
of
infrastructures
•
Users
are
generally
not
IT
specialists
⇒
User
interfaces
need
to
be
intui8ve
and
self-­‐
explanatory
⇒
Science
gateways
Sandra
Gesing
Science
Gateways
for
Life
Sciences
16

17. Science
Gateways
“A
Science
Gateway
is
a
community-­‐developed
set
of
tools,
applica9ons,
and
data
that
is
integrated
via
a
portal
or
a
suite
of
applica9ons,
usually
in
a
graphical
user
interface,
that
is
further
customized
to
meet
the
needs
of
a
specific
community.”
TeraGrid/XSEDE
Community
Sandra
Gesing
Science
Gateways
for
Life
Sciences
17

18. Web-­‐based
Science
Gateways
•
Single
point
of
entry
•
Possibility
to
customize
views
and
tools
•
Store
user
preferences
•
No
installa?on
of
so`ware
on
the
user’s
side
•
No
firewall
issues
Slar9barGast:
“I
must
warn
you,
we're
going
to
pass
through,
well,
a
sort
of
gateway
thing.”
Arthur
Dent:
„What?“
Slar9barGast:
“It
may
disturb
you.
It
scares
the
willies
out
of
me.”
(Douglas
Adams
in
“The
Hitchhiker's
Guide
to
the
Galaxy”)
Sandra
Gesing
Science
Gateways
for
Life
Sciences
18

19. Goal
of
Science
Gateways
Usability
of
so`ware
"AOer
all,
usability
really
just
means
that
making
sure
that
something
works
well:
that
a
person
…
can
use
the
thing
-­‐
whether
it's
a
Web
site,
a
fighter
jet,
or
a
revolving
door
-­‐
for
its
intended
purpose
without
geSng
hopelessly
frustrated."
(Steve
Krug
in
“Don't
make
me
think!:
A
Common
Sense
Approach
to
Web
Usability”,
2005)
Sandra
Gesing
Science
Gateways
for
Life
Sciences
19

20. Re-­‐Usability
• Sharing
of
knowledge
and
data
• Re-­‐Using
of
„recipes“
and
workflows
• Re-­‐Usability
of
so`ware
“The
key
to
produc9vity
is
reusability.
The
easiest
way
to
produce
code
is
obviously
to
have
it
already!"
(John
R.
Bourne
in
“Object-­‐oriented
Engineering:
Building
Engineering
Systems
Using
Smalltalk-­‐80”,
1992)
Sandra
Gesing
Science
Gateways
for
Life
Sciences
20

21. Re-­‐Usability
Re-­‐inven?ng
is
not
always
necessary...
Sandra
Gesing
Science
Gateways
for
Life
Sciences
21

22. Re-­‐Usability
...
but
the
model
should
fit
to
the
demands
of
the
community
Sandra
Gesing
Science
Gateways
for
Life
Sciences
22

23. Diverse
Approaches
•
Science
gateway
frameworks
•
Sta?c
layout
•
Layout
extendable
•
Workflow-­‐enabled
•
Portal
frameworks
•
Content
management
systems
•
Libraries
for
implementa?on
Sandra
Gesing
Science
Gateways
for
Life
Sciences
23

24. Galaxy
Python
framework
Sandra
Gesing
Science
Gateways
for
Life
Sciences
24

25. Galaxy
Sandra
Gesing
Science
Gateways
for
Life
Sciences
25

26. Parametriza?on
Sandra
Gesing
Science
Gateways
for
Life
Sciences
26

27. Workflows
Sandra
Gesing
Science
Gateways
for
Life
Sciences
27

28. Administra?on
Sandra
Gesing
Science
Gateways
for
Life
Sciences
28

29. WS-­‐PGRADE
User
Interface
WS-­‐PGRADE
Liferay
High-­‐Level
Middleware
Service
Layer
gUSE
DCI
Resources
Middleware
Layer
Sandra
Gesing
Science
Gateways
for
Life
Sciences
29

30. WS-­‐PGRADE
Sandra
Gesing
Science
Gateways
for
Life
Sciences
30

31. Job
Configura?on
Sandra
Gesing
Science
Gateways
for
Life
Sciences
31

32. Monitoring
Sandra
Gesing
Science
Gateways
for
Life
Sciences
32

33. MoSGrid
Molecular
Simula?on
Grid
•
Science
gateway
integrated
with
underlying
compute
and
data
management
infrastructure
•
Distributed
workflow
management
•
Data
repository
Sandra
Gesing
Science
Gateways
for
Life
Sciences
33

34. Tools
Sandra
Gesing
Science
Gateways
for
Life
Sciences
34

35. File
Management
Sandra
Gesing
Science
Gateways
for
Life
Sciences
35

36. MoSGrid
–
Applica?on
Areas
Molecular
Dynamics
•
Study
and
simula?on
of
molecular
mo?on
Quantum
Chemistry
•
Study
and
simula?on
of
molecular
electronic
behavior
rela?ve
to
their
chemical
reac?vity
Docking
•
Main
focus
on
evalua?on
of
ligand-­‐receptor
interac?ons
(e.g.,
for
drug
design)
Sandra
Gesing
Science
Gateways
for
Life
Sciences
36

37. MD
Portlet
Sandra
Gesing
Science
Gateways
for
Life
Sciences
37

38. MD
Portlet
Sandra
Gesing
Science
Gateways
for
Life
Sciences
38

39. MD
Portlet
Sandra
Gesing
Science
Gateways
for
Life
Sciences
39

40. QC
Portlet
Sandra
Gesing
Science
Gateways
for
Life
Sciences
40

41. QC
Portlet
Sandra
Gesing
Science
Gateways
for
Life
Sciences
41

42. Docking
Portlet
Sandra
Gesing
Science
Gateways
for
Life
Sciences
42

43. Docking
Portlet
Sandra
Gesing
Science
Gateways
for
Life
Sciences
43

44. VectorBase
Sandra
Gesing
Science
Gateways
for
Life
Sciences
44

45. Tools
Sandra
Gesing
Science
Gateways
for
Life
Sciences
45

46. Tools
Sandra
Gesing
Science
Gateways
for
Life
Sciences
46

47. Tools
Sandra
Gesing
Science
Gateways
for
Life
Sciences
47

48. VECNet
Sandra
Gesing
Science
Gateways
for
Life
Sciences
48

49. Data
Sandra
Gesing
Science
Gateways
for
Life
Sciences
49

50. Modeling
Plarorm
Sandra
Gesing
Science
Gateways
for
Life
Sciences
50

51. Risk
Mapper
Sandra
Gesing
Science
Gateways
for
Life
Sciences
51

52. Risk
Mapper
Sandra
Gesing
Science
Gateways
for
Life
Sciences
52

53. Usability
vs.
Re-­‐Usability
• User
side
• Methods
• Workflows
• Data
è Re-­‐usability
increases
usability
on
the
user
side
• Admin/Developer
side
• Frameworks
• Libraries
• Source
code
è Usability
and
re-­‐usability
depend
on
support,
documenta?on
and
scalability
Sandra
Gesing
Science
Gateways
for
Life
Sciences
53

54. Usability
vs.
Re-­‐Usability
• User
side
• Layout
• Visualiza?on
• Security
è Re-­‐used
parts
may
be
not
sufficient,
usability
depends
on
the
features
needed
in
the
community
• Admin/Developer
side
• Integra?on
with
compu?ng
and
data
infrastructures
• Security
è Usability
and
re-­‐usability
depend
on
available
infrastructures
Sandra
Gesing
Science
Gateways
for
Life
Sciences
54

55. New
Science
Gateway
-­‐
Checklist
•
•
•
•
•
Demands
of
the
user
community
on
the
user
interface
Demands
on
security
Demands
on
compu?ng
and
data
resources
Workflows
Performance
•
•
•
•
Exis?ng
tools
and
models
Available
underlying
infrastructure
Available
documenta?on
and
support
Effort
on
development
and
maintenance
Sandra
Gesing
Science
Gateways
for
Life
Sciences
55

56. sandra.gesing@nd.edu
Sandra
Gesing
Science
Gatewazs
for
Life
Sciences
56