iPlant Presentation given at NESCent in June 2012 for the phylotastic participants of Phylotastic

1. The iPlant Collaborative:
A Cyberinfrastructure for the Life
Sciences
Naim Matasci
BIO5 / The iPlant Collaborative

2. What is iPlant?

3. http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html

5. Problem 1: Data Volume
• Cost of analysis follows Moore's Law:
– 1 Student with 1 computer to analyze 1 Mb of
data produced in 2001
– 200 Students and 200 computers to analyze all
data produced for the same cost today (10 Gb)

6. Problem 2: Fragmented Analytical Landscape
1. Tools separated by compute
platform, data format, integration
issues, and programming model.
1. Mixture of desktop, command
line, database, and web-based
tools
2. Labor intensive, fragile solutions
devised to reach scientific
objectives
3. Little ability to share results,
analytical methods
4. Lack of reproducibility

7. Scalability
ABI 3730 DNA Analyzer, illumina Genome Analyzer, Joe Felesenstein ca. 1980, Ranger Cluster at TACC

10. Major Ways to Access iPlant
• Storing and sharing data large and small: iPlant Data
Storage
• Integrated web-based analysis: The Discovery Environment
• Cloud computing: Atmosphere
• Applications: TNRS, TreeViewer, PhytoBisque, etc
• Scientific networking, knowledgebase and information
exchange: My-Plant.org
• Educational tools: DNASubway
• Embedding iPlant CI capabilities into software: The
Foundation API
• High Performance Computing for experts: TeraGrid/XSEDE
10

11. Why is the tree of life important?
“Knowledge of evolutionary relationships is
fundamental to biology, yielding new insights
across the plant sciences, from comparative
genomics and molecular evolution, to plant
development, to the study of adaptation,
speciation, community assembly, and
ecosystem functioning.”

12. Nothing in biology makes
sense except in the light
of evolution.
T. G. Dobzahnsky

14. C3 to C4 Photosynthesis
Xin-Guang et al. 2008

15. "We combined geospatial and molecular
sequence data from two public archives to
produce a 1,230-taxon phylogeny of the grasses
with accompanying climate data for all species,
extracted from more than 1.1 million herbarium
specimens."
Edwards and Smith, 2010

16. "Here we show that grasses are ancestrally a
warm-adapted clade and that C4 evolution
was not correlated with shifts between
temperate and tropical biomes. Instead, 18
of 20 inferred C4 origins were correlated with
marked reductions in mean annual
precipitation."

17. New Possibilities
Acer glabrum
Acer saccharinum
Acer rubrum
Acer distylum
Acer macrophyllum
Acer nipponicum
Acer spicatum
Acer carpinifolium
Acer diabolicum
Acer circinatum
Acer sieboldianum
Acer palmatum
Acer saccharum
Acer tschonoskii
Acer rufinerve
Acer pensylvanicum
Acer crataegifolium
Acer mono
illumina Genome Analyzer, Ranger Cluster at TACC, Acer phylogeny (Ackerly 2009), Green Plant ToL

19. Just Ask

20. Atmosphere

24. iPlant's APIs – The Foundation API
Service Role
Endpoint
IO File storage, retrieval and management. Database
interoperability
DATA File format conversion
APPS Registration and discovery of HPC applications
JOB Submission and management of compute jobs
SYSTEMS Availability and info about XSEDE hosts
PROFILE User profile discovery
AUTH Token based secure authentication
POSTIT URL shortener

25. Consumer Applications
25

28. iPlant Data Store
Dramatization: Not the actual iPlant Data Store

29. Overview of the iPlant Data Store
Some important items we won’t see in the demo
Source Destination Copy Method Time (seconds)
CD My Computer cp 320
Berkeley Server My Computer scp 150
External Drive My Computer cp 36
USB2.0 Flash My Computer cp 30
iDS MyComputer iget 18
My Computer My Computer cp 15
Close to optimum conditions; transfer between
Univ. of Arizona and UC Berkeley
100GB: 29m15s
1 GB / 17.5 seconds

31. Tree Visualization
• > 500K Taxa
• Fast
• Web based, platform independent
• Semantic zooming
• Metadata driven display of information

32. iPlant Tree Viewer
http://portnoy.iplantcollaborative.org/

33. LIVE TREE VIEW DEMO

34. Obstacles
Lobelia_kauaensis
Lobelia_villosa
Lobelia_gloria-montis
Trematolobelia_kauaiensis
Trematolobelia_macrostachys
Lobelia_hypoleuca
Lobelia_yuccoides
Lobelia_niihauensis
Brighamia_insignis
Brighamia_rockii
Delissea_rhytidosperma
Delissea_subcordata
Cyanea_pilosa
Cyanea_acuminata
Cyanea_hirtella
Cyanea_coriacea
Cyanea_leptostegia
Clermontia_kakeana
Clermontia_parviflora
Clermontia_arborescens
Clermontia_fauriei
Number of taxa Taxa names

35. Taxonomic uncertainty
1. Non-existent names
• Misspellings
• Contamination
• Annotations
• Morphospecies
• Digitization issues (frame shifts, character
encoding)Lexical variants (digitization conventions)
2. Synonymy
• Nomenclatural synonyms
• Taxonomic synonyms / concepts
3. Misidentifications, incomplete identifications

36. a) Centaurium curvistamineum
(Wittr.) Abrams (1951)
b) Centaurium minimum (Howell)
Piper (1915)
c) Centaurium muhlenbergii (Griseb.)
Wight ex Piper (1906)
d) Centaurium muhlenbergii (Griseb.)
Wight ex Piper forma albiflorum
(Suksd.) St. John (1937)
e) Centaurium muhlenbergii (Griseb.)
Wight ex Piper var. albiflorum
Suksd. (1927)
f) Centaurodes muhlenbergii
(Griseb.) Kuntze (1891)
g) Erythraea curvistaminea Wittr.
(1886)
h) Erythraea minima Howell (1901)
i) Erythraea muhlenbergii Griseb.
(1839)
Image: Gordon Leppig & Andrea J. Pickart

39. Request Tool Installation
Apps -> Create -> New App
Create New -> Request Tool Installation
Fill out forms and submit.
Receive response in 2-5 days.