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iPlant cyberifrastructure to support ecological modeling
Presented at the Species Distribution Modeling Group at the American Museum of Natural History
May 30, 2014Ramona Walls
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iPlant Collaborative Vision
Enable life science researchers and educators to use and extend cyberinfrastructure to understand and ultimately predict the complexity of biological systems.
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What is cyberinfrastructure?
Data Storage
Software HPC People
iPlant CI
Storage and compute
Platforms, tools, datasets
Training, support, expertise
Software Hardware People
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iPlant CI supports synthetic biology
Genotypic
Phylogenetic Tools for inference
Ecological Models
Crop Models
Association Studies
Molecular Networks
Environmental
Comparative Genomics
Sequencing & Assembly
Annotation
Environmental datasets
Phenotypic
Image-based Phenotyping
Molecular Phenotyping
Trait Data
Climate model products
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iPlant is a collaborative virtual organization
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iPlant collaborates to enable access to the solutions that work
the best for you.
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OVERVIEW OF IPLANT TOOLS AND SERVICES
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iPlant Data Store
Initial 100 GB allocation – TB allocations available
Automatic data backup
Easy upload /download and sharing
The resources you need to share and manage data with your lab, colleagues and community
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AtmosphereCloud computing for the life sciences
Simple: One-click access to more than 100 virtual machine images
Flexible: Fully customize your software setup
Powerful: Integrated with iPlant computing and data resources
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Discovery EnvironmentHundreds of bioinformatics Apps in an easy-to-use interface
A platform that can run almost any bioinformatics application
Seamlessly integrated with data and high performance computing
User extensible – add your own applications
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BisqueImage analysis, management, and metadata
Secure image storage, analysis, and data management
Integrate existing algorithms or create new ones
Custom visualization and image handling routines and APIs
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Agave APIFully customize iPlant resources
Science-as-a-service platform
Define your own compute and storage resources (local and iPlant)
Build your own app store of scientific codes and workflows
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DNA SubwayEducational workflows for Genomes, DNA Barcoding, RNA-Seq
Commonly used bioinformatics tools in streamlined workflows
Teach important concepts in biology and bioinformatics
Inquiry-based experiments for novel discovery and publication of data
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SUPPORT FOR ECOLOGICAL MODELING
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Project Goals
• Provide computational support for scalable:– modeling of species’ geographic distribution
(SDM)– mechanistic eco-physiological modeling
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Major limitations in the field of ecological modeling
• Access to data– environmental and organismal
• Access to high performance computing (HPC) tools that can support compute-intensive models
• Model development
iPlant can provide infrastructure to help overcome the first two challenges and partner with the community on the third challenge.
?
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iPlant’s long-term vision for an ecological modeling infrastructure
• Modular access to climate layers• A query interface for finding and extracting
relevant occurence and trait data for the taxa of interest from iPlant’s Data Commons
• Powerful, flexible modeling tools• Sophisticated visualization of geospatial data
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Initial plan is to provide access to:
• Environmental data• Organismal locality (occurence) data• High performance computing environment for
running models
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Environmental Data
• Data layers are often large and difficult to work with, even though the researcher only needs a subset of the layer.
• Web services (e.g., GeoNode.org and GeoServer.org) can be harnessed to allow researchers to work with data layers stored remotely.
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iPlant will make environmental data layers available through the Data Commons and GeoServer
• University Corporation for Atmospheric Research (UCAR)
• Oakridge National Laboratory’s Distributed Active Archive Center for Biogeochemical Dynamics (ORNL DAAC)
• NASA Earth Observing System Data and Information System (EOSDIS) available through the Data Commons.
• High-res layers from iPlant collaborators?
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Organismal locality (occurence) data
• For many modeling efforts, users will supply their own list of species’ localities.
• Through the BIEN3 database, iPlant users will also have access to data for North American plants– includes cleaned-up Global Biodiversity Information
Framework (GBIF) data. – iPlant will provide a query interface for extracted
subsets of the BIEN data for use in ecological modeling.
• Some trait data will also available
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Modeling tools 1
• Initially, iPlant will make an HPC version of Maxent available to users.
• Investigating the utility of making popular R packages for modeling (biomod2, Maxlike, and IPMpack) available through rPlant and wrapR, so that they can run on HPC resources.
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Modeling tools 2
• More generally, ecological modeling will be supported through an HPC version Matlab.
• Because of licensing restrictions, users will initially be restricted to running Matlab models which they build on their own, licensed system.
• Stan and OpenBUGS are being considered to support Bayesian modeling.
?
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Links
• http://www.iplantcollaborative.org/
• contact: rwalls_at_iplantcollaborative.org
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Timeline• Q3 2014:
– HPC version of Maxent available through iPlant (DE or Atmosphere)– Availability of BIEN occurence data– Scope work on query and subsetting services for data layers*– Metadata template for environmental layers
• Q4 2014:– HPC version of Matlab for running models– Query interface for BIEN occurence data– Continue development of query and subsetting services for data layers*
• Q1 2015:– Ability to query environmental layers through Data Commons*– Ability to subset environmental layers through iPlant CI (DE, Atmosphere, or
API)– Species distribution modeling tutorial.
*May happen sooner through GeoNode