iPlant cyberifrastructure to support ecological modeling Presented at the Species Distribution Modeling Group at the American Museum of Natural History May 30, 2014 Ramona Walls

iPlant Collaborative Vision Enable life science researchers and educators to use and extend cyberinfrastructure to understand and ultimately predict the complexity of biological systems.

What is cyberinfrastructure? Data Storage SoftwareHPCPeople iPlant CI Storage and computePlatforms, tools, datasets Training, support, expertise Software HardwarePeople

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

iPlant is a collaborative virtual organization

iPlant collaborates to enable access to the solutions that work the best for you.

OVERVIEW OF IPLANT TOOLS AND SERVICES

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

Atmosphere Cloud 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

Discovery Environment Hundreds 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

Bisque Image 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

Agave API Fully 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

DNA Subway Educational 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

SUPPORT FOR ECOLOGICAL MODELING

Project Goals Provide computational support for scalable: – modeling of species’ geographic distribution (SDM) – mechanistic eco-physiological modeling

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. ?

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

Initial plan is to provide access to: Environmental data Organismal locality (occurence) data High performance computing environment for running models

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.

iPlant will make environmental data layers available through the Data Commons and GeoServer University Corporation for Atmospheric Research (UCAR)UCAR Oakridge National Laboratory’s Distributed Active Archive Center for Biogeochemical Dynamics (ORNL DAAC)ORNL DAAC NASA Earth Observing System Data and Information System (EOSDIS) available through the Data Commons.EOSDIS High-res layers from iPlant collaborators ?

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

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.

Modeling tools 2 More generally, ecological modeling will be supported through an HPC version Matlab. 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. Stan OpenBUGS ?

Links contact: rwalls_at_iplantcollaborative.org

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