Jeff Grethe: CAMERA

Jeffrey S. Grethe, Ph.D. Center for Research in Biological Systems University of California, San Diego ,[object Object]

Global Scientific Research Cyber-Community

CAMERA 2.0 Objectives ,[object Object],[object Object],[object Object],[object Object],[object Object]

Creating CAMERA 2.0 - Advanced Cyberinfrastructure Service Oriented Architecture

The Semantically Aware DB Schema ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Integration of External Data ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

NASA Aqua-MODIS satellite data ,[object Object],Sea Surface Temp Chlorophyll MODIS Images covering GOS sites #8 – 12, mid November, 2003

Integration of Enhanced Metadata

Integrate and browse additional sources of microbial data

Community Data Requirements ,[object Object],[object Object],[object Object],[object Object],[object Object]

CAMERA 2.0 (Data Submission) Growing the CAMERA Community and Resource…

Data Standards ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

User Friendly Compute Environment

CAMERA 2.0 (Computation) From simple job submission to community developed and published workflows…

The Big Picture: Supporting the Scientist Conceptual Workflow Executable Workflow From “Napkin Drawings” … … to Executable Workflows Source: Mladen Vouk (NCSU)

Scientific Workflow Systems … ,[object Object],[object Object],[object Object],[object Object],www.kepler-project.org ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Ptolemy II: A laboratory for investigating design KEPLER: A problem-solving environment for Scientific Workflow KEPLER = “Ptolemy II + X” for Scientific Workflows

Personalized (Collaborative) Workflow and Data Spaces

RAMMCAP – Rapid clustering and functional annotation for metagenomic sequences ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],CD-HIT, 90-95% More in-depth analysis and further annotation Metagenomic Raw reads CD-HIT-EST, 95% DNA clusters Protein clusters Representative sequences Unique DNA sequences ORF Annotation 1. ORF_finder 2. Metagene CD-HIT, 60 or 30% COG Pfam Tigrfam HMMER HMMERHEAD RPS-BLAST Cluster Annotation 1. tRNA scan 2. rRNA scan 3. meta_RNA ORFs Non-redundant ORFs tRNAs rRNAs

Annotation workflow A green box is called an ‘actor’ , which performs a task. This special actor represents an annotation component, such as BLAST search. Workflow parameters, which can be specified by users in the portal, are passed to workflow components. Data flow is divided.

Run branches within workflow A ORF clustering branch A functional annotation branch

Provenance of Workflow Related Data ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Provenance Schema and Viewer in CAMERA 2.0

Jeff Grethe: CAMERA

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Jeff Grethe: CAMERA