February 12, 2011 NEMO All-Hands Meeting: Database and Portal Kurt Mueller and Jason Sydes

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Presentation transcript:

February 12, 2011 NEMO All-Hands Meeting: Database and Portal Kurt Mueller and Jason Sydes

Agenda FTP site / file database overview NEMO portal – Present – Future

Database – FTP site Place to store files – Raw waveforms (input files) – Intermediate analysis results – Parameter files – Final output files

Organization Organize files by lab, experiment, file type: LAB DIRECTORY EXPERIMENT DIRECTORY INPUT_DATA DIRECTORY ANALYSIS_1 DIRECTORY ANALYSIS_2 DIRECTORY

Example JTC (lab-level folder) JTC-PMN1 (experiment-level folder) JTC-PMN1_Input_Data (subdir) 'JTC-PMN1.raw' (input data file) JTC-PMN1_Decomposition_ (subdir) 'JTC-PMN1_tPCA.m' (metascript file) 'JTC-PMN1_DecompObj mat' (MATLAB output file) 'JTC-PMN1_tPCA.raw' (simple binary output data file)

Uploading files – ftp client

Data in FTP is both managed and unmanaged Mixture of two different areas – Unmanaged – Portal managed Possible area for documentation? What role will FTP server will serve in future? Can browse and download portal data via FTP – Readonly!

Data in portal accessible via FTP

Graphical ftp clients Mac OS X + Windows + Linux – Filezilla - Mac OS X + Windows – Cyberduck – free - Mac OS X – Transmit - $34 -

Goals of portal 1.Online record of experiment metadata 2.Repository of experiment data files 3.Tight coupling to NEMO ontology 1.Provenance of all data 2.NEMO analysis pipeline execution 3.Querying on metadata now in progress

Record experiment metadata Experiment Conditions Sessions Publications Subject groups Data files Task Stimuli Responses

Quick Sampling of Portal

Portal database tables

Repository of experiment data files New upload widget provides progress feedback (standard http upload does not)

OpenID access to NEMO resources SSO: Single Sign On Login once, get access to – NEMO portal – NEMO wiki – NEMO sourceforge page Learn about it: How to create a new SSO account:

Role-based access control (RBAC)

Database coupled to Ontology Example Table: Stimulus

Database coupled to Ontology Example “Ontology”: Stimulus

Database coupled to Ontology

Database coupled to Ontology Example mapping: Stimulus

Database coupled to Ontology Example term: stimulus_intensity

Database coupled to Ontology Example tooltip

Database coupled to Ontology Quick syncing

Open Provenance Model (

Open Provenance Model – subset used –

Open Provenance Model Example

Open Provenance Model Simplified Example

Workflow – MATLAB in portal Current workflow: 1.Conduct experiment, producing raw waveforms 2.Process data with NEMO Toolkit scripts, locally 3.Upload raw and processed data to ftp or portal 4.Create an experiment in the portal, associate data with experiment

Worfklow – MATLAB in portal Future workflow (in design) 1.Conduct experiment, producing raw waveforms 2.Create an experiment in the portal 3.Upload raw data through portal 4.Execute MATLAB pipeline through portal Automatic storage of output data Automatic provenance tracking Single place for MATLAB scripts to live Run on big iron

Questions?

Thank you!