CaNanoLab Users Group Use of Informatics to Expedite and Validate the Application of Nanotechnology in Biomedicine August 2, 2012.

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Presentation transcript:

caNanoLab Users Group Use of Informatics to Expedite and Validate the Application of Nanotechnology in Biomedicine August 2, 2012

Agenda caNanoLab Release Status caNanoLab Release Status ISA-TAB-Nano Wireframe Review Next Steps

caNanoLab Release Status Completed and deployed caNanoLab on Production in May 2012: – Software available for download on the NCI CBIIT Download Site: –

caNanoLab Release Status Completed technology stack upgrade: JBoss 5.1, JDK 6, CSM/UPT Implemented defect fixes –Deleting an item in caNanoLab returns “no access” warning (caNanoLab-47/50) –Delete button doesn’t work in Characterization form (caNanoLab- 48) –InterNano External Link broken (caNanoLab-51) –Basic Sample Search giving same results for Sample Name equals/contains (caNanoLab-52) Implemented data updates –Updated 20 samples in the production database that have invalid XML characters –Update the NCL protocol files uploaded in previous releases to use protocol URLs provided by the NCL assay cascade protocols at Currently on QA and plan to be on Production mid-August 2012

caNanoLab Release Status Implemented a grid client for Thomson Reuters –Generated tab-delimited output file for all 921 samples –Mapping between Thomson Reuters fields and caNanoLab fields:

caNanoLab Release Status Requirements Analysis and Design for ISA-TAB-Nano support –Drafted use cases for ISA-TAB-Nano file management –Drafted wireframes for ISA-TAB-Nano file management Feature Request Analysis –Add field(s) to support the description of sample synthesis (caNanoLab-49): Important to capture information about nanoparticle synthesis to support the reproducibility of particle creation. Sometimes, this description can be captured as a descriptive paragraph; other times, a lengthy process is involved and reference to a publication will be more appropriate.

Wireframe Review ISA-TAB-Nano File Management

Wireframe Review Submit ISA-TAB-Nano Files

Wireframe Review Search ISA-TAB-Nano Files

Wireframe Review ISA-TAB-Nano File Search Results

Next Steps Complete caNanoLab Release Production deployment Modify ISA-TAB-Nano support wireframes based on feedback Study the ISA-TAB Validator Tool –Design object model changes supporting investigations and studies –Design object model changes supporting sample synthesis Host next caNanoLab Users Group Meeting: –Users Group Meeting: October 4, :00 AM EST –Agenda: Discuss caNanoLab status Review ISA-TAB-Nano wireframe changes Review object model changes in support of ISA-TAB-Nano investigations and studies Review object model changes in support of sample synthesis

caNanoLab Team NCI Project Sponsor – Juli Klemm NCI Project Officer - JJ Pan SAIC-F COTR – Deb Hope SAIC Technical Lead – Sue Pan NCI Quality Assurance – Quy Phung

References caNanoLab Portal – caNanoLab Wiki – ki+Home+Pagehttps://wiki.nci.nih.gov/display/caNanoLab/caNanoLab+Wi ki+Home+Page caNanoLab JIRA Tracker – ISA-TAB-Nano Data Standard – ISA-TAB –

caNanoLab Curation Activities Sponsored by the NCI Alliance for Nanotechnology in Cancer Focused on structuring public data – primarily published data - from Alliance investigators Effort is two-fold –Represent data in ISA-TAB-nano –Load data into caNanoLab ISA-TAB-nano files available at

Progress and plans 15