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

Agenda caNanoLab Release Status caNanoLab Release Timeline Results of Users Group Feature Prioritization caNanoLab Collaborations Next Steps

caNanoLab Release Status Completed Section 508 Compliance remediation (caNanoLab-8) Implemented feature requests Added display of creation date for samples, protocols, and publications (caNanoLab-29) Added URL to protocol submission/retrieval (caNanoLab-32) Disable polling statistics on home page (caNanoLab-33) Added external link disclaimer (caNanoLab-34) Implemented defect fixes Back button on sample search results (caNanoLab-3) Set column order before saving data matrix (caNanoLab-5) Modified the PubMed interface based on PubMed API changes (caNanoLab-31) Implemented Technology Stack Upgrade Upgraded to BDA-Lite (caNanoLab-13) Provided support for ISA-TAB-Nano Modified ISA-TAB-Nano manuscript and supporting information Deployed to QA for testing

Creation Date Addition (caNanoLab-29)

Protocol URL Addition (caNanoLab-32)

Disable Stats Polling (caNanoLab-33)

External Link Disclaimer (caNanoLab-34)

caNanoLab Release Timeline QA Deployment:4/6/2012 STAGE Deployment:4/27/2012 Production Deployment:5/9/2012

Results of Feature Prioritication (1 of 3) Jira number caNanoLab-2: Feature: Provide support for in vivo characterization data Description: Support the NCI Alliance use case for understanding the effects of nanomaterial size and shape on biodistribution. Requires support for studies, animal and treatment information, pharmacokinetics, and toxicology. 10 votes, Priority High. Jira number caNanoLab-19: Feature: Provide support for the ISA-TAB-Nano standard Description: Support the validation, import, and export of ISA-TAB-Nano files. Leverage existing ISA-Tools where possible. Requires support for studies. 8 votes, priority High. Jira number caNanoLab-20: Feature: Provide a Java and SOAP API, including RESTful services for accessing caNanoLab data Description: Expose the caCORE SDK generated APIs and add the security filter. 3 votes, priority Low.

Results of Feature Prioritization (2 of 3) Jira number caNanoLab-21 Feature: Interface with analysis and visualization tools such as GenePattern Description: Allow users to view data queried from caNanoLab in GenePattern (e.g. heatmap displaying particle size vs. toxicity) 0 votes, priority Low. Jira number caNanoLab-22 Feature: Interface with the National Biomedical Imaging Archive (NBIA) and the Molecular Imaging and Contrast Agent Database (MICAD) database in support of nanomaterial images Description: Allow users to upload biomedical images into NBIA and link caNanoLab to NBIA. Provide links from nanomaterials used as image contrast agents to MICAD. 4 votes, priority Medium. Jira Number caNanoLab-23 Feature: Interface with the cancer Models Organism Database (caMOD) in support of animal models used in nanomaterial characterizations Description: Provide links from nanomaterial characterizations to animal models 3 votes, priority Low.

Results of Feature Prioritization (3 of 3) Jira number caNanoLab-24 Feature: Add support for Structure-Activity-Relationships (SARs) Description: Interface with the Collaboratory for Structural Nanotechnology (CSN) 9 votes, priority High. Jira number caNanoLab-25 Feature: Integrate with the Nanoparticle Ontology (NPO) Description: Allow users to submit and browse caNanoLab terms leveraging the NPO. 8 votes, priority High. Jira number caNanoLab-26 Feature: Provide support for automatic report generation Description: Allow researchers to export data in a customized report leveraging a report template. 2 votes, priority Low. Jira number caNanoLab-27 Feature: Add Google-like Search Description: Add capability to perform freestyle search. 2 votes, priority Low. Jira number caNanoLab-28 Feature: Provide links to clinically validated biomarkers in support of nanomaterial design Description: Provide links to biomarker repositories. 5 votes, priority Medium.

caNanoLab Priorities

caNanoLab Collaborations Collaborating with Thomson Reuters on accessing caNanoLab data within publications Providing Thomson Reuters with information on querying for caNanoLab data using the caNanoLab grid API to obtain information on nanomaterial samples and publications

Next Steps Deploy caNanoLab to Production Begin caNanoLab Technology Stack Upgrades Begin Prioritization Discussion on In Vivo Characterization Components Host next caNanoLab Users Group Meeting: Users Group Meeting: June 7, :00 PM EST Agenda: Discuss caNanoLab status Discuss prioritization of in vivo characterization components

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

References caNanoLab Portal caNanoLab Wiki caNanoLab JIRA Tracker ISA-TAB-Nano Data Standard ISA-TAB