NIH | National Cancer Institute | NCI Wiki  

Versions Compared

Old Version 20

changes.mady.by.user Gaheen, Sharon (NIH/NCI) [C]

Saved on

compared with

New Version Current

changes.mady.by.user Bleich, Deena (NIH/NHLBI) [C]

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Add version 3.1.14
Section

caNanoLab logoImage Added


caNanoLab Overview

Image Removed
caNanoLab Portal Image Removed

The cancer Nanotechnology Laboratory portal (caNanoLab) is a web-based portal designed to facilitate data sharing in the research community to expedite and validate the use of nanomaterials in biomedicine. caNanoLab provides support for the annotation of nanomaterials with characterizations resulting from physico-chemical and in vitro nanomaterial assays and the sharing of these characterizations and associated nanotechnology protocols in a secure fashion.

caNanoLab is a collaboration between the
Column
width20%40%
Panel
titleContents of this Page

Table of Contents

maxLevelinfo

minLevel2

Tip
iconfalse
titleKeeping Up With caNanoLab Documentation
Panel
titlecaNanoLab Project Links
Panel
titleNanotechnology CDE and Terminology Development
Panel
titleNanotechnology Resources
Column

For information about this caNanoLab release:

Column
Panel
titleAt a Glance Details
  • Version Number: 3.1.14
  • Release Date: February 14, 2024
  • Primary audience: Investigators and researchers interested in information about the characterizations of nanomaterials used in biomedical research.
  • The new release 3.1 has been moved to deploy on the Google Cloud App Engine Flex system. For now, use the 3.0 release for local installations.
  • Installation Level (for 3.0): Intermediate - technical assistance may be required, download may require supporting infrastructure or software.
  • System Requirements (for 3.0): This is a web-based application that can be accessed through an industry standard browser. Installation requires:
    • Memory 1GB or more (Linux, Solaris, or Windows)
    • Disk storage 36 GB (minimum)
    • Database Server: MySQL v 5.5.x
    • JBoss Wildfly, 8
    • Java 1.8

Include Page
wikicontent:Included Help Downloading Files Panel
wikicontent:Included Help Downloading Files Panel

Tool Overview

Include Page
Introduction
Introduction

caNanoLab provides access to information on:

  • Nanotechnology protocols in biomedicine
  • Composition of nanomaterials
  • Functions of nanomaterials (for example, therapeutic, targeting, diagnostic imaging)
  • Physico-chemical characterizations including size, molecular weight, shape, physical state, surface chemistry, purity, solubility, and relaxivity
  • In Vitro characterizations such as cytotoxicity, blood contact properties, oxidative stress, and immune cell functions
  • Publications and reports from nanotechnology studies in biomedicine

caNanoLab was developed as a collaboration between the NCI Center for Biomedical Informatics and Information Technology (CBIIT),

...

the NCI Nanotechnology Characterization Laboratory (NCL), and

...

the NCI

...

caNanoLab and Standards Development

The caNanoLab project is actively involved in a variety of efforts supporting the development of standards for representing nanomaterials and their characterizations as applied to the field of nanomedicine. The caNanoLab project participates in the caBIG® Integrative Cancer Research (ICR) Nanotechnology Working Group (Nano WG) which is chartered to integrate nanotechnology information and tools to aid discovery and clinical translation in the cancer research community leveraging caBIG infrastructure components. The primary objectives of the caBIG ICR Nano WG are to:

  • Define and prioritize development and governance needs for the cancer nanotechnology ontology
  • Adopt and collect data sharing standards and protocols for cancer nanotechnology data
  • Develop a vision for nanoinformatics enabling information exchange with nanotechnology resources leveraging data standards

The caNanoLab project participates in working group objectives by assisting in the development of nanotechnology standards and the application of these standards in the caNanoLab nanotechnology resource. Information on caBIG ICR Nano WG standards leveraged by caNanoLab is provided in the subsections below.

Nanotechnology Data Sharing Standards

The caNanoLab project worked with the caBIG ICR Nano WG to develop a Nanotechnology Data Sharing Standards document which identifies common data elements leveraged across nanotechnology resources.
Nanotechnology Data Sharing Standards includes support for:

  • Nanomaterials and their Composition - Nanomaterials (e.g. dendrimer) and their associated properties (e.g. branch, generation) and composing elements (e.g. core). Includes functionalizing entities (e.g. small molecule, antibodies) associated with the nanomaterial that allow the material to function as a targeting, therapeutic, and/or diagnostic agent.
  • Physico-Chemical Characterizations - Assay conditions and measurements associated with the physical (e.g. size, molecular weight) and chemical (e.g. surface chemistry) properties of nanomaterials.
  • In Vitro Characterizations - Assay conditions and measurements that assess a nanomaterial's interaction with cellular components including cytotoxicity and blood contact properties.
  • In Vivo Characterizations - Characterizations performed on nanomaterials to determine the safety, efficacy, pharmacokinetics, and toxicology properties of nanomaterials in animal models so that nanomaterials can be transitioned for use in clinical applications.
NanoParticle Ontology

caNanoLab consumes of and contributes to the NanoParticle Ontology (NPO). Information on the NPO is available on the caBIG ICR Nano WG Ontology Development and Governance Site.

nano-TAB

nano-TAB is a tab-delimited spreadsheet type of format facilitating the submission and exchange of data pertaining to nanomaterial composition and their characterizations. The caNanoLab project participates on the caBIG ICR Nano WG sub-group supporting the development of nano-TAB which leverages and extends the ISA-TAB standard.

To become a member of the nano-TAB sub-group, please subscribe to the nano-TAB Listserv. Artifacts from the sub-group are available on the nano-TAB project site

LS DAM Nano Sub-Domain

caNanoLab has been working with the caBIG Life Sciences Domain Analysis Modeling (LS DAM) team to develop a nano sub-domain. The nano sub-domain is based on the caNanoLab object model (nano-OM) extended to support existing LS DAM concepts. The caNanoLab project aims to develop future services leveraging the NCI's Enterprise Compliance and Conformance Framework (ECCF).

Data Curation

Data curation is a key component for ensuring that data is appropriately annotated to facilitate data sharing in a semantically interoperable fashion. Data curation activities on caNanoLab are currently performed by nanotechnology data scientists at Washington University and the Nanotechnology Characterization Laboratory (NCL). Data curators assist in extracting data from publications and nanotechnology experiments, annotating extracted data, and providing overall data quality control. If you are interested in submitting your data into caNanoLab, please contact the caNanoLab Users Listserv.

caNanoLab Architecture

caNanoLab leverages the caCORE SDK and caGrid technologies to develop, deploy, and advertise common services for nanomaterials and characterizations. caNanoLab grid services are available through caB2B and other caBIG resources consuming of caGrid services.

caNanoLab Users Group

caNanoLab hosts data from a variety of organizations conducting nanomaterial characterizations. caNanoLab feature requests are obtained by working with the nanotechnology community through the caNanoLab Users Group and the caBIG ICR Nano WG.

caNanoLab Users Group meetings occur the 3rd Friday of every month from 1:30PM-2:30PM ET. caNanoLab Users Group Presentations are available on the caNanoLab Project Site. To become a caNanoLab Users Group member, please subscribe via the caNanoLab Users Listserv.

Using the caNanoLab Wiki

...

Office of Cancer Nanotechnology Research (OCNR).

Data Curation

Data curation is a key component for ensuring that data is appropriately annotated to facilitate data sharing in a semantically interoperable fashion. Data curation activities on caNanoLab are currently performed by the NCI Alliance for Nanotechnology in Cancer Data Coordinators and the NCI data curator. Data curators assist in extracting data from publications and nanotechnology experiments, annotating extracted data, and providing overall data quality control. If you are interested in submitting your data into caNanoLab, contact caNanoLab-Support@ISB-CGC.org.

Detailed data curation steps are explained in the Curation of Biomedical Data into ISA-TAB-Nano and caNanoLab Standard Operating Procedure.

Installation and Downloads

caNanoLab 3.1.14 Artifacts

caNanoLab 3.1.13 Artifacts

caNanoLab 3.1.12 Artifacts

caNanoLab 3.1.11 Artifacts

caNanoLab 3.1.10 Artifacts

caNanoLab 3.1.9 Artifacts

caNanoLab 3.1.8 Artifacts

caNanoLab 3.1.7 Artifacts

caNanoLab 3.1.6 Artifacts

caNanoLab 3.1.5 Artifacts

caNanoLab 3.1.4 Artifacts

caNanoLab 3.1.3 Artifacts

caNanoLab 3.1.2 Artifacts

caNanoLab 3.1.1 Artifacts

caNanoLab 3.1.0 Artifacts

caNanoLab 3.0 Artifacts

caNanoLab 2.4.1 Artifacts

caNanoLab 2.4 Artifacts

caNanoLab 2.3.11 Artifacts

Forum and Support

Presentations, Demos and Other Materials

The caNanoLab Data Submission Video and accompanying transcript is available to assist people in submitting data in caNanoLab. 

Note: Materials for previous caNanoLab releases are available from the caNanoLab Presentations, Demos and Other Materials archive. 

Documentation and Training

To access online help in the application, click the Help button.

Note: Documents for previous caNanoLab releases are available from the caNanoLab Presentations, Demos and Other Materials Archive and the Docs Archive Page - calab. 

Related Tools and Terminology

Include Page
wikicontent:Included Help Downloading Files Panel
wikicontent:Included Help Downloading Files Panel