Managing Samples in caNanoLab | caNanoLab User's Guide| Managing Sample Characterizations
This chapter describes how to manage the samples' information accessible from the Navigation Tree. Topics in this chapter include
Sample Composition Overview
Sample composition records information associated with the way a sample is made, especially in terms of its different parts, its constituents. Composition for a sample in caNanoLab consists of information categorized by nanomaterial entity, functionalizing entity, and chemical association(s). You can also add files relevant to the sample composition or derivation of its data.
- Nanomaterial Entity composition describes the component of a sample that is a nanoparticle.
- Functionalizing Entity composition describes the substance, physical or biological factor, etc. of the sample that produces a specific effect.
- Chemical Association composition annotations describes the chemical association(s) of the nanoparticle/functionalizing entities of the sample.
- Composition File enables you to add files relevant to the sample independently of the entity or chemical associations.
Accessing the Sample Composition Summary
If you have read-only access, you can review the sample composition summary.
To access characterization functions in the Navigation Tree
- Click Samples and Search Existing Samples.
- Fill in criteria, and click Search.
- Click Edit in the search results.
- The Navigation Tree appears on the left sidebar and comprises functions which you can use to add annotations to the sample.
NAVIGATION TREE GENERAL INFO COMPOSITION CHARACTERIZATION PUBLICATION - General Info appears after you click the sample name and shows the Update Sample page.
- Composition defines Nanomaterial Entity, Functionalizing Entity, and Chemical Associations.
- Characterization defines essential physical characteristics that identify the material and structural properties via the Protocol and Physico-Chemical, In Vivo, and In Vitro Characterization.
- Publication displays articles, books chapters, reviews and reports already added to a sample.
Click Composition.
The All tab displays compositions already added to the sample by category. Additional tabs show items added to the sample for each subcategory.
Adding Nanomaterial Entity Composition Annotations
To add a nanomaterial entity
- Access a sample and composition.
Click the Nanomaterial Entity tab or the All tab and click Add next to Nanomaterial Entity.
Both tabs provide customizations based on your Nanomaterial Entity Type* selection.
To enter an alternative to an option, select other if available and enter a value. The value is added to the list of options.
Follow these steps to fill in the composition. Links are provided for additional details.
Step... What to Do.. Nanomaterial Entity Type* Fill in the entity type (required) and add a Description for the entity.
A Biopolymer nanoparticle is a type of polymer that is produced by living organisms. In the context of nanotechnology, a biopolymer can also be a nanomaterial entity or a functionalizing entity.
A Carbon Nanotube (CNTs) is a fullerene-like nanostructure that consist of graphene cylinders. The ends of the construct are closed with pentagonal-shaped rings.
Dendrimer is a polymeric molecule which has a highly-branched, three-dimensional architecture. Dendrimers are synthesized from monomers and new branches are added in discrete steps to form a tree-like architecture. A high level of synthetic control is achieved through iterative reactions and purification at each step to regulate the size, architecture, functionality and monodispersity of the molecules. These polymers have desirable pharmacokinetic properties and a polyvalent array of surface groups that make them potential drug delivery vesicles.
An Emulsion is a suspension of liquid within another liquid or a dispersion consisting of two or more liquid phases. In the context of caNanoLab, an emulsion nanoparticle consists of nanoparticles suspended in an emulsifying liquid.
A Fullerene is one of three known pure forms of carbon that exhibits a spherical shape with a hollow interior; named after Buckminster Fuller. The number of carbon atoms comprising fullerenes is variable; several stable spherical carbon structures containing 70 or more atoms have been documented.
A Liposome is a substance composed of layers of lipid that form hollow microscopic spheres within which drugs or agents could be contained for enhanced safety and efficacy. Based upon its size measured in nanometer range, a liposome can be categorized as a nanoparticle.
A Metal Particle is a nanoparticle composed of electropositive chemical elements characterized by ductility, malleability, luster, and conductance of heat and electricity. They can replace the hydrogen of an acid and form bases with hydroxyl radicals.
A Quantum Dot is a nanometer-sized semiconductor particle, made of cadmium selenide (CdSe), cadmium sulfide (CdS) or cadmium telluride (CdTe) with an inert polymer coating. The semiconductor material used for the core is chosen based upon the emission wavelength range being targeted: CdS for UV-blue, CdSe for the bulk of the visible spectrum, and CdTe for far red and near-infrared. The size of the particle determines the exact color of a given quantum dot. The polymer coating protects cells from cadmium toxicity but also facilitates the attachment of a variety of targeting molecules, including monoclonal antibodies directed to tumor-specific biomarkers. Because of their small size, quantum dots can function as cell- and even molecule-specific markers that will not interfere with the normal cellular functions.
A key feature that distinguishes a Polymer from other molecules is the repetition of a linked series of many identical, similar, or complementary monomers. A polymer nanoparticle is just that--a polymer measured in nanometer range.
Nanomaterial Properties Based on the Entity Type, fill in the appropriate Properties. Composing Elements Add information regarding the elements that compose the nanomaterial entity of the sample. Composition File Click Add to expand the page to add one or more files whose data is relevant to the nanomaterial entity or the derivation of its data.
Copy to other samples with the same primary organization? Select samples in the list to which you want this physico-chemical data transferred. This option copies files and data to one or more selected samples "owned" by the same point of contact. When you finish, click Submit to save the data to the sample.
Defining Nanomaterial Entity Properties
If you selected one of the Nanomaterial Entity Types listed in the following table, the Properties section opens, and you must fill in additional information.
| Nanomaterial Entity Type | Properties to Complete |
|---|---|
Biopolymer |
|
Carbon Nanotube | Enter the Average Length of the nanotube. Enter the Length Unit of measurement for the average length measurement of the nanotube.
Enter information about the Chirality in the nanotube and its effect on the orientation of functional groups located on the particle. Enter the measurement of the nanotube Diameter, as measured from one side of the tube wall through the center of the nanotube to the opposite point on the circumference. Enter the Diameter Unit of measurement for the nanotube diameter. Select the appropriate description of the nanotube Wall Type.
|
Dendrimer | Branches are molecules that branch off of the core (like tree branches).
Generations are shells layered on the core of a dendrimer. Dendrimers consist of layers of chemical shells built on a core module. Each shell consists of two chemicals in the same order (A-B) and each shell is called a generation. The generations are labeled in decimal to illustrate the shell layering/consistency. For example, Generation 2.5 (G2.5) = 1 shell of A-B (1), surrounded by a second shell of A-B (2), topped off with only one chemical A within the shell (.5). As such, the layering structure would be (A-B, A-B, A) = 2.5.
|
Emulsion | Specify whether the composition Is Polymerized (required). Polymerization consists of enzymatic reactions that link a series of monomers, forming a polymerized compound (polymer), usually of high molecular weight, by combination of simpler molecules (monomers). Enter the name of the polymer (Polymer Name) suspended in the emulsion (required). |
Fullerene | Enter the Average Diameter measurement, as measured from one side of the nanoparticle through its center to the opposite point on the circumference. Enter the Average Diameter Unit of measurement for the fullerene diameter. Enter the Number of Carbon molecules comprising the fullerene. |
Liposome | Enter the name of the liposome polymer (Polymer Name). Polymerization consists of enzymatic reactions that link a series of monomers, forming a polymerized compound (polymer), usually of high molecular weight, by combination of simpler molecules (monomers).
|
Polymer | In Initiator, enter the agent that initiated the polymerization. Examples are free radicals or peroxide. Crosslinking is a covalent bond between two polymers or two different regions of the same polymer.
In Crosslink Degree, enter the percentage level of covalent linkage in the polymer. |
Defining Nanomaterial Composing Elements
Define the following composing elements for the nanomaterial entity.
| Complete... | How to... |
|---|---|
| Composing Element Type* | Select the type of composing element comprising this nanomaterial (required).
|
| Chemical Name* | Enter the chemical name given to the atomic or molecular structure that composes the center of the nanoparticle (required). |
| Crosslink Degree | Enter the percentage level of covalent linkage in the polymer. |
| PubChem Data Source/PubChem ID | Select one of the three PubChem data sources: Compound, Substance, or BioAssay. The database is located here: http://pubchem.ncbi.nlm.nih.gov/. Enter the PubChem ID which is the PubChem identifier for a compound, a substance, or a bioassay. |
| Amount/Amount Unit | Select the appropriate values and unit for this composing element information. |
| Molecular Formula Type | |
| Molecular Formula | Enter the chemical formula of the nanoparticle. |
| Description | Enter a description for the composing element. |
| Inherent Function | Inherent function is the characteristic behavior of a sample that results from the chemical and physical composition and properties of the entity. Click Add to expand the page where you can enter this information. |
| Function Type | Select the function type category which best fits the nanomaterial entity. If you select imaging function, you must specify an Imaging Modality Type. |
| Description | Enter any additional function information for the nanomaterial entity that the form does not already include. |
Once you add the composing element, click Save or Cancel to close the window.
Adding Functionalizing Entity Composition Annotations
To add a functionalizing entity
- Access a sample and composition.
- Click the Functionalizing Entity tab or the All tab and click Add next to Functionalizing Entity.
Both tabs provide customizations based on your Functionalizing Entity Type* selection.
To enter an alternative to an option, select other if available and enter a value. The value is added to the list of options.
Follow these steps to fill in the composition. Links are provided for additional details.
Step... Description... Functionalizing Entity Select the Entity Type and complete the entity information.
Functionalizing Entity Properties Based on the Entity Type, you may need to fill in additional Properties. Inherent Function Information Add information about the functionalizing elements of the sample. Composition File Add one or more files containing data that is relevant to the functionalizing entity or the derivation of its data.
Copy to other samples with the same primary organization? Select one or more samples in the list to which you want this composition data transferred. This option copies files and data to one or more selected samples "owned" by the same point of contact. When you finish, click Submit to save the data to the sample.
Defining a Functionalizing Entity
Fill in the following functionalized entity information as needed.
| Complete... | How to... |
|---|---|
| Chemical Name | Enter the chemical name for the functionalizing entity whose type you just selected. |
| PubChem Data Source/PubChem ID | Select one of the three PubChem data sources: Compound, Substance, or BioAssay. The database is located here: http://pubchem.ncbi.nlm.nih.gov/. Enter the PubChem ID which is the PubChem identifier for a compound, a substance, or a bioassay. |
| Amount/Amount Unit | Select the appropriate values and unit for this composing element information. |
| Molecular Formula Type | |
| Molecular Formula | Enter the chemical formula of the functionalizing entity. |
| Activation Method | Select the method used to activate the functionality of the sample from the list. If you do not have to activate the entity, select does not require activation.
|
| Activation Effect | Enter the functional effect of the entity. |
| Description | Enter any additional composition information that the form does not include. |
Once you add the inherent function, click Save or Cancel to close the window.
Defining Functionalizing Entity Properties
If you selected one of the Functionalizing Entity Types listed in the following table, the Properties section opens, and you must fill in additional information.
| For Entity Type | Complete the Properties... |
|---|---|
| Antibody | Select the Type of antibody functioning for this sample. Select the Isotype for this antibody. Select the animal Species from which the antibody was derived. |
| Biopolymer | Select the Biopolymer type of antibody functionalizing entity for this sample. Using the appropriate format, enter the complete Sequence of the biopolymer. |
| Small Molecule | Add an Alternate Name for the Small Molecule. |
Defining Function Information
Fill in the following inherent function information for the functionalizing entity.
| Complete... | How to... |
|---|---|
| Function Type | Select the function type category which best fits the nanomaterial entity. If you select imaging function, you must specify an Imaging Modality Type. |
| Description | Enter any additional composition information that the form does not include. |
When you are done, click Save or Cancel to close the window.
Adding Chemical Association Composition Annotations
You can enter basic annotation information describing the chemical association(s) of the sample and/or functionalizing entities of the sample.
Chemical association requirement
To enter chemical association information, you must enter at least two composing elements and/or at lease one functionalizing entity to the sampe entity.
To add a chemical association
Click the Chemical Association tab or the All tab and click Add next to Chemical Association.
Both tabs provide customizations based on your Association Type* selection.
Follow these steps to fill in the association. Links are provided for additional details.
Complete... How to... Association Type* Select a chemical association type (required).
- Association
- Encapsulation
- Entrapment
- Intercallation
Description Enter any additional information that describes the chemical association of the two elements.
Elements Information In the Elements Information section, both Element boxes list the nanomaterial or functionalizing entities you defined while annotating the sample.
Each time you select an option, a list displays entities relating to your previous selection.
Select an option from each list.
The arrow between the Element text boxes symbolizes the association between the two.
Composition File Click Add to expand the page where you can add one or more files whose data is relevant to the functionalizing entity or the derivation of its data.
When you are finished, click Submit to save the association to the sample.
Adding Composition Files
You can add results in the form of supporting documents, such as a graphic, spreadsheet or images, to a sample or files relevant to the sample independent of the entity or chemical associations that you defined.
To add files to a sample
To add a file, click the Composition File tab or the All tab and scroll to the File section.
Click Add next to File.
- Upload, browse, and select the file or enter the file's URL where the document is located.
- Complete the following.
- Select the File Type (required), Document, Graph, Image, Movie, or Spreadsheet.
- Enter the File Title (required).
- Specify Keywords to associate with the file
- Enter a Description of additional information of the file.
Click Submit to add the file(s) to the sample.
Editing and Deleting a File
Once you add a composition file, you can remove the file or edit the composition file information.
To delete a file, click Edit and on the Edit Composition File page, click Delete.
To update the file information, click Edit and on the Edit Composition File page, make the changes and click Update. The list of files is updated.
