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Managing Samples in caNanoLab | caNanoLab User's Guide| Managing Sample Characterizations
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If you have read-only permissions, see Viewing a refer to Accessing the Sample Composition Summary. If you are a curator with appropriate security permissions, you can perform all the tasks described in this chapter. |
This chapter describes how to manage the samples' information accessible from the Navigation Tree. This section includes the following topics:
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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.
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With the appropriate security permissions, you can add or delete composition details. If the buttons do not display, you have read-only access to the item. |
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With read-only access, you can review the sample composition summary.
To access characterization functions in the Navigation Tree
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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.
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To add a nanomaterial entity
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Click the All or Nanomaterial Entity tab to enter data or add files pertaining to the nanomaterial component of the sample. Both tabs display five sections, but the All tab provides customizations based what you select in the Nanomaterial Entity Type* field.
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Fill in the entity type (required) and add a Description for the entity.
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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.
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When you finish, click Submit to save the data to the sample.
Defining Nanomaterial Entity Properties
The following nanomaterial entity types can be selected in the Nanomaterial Entity Summary. Once selected, a Property section appears on the page. You can describe properties for each type by following these links.
After defining the particle properties, continue to define Biopolymer information.
Biopolymer
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.
Define biopolymer properties.
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Enter the name of the biopolymer.
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Using the appropriate format, enter the complete sequence of the biopolymer.
After defining the particle properties, continue to define Carbon Nanotube information.
Carbon Nanotube
Carbon nanotubes (CNTs) are fullerene-like nanostructures that consist of graphene cylinders. The ends of the construct are closed with pentagonal-shaped rings.
Fill in the carbon nanotube properties as needed.
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Enter the average length of the nanotube.
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Select or enter the measurement unit type for the average length measurement of the nanotube.
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The spatial position or orientation of functional groups located within a molecule. Enter information about the chirality in the nanotube and its effect on the orientation of functional groups located on the particle.
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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.
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Enter the measurement unit type of the nanotube diameter.
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- Select the appropriate description of the nanotube wall:
- DWNT (Double-Wall Nanotube) Nanotube wall consists of two layers of graphitic carbon.
- MWNT (Multiple-Wall Nanotube) Nanotube consists of single-walled nanotubes layered inside each other
- SWNT (Single-wall Nanotube) Wall consists of a single layer of graphitic carbon
After defining the particle properties, continue to define Dendrimer information.
Dendrimer
A 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.
Fill in the dendrimer properties.
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Branches are molecules that branch off of the core (like tree branches). Enter a description that represents the number of branches in the dendrimer.
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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.
List the generations reflected in this dendrimer.
After defining the particle properties, continue to define Emulsion information.
Emulsion
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.
Fill in the emulsion properties as needed.
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Specify whether the composition is polymerized. 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).
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- Enter the name of the polymer suspended in the emulsion.
After defining the particle properties, continue to define Fullerene information.
Fullerene
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.
Fill in the fullerene properties as needed.
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Enter the measurement unit type of the fullerene diameter.
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Enter the number of carbon molecules comprising the fullerene.
After defining the particle properties, continue to define Liposome information.
Liposome
Liposomes are substances 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.
Fill in the liposome properties as needed. After defining the particle properties, continue to define Metal Particle information.
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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).
Select Yes or No, reflecting whether or not the liposome is polymerized.
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After defining the particle properties, continue to define Metal Particle information.
Metal Particle
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.
There are no unique metal particle properties to be defined. Continue to define Polymer information.
Polymer
A key feature that distinguishes polymers 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.
Define the polymer properties.
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After defining the particle properties, continue to define Quantum Dot information.
Quantum Dot
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.
There are no unique quantum dot properties to be defined. Continue to define Nanomaterial Composing Elementsinformation.
Defining Nanomaterial Composing Elements
Define the composing elements for the nanomaterial entity.
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Inherent function is the characteristic behavior of a sample that results from the chemical and physical composition and properties of the entity.
Click the Add button to expand the page where you can enter this information.
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Click Save to add the inherent function details to the nanomaterial entity or Cancel to just close the window.
After defining composing elements, continue to define Add supporting documentation files.
Adding a File
To add results in the form of supporting documentation to the nanomaterial entity
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After adding one or more files, return to the steps described in Adding Nanomaterial Entity Composition Annotations.
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Click the All or Functionalized Entity tab to enter data or add files pertaining to the nanomaterial component of the sample. Both tabs display five sections, but the All tab provides customizations based what you select in the Functionalized Entity Type* field.
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Fill in the entity type (required).
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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.
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When you finish, click Submit to save the data to the sample.
Defining a Functionalizing Entity
To define a functionalized entity
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Continue to define Functionalizing Entity type] Properties.
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The [Funtionalizing Entity Type] Properties section opens for some Functionalizing Entity types as you make that selection. To define properties for each unique functionalizing entity, enter information for the following fields.
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Antibody – Select from the following fields:
- Type: Select from the drop-down list the type of antibody functioning for this sample.
- Isotype: Select from the drop-down list the isotype for this antibody:IgA
- Species:Select from the drop-down list the animal species from which the antibody was derived.
Biopolymer – Select from the following fields:
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Small Molecule: Add an Alternate Name for the Small Molecule.
Continue to define Function information.
Defining Function Information
To define function information for the functionalizing entity
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In the Navigation Tree, a hyperlink for the new Composition characterization is added under Functionalizing Entity.
Continue to Add files, if needed.
Adding a File
To add results in the form of supporting documents to the functionalizing entity, follow these steps:
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As appropriate, continue the process described in Adding Functionalizing Entity Composition Annotations or Adding Chemical Association Composition Annotations.
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Using the [Sample] Composition Chemical Association subcategory, you can enter basic annotation information describing the chemical association(s) of the sample and/or functionalizing entities of the sample.
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To enter chemical association information, you must have entered at least two composing elements and/or at least one functionalizing entity for the sample entity. |
To enter chemical association information
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- Once you enter the essential nanomaterial entity and functionalizing entity information under the Composition category, click the Add button corresponding to Chemical Association on the All tab or select the Chemical Association tab itself where you can click the Add button.
- The page that opens is organized into three sections. Select from the drop-down list the Association Type (required). Options include:
Description: Enter any additional information that describes the chemical association of the two elements. - In the Elements Information section, both Element boxes select the nanomaterial or functionalizing entities for which you are defining the chemical association. These have been previously defined for the sample you are annotating. For each selection you make, another drop-down list appears displaying entities relating to your previous selection. Make the appropriate selections in each.The arrow between the Element text boxes symbolizes the association between the two.
- In the File section, click Add to expand the page where you can add one or more files whose data is relevant to the nanomaterial entity or the derivation of its data.
Adding Composition Files
This section of the [Sample] Composition category allows you to add files relevant to the sample independently of the entity or chemical associations that you defined. You can add as many files as you wish.
To add a file
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- After you click the Composition button on the Navigation Tree, click the Composition File Add button.
The Composition File page opens. - Select the Upload button, then click the Browse button to navigate to the report or publication to be associated with the sample,
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Click the Enter File URL button and enter the URL where the document is located. - For the file to be added, specify or enter the following:
- File Type (required): Document, Graph, Image, Spreadsheet
- File Title (required)
- Keywords to associate with the file
- Description: Enter any additional information for the file that the form does not already include.
- In the Visibility field, select the group(s) to be granted access to the selected file.
- When you finish, click Submit to add the referenced file(s) to the sample or click Reset to clear all fields on the form.
After adding one or more files, continue the process described in Adding Chemical Association Composition Annotations.
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You can add as many files as you wish. |
For more information about working with publications, see Managing Publications.
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