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This chapter describes how to manage synthesis information in caNanoLab samples. 

  • If you have a read-only account, you can view, print, or export sample information. For details, refer to (link TBD). 
  • If you have a curator account associated with an existing sample, you can also add, edit, or delete information in that sample.

This chapter includes the following topics. (TBD: I might split this page into multiple pages, one page for each topic.)

Viewing, Printing, or Exporting Synthesis Information in a Sample

You can view information in an existing sample. 

  1. Search for the sample, as described in Managing Samples in caNanoLab. The Sample Search Results page appears.

  2. In the row for the sample you want to view, click View. The Sample page appears.

  3. In the Navigation Tree, click Synthesis. The Sample (sample name) Synthesis page appears.
  4. Select the tab for the category of information you want to view (Materials, Functionalization, or Purification), or remain on the default tab (All).
  5. To print the information, click Print at the top right of the page.
  6. To export the information to a spreadsheet, click Export at the top right of the page.


To export all sample information to JSON or XML, refer to Managing Samples in caNanoLab.

Adding, Editing, or Deleting Synthesis Information in a Sample

If you are logged into caNanoLab, and if you have a curator account associated with an existing sample, you can add or edit information in that sample. 

  1. Search for the sample, as described in Managing Samples in caNanoLab. The Sample Search Results page appears.

  2. In the row for the sample you want to edit, click Edit. The Update Sample page appears. 

  3. In the Navigation Tree, click Synthesis. The Sample (sample name) Synthesis page appears. 

  4. Select the tab for the category of information you want to add or edit (Materials, Functionalization, or Purification), or remain on the default tab (All).

  5. To add or edit an item, click Add or click Edit next to that item. The Add page or Edit page for that item appears. For details, refer to the following topics: (links TBD)

  6. To delete an item, click Edit next to that item. The Edit page for that item appears. Click Delete. The system moves the deleted item to the sample archive for historical purposes.


If you are logged in and an Add or Edit button is not available, you have read-only access to the data.

Adding or Editing Synthesis Materials in a Sample

  1. Display the Add or Edit page for synthesis material of a sample, as described in (link TBD).
  2. In the Materials tab of the Sample (sample name) Synthesis page, click Add, or click Edit next to the item you want to edit. The Add page or Edit page for that item appears.
  3. Select a protocol and provide a description. (TBD: What guidance can we provide here for specifying a protocol & description?)

  4. In the Materials panel, click Add and fill in the following information.

    CompleteHow to
    Material Type*

    Select the type of material 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).
    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.
     

    (TBD: This panel is similar to composition, but Dev GUI doesn't have PubChem ID field. Is that intentional?)

    Amount/Amount Unit

    Select the appropriate values and unit for this composing element information.

    Molecular Formula Type

    Select the molecular formula type found in this biopolymer.

    Molecular FormulaEnter the chemical formula of the nanoparticle.
    Supplier NameSelect the supplier name. (TBD: What guidance can we provide here for selecting the supplier name?)
    LotSpecify the lot. (TBD: What guidance can we provide here for specifying the lot?)
    Material DescriptionEnter a description for the composing element.
    Inherent Functions

    Next to Inherent Functions, click Add to expand the panel. An inherent function is the characteristic behavior of a sample that results from the chemical and physical composition and properties of the entity. For details, refer to (link TBD).

  5. Click Save Material Element. 
  6. Add files. For details, refer to (link TBD).
  7. Click Update. 

Adding or Editing Synthesis Functionalization in a Sample

  1. Display the Add or Edit page for synthesis functionalization of a sample, as described in (link TBD).
  2. In the Functionalization tab of the Sample (sample name) Synthesis page, click Add, or click Edit next to the item you want to edit. The Add page or Edit page for that item appears.
  3. Select a protocol and provide a description. (TBD: What guidance can we provide here for specifying a protocol & description?)

  4. In the Functionalization Materials panel, click Add and fill in the following information: 

    CompleteHow to
    Functionalization Type*

    Select the type of material 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).
    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.

    (TBD: This panel is similar to composition, but Dev GUI doesn't have PubChem ID field. Is that intentional?)

    Amount/Amount Unit

    Select the appropriate values and unit for this composing element information.

    Molecular Formula Type

    Select the molecular formula type found in this biopolymer.

    Molecular FormulaEnter the chemical formula of the nanoparticle.
    Functionalization DescriptionEnter a description for the composing element.
    Inherent Functions

    Next to Inherent Functions, click Add to expand the panel. An inherent function is the characteristic behavior of a sample that results from the chemical and physical composition and properties of the entity. For details, refer to (link TBD).

  5. Click Save Functionalization Element. 
  6. Add files. For details, refer to (link TBD).
  7. Click Update.

Adding or Editing Synthesis Purification in a Sample

  1. Display the Add or Edit page for synthesis purification of a sample, as described in (link TBD).

  2. Fill in the information as described in the following table: 

    PanelWhat to Do
    Purification Type

    Fill in the general information about the purification.

    • Select a Purification Type. (TBD: What guidance can we provide here for choosing interim or final?)

    • Select a Protocol. (TBD: In the Dev tier, no values show up in this drop-down list for me. Do we need to provide guidance for choosing a value?)

    • Specify the Yield. (TBD: What guidance can we provide here for specifying a value?)

    Design and Methods

    Fill in the design and methods information about the purification.

    • In the Design and Methods Description field, enter a description for the purification design and methods.

      Adding extra lines

      If you include an extra line between text in the Design and Methods Description, the line separation is preserved when you save or update the purification information.

    • Next to Technique and Instruments, click Add to expand the panel. For details on specifying techniques and instruments used to derive the data, refer to (link TBD).
    Finding

    Click Add to expand the panel. Add data findings and supporting documentation relating to the purification. Import as many .csv files as you wish or add derived data manually. For details, refer to (link TBD).

    Analysis and ConclusionEnter any relevant analyses and conclusions reached by the data. 
    Files

    Click Add to expand the panel. (TBD: On the Dev tier, nothing happens when I click Add in the purification Files panel.) Add supporting documentation relating to the purification. Import as many files as you wish. For details, refer to (link TBD).

  3. Click Update.

Defining Inherent Functions

You can add inherent functions to a sample. (TBD: You can add as many as you wish?)

To add each function:

  1. In the Add or Edit page for synthesis (materials or functionalization) of a sample, expand the Inherent Functions panel, as described in (links TBD).

  2. Fill in the following information. 

    CompleteHow to
    Type

    Select the function type category which best fits the nanomaterial entity.
    If you select imaging function, you must specify an Imaging Modality Type.

    DescriptionEnter any additional function information for the nanomaterial entity that the form does not already include.
  3. Click Save Inherent Function. 

Defining Purification Techniques and Instruments

You can add purification techniques and instruments to a sample. (TBD: You can add as many as you wish?)

To add each technique:

  1. On the Add or Edit page for synthesis purification of a sample, expand the Technique and Instruments panel, as described in (link TBD).

  2. Fill in the following information.

    Technique and Instruments PanelDescription

    Technique*

    Select the technique (required).

    Abbreviation

    When you select a technique, Abbreviation populates automatically if an abbreviation is known. If not, enter an abbreviation.

    DescriptionEnter a description of the technique and instruments.
    Instruments

    Click Add to expand the Instruments panel. Enter or select identifying information about the instrument used to obtain data.
    • Select the instrument Manufacturer.
    • Enter the instrument Model Name.
    • Enter the model Type.
     (TBD: On the Dev tier, nothing happens when I click Add next to Instruments.)

  3. When you are finished, click Save Technique. (TBD: On the Dev tier, nothing happens when I click Save Technique.)

Adding Data Findings to Synthesis Purification 

You can add purification data findings to a sample. (TBD: You can add as many as you wish?)

To add each finding:

  1. On the Add or Edit page for synthesis purification of a sample, expand the Finding  panel, as described in (link TBD). 
  2. Under Data and Conditions, add findings such as laboratory conditions, pH, or temperature. You can add data manually or you can import as many .csv files as needed. (TBD: May I have a sample CSV file to import, to test these instructions?)

    • To import a file of data values

      1. Save a spreadsheet of data values to a csv (comma-separated value) file.

      2. Click Import csv. Select the data file and follow the prompts to add it. The system adds columns and data under Data and Conditions.

    • To add the data values manually

      1. Specify the number of columns and rows for the matrix, and click Update.

      2. Add the data values to the rows.

  3. Whether you imported values or added values manually, you can preface each data value with one of the following: Maintain the default, equal to (=), or select greater than (>), less than (<), or infinity (approximate). (TBD: On the Dev tier, these drop-down lists are empty.)

  4. To define a column, click an underlined column heading. The Column Definition panel appears.
  5. Select a Column Type, Datum or Condition.

  6. Select a Column Name or select other and add a new one. You can add up to three cell viability Column Names, including cell viability, cell viability B, and cell viability C. You can further identify the column with the Column Value Type.

    • For Column Type Datum, (Column Name options TBD: What column types are available for each column name?).

    • For Column Type Condition, (Column Name options TBD: Same table as for Characterization?). 

  7. To further identify a column, select a Column Value Type. Once the column information is saved, the Column Type is shown in parentheses after the Column Name, such as cell viability (mean). (TBD: In Dev tier, for condition, no values show up in this drop-down list for me.)

  8. Select a Column Value Unit, or select other and add one.

  9. If you want the same value to fill all rows in a column, add a Constant Value. For Column Value Type, boolean, enter a Constant Value of 1 for true and 0 for false.

  10. Click Save. The system updates the columns. If needed, click Set Column Order to change the order of the column headings in the matrix.

  11. Click Save in the Finding panel.

Adding Supporting Documents to a Sample

You can add supporting documents to a sample. You can add as many files as you wish.

To add each file

  1. In the Add or Edit page for synthesis (materials, functionalization, or purification) of a sample, expand the Files panel, as described in (links TBD).
  2. Select Upload or Enter File URL.
    • For Upload, click Choose File. Browse to the file and select it. 
    • Otherwise, enter the file's URL where the document is located.
  3. Complete the following fields.
    1. Select the File Type (required): Document, Graph, Image, Movie, PDF, or Spreadsheet.
    2. Enter the File Title (required).
    3. Specify Keywords to associate with the file.
    4. Enter a Description of the file or additional information.

  4. Click Save File. The system adds the file to the sample.


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