Managing Synthesis - 2021-07-12

This chapter describes how to manage synthesis information in caNanoLab samples. Topics in this chapter include:

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.

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.

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 sections: (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.

Adding or Editing Synthesis Materials in a Sample

1. 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.
2. (Protocol and description details TBD.)
3. (Materials details TBD.)
4. Add files. For details, refer to (link TBD).
5. Click Update. 

Adding or Editing Synthesis Functionalization in a Sample

1. 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.
2. (Protocol and description details TBD.)
3. (Functionalization details TBD.)
4. Add files. For details, refer to (link TBD).
5. Click Update.

Adding or Editing Synthesis Purification in a Sample

1. In the Purification 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.

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

   Section	What to Do
   Purification Type	Fill in the general information about the purification. Select a Purification Type. (TBD: Do we need to provide guidance for choosing interim or final?) Select a Protocol. (TBD: 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: Do we need to provide guidance for specifying a value?)
   Design and Methods	Complete the fields describing techniques and instruments used to derive the data. For details, refer to (link TBD).
   Finding	Click Add to expand the section. 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 Conclusion	Enter any relevant analyses and conclusions reached by the data.
   Files	Add supporting documentation relating to the purification. Import as many files as you wish. Click Add to expand the section. For details, refer to (link TBD).

3. Click Update.

Defining Purification Techniques and Instruments

When you are adding purification information, fill in the following design, methods, and techniques used.

When you are finished, click Save.

Adding Data Findings to Synthesis Purification 

To add findings to purification information, you can add data directly to Data and Conditions by creating columns and adding data manually or you can import as many .csv files as needed. Information can include laboratory conditions, pH, or temperature. You can add as many files as you wish.

1. Add data values to Data and Conditions.

   1. To import a file of data values

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

      2. Click Import csv and select and follow the prompts to add the data file to the Findings Info.

      3. The columns and data are added to Data and Conditions.

   2. 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.

2. Whether you imported or added information 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).

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

5. 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).

   • For Column Type Condition, (Column Name options TBD). 

6. 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).

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

8. 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.

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

10. Click Save in the Finding section.

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 File section of the page, next to Files, click Add.
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.