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For a new project, where no samples have yet been added, the Data tab will automatically prompt you to add samples (Figure 21). To add samples to the project, click Import data. Four options will be displayed.

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Select the Automatically create samples from files button. The next screen will feature a file browser that will show any folders you have access to in the Partek Flow server (Figure 32). Select a folder by clicking the folder name. Files in the selected folder that have file formats that can be imported by Partek Flow will be displayed and tick-marked on the right panel (Figure 3). You can exclude some files from the folder by unselecting the check mark on the left side of the filename. When you have made your selections, click the Create sample button.

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Alternatively, files can also be uploaded and imported into the project from the user's local computer. Select the My computer radio button (Figure 43) and the options of selecting the local file and the upload (destination) directory will appear. Only one file at a time can be imported to a project using this method.

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Please be aware that the use of the method illustrated in Figure 4 3 highly depends on the speed and latency of the Internet connection between the user's computer and the server where Partek Flow is installed. Given the large size of most genomics data sets, is not recommended in most cases.

After successful creation of samples from files, the Data tab now contains a Sample management table (Figure 54). The Sample name column in the table is automatically generated based on the filenames and the table is sorted in alphabetical order.

Clicking the on the Show data files link on the lower right side of the sample management table will expand the table and reveal the filenames of the files associated with each sample (Figure 5). Conversely, clicking on Hide data files will hide the file information.

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Select the Import samples from another project button. A dialog box will allow selection of the samples (Figure 65). The drop down menu Project lists the existing projects that the current user has access to. They may be previous projects from the same user, previous projects from collaborators, or (if the user has an administrative account) all the projects in the Partek Flow server.

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Samples can be added one at a time by selecting the Create a new blank sample option (Figure 76). In the following dialog box, type a sample name and click Create. This process creates a sample entry in the sample management table but there is no associated file with it, hence it is a "blank sample."

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Additional samples can be added to any existing project simply by opening the project, going to the Data tab, and clicking the Import data button (Figure 87). Three options to add samples will be revealed.

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Alternatively, if you have a matrix of data, such as raw read count data in text format, select Import feature counts. This will bring up the Input options page (Figure 98).

A box showing a text preview of the first 15 rows of the text file should help you determine on which row the relevant feature counts are located. Inspect the text preview and indicate which row the data header begins.

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Otherwise, manually specify the orientation of the data matrix by changing the Input format drop-down menu (Figure 109). If the data has been log transformed, specify the base under Counts format.

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Attributes can be managed or created within a project. Under the Data tab, click the button to open the Manage attributes page (Figure 1110).

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To add a categorical attribute in the Manage attributes page, click the Add new attribute (Figure 1211). In the dialog box, type a Name for the attribute, select the Categorical radio button next to Attribute type, select the visibility of the attribute and then click the Add button.

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Individual categories for the attribute must then be entered. Enter a name of the New category and click Add. The Name of the new category will show up in the table. The category can also be edited by clicking  or deleted by clicking  . Additionally, sub-categories can be added by clicking Image RemovedImage Added in the Options column. After all the categories have been added to this attribute, click Close to proceed.

Repeat the process for additional attributes of the samples in your study. When done, click Back to sample management table. Categorical attributes will default to Project-specific visibility. 
An additional feature to facilitate the controlled vocabulary in Partek Flow is the integration of terms used by SNOMED CT, a healthcare terminology used for electronic health records. They can be added easily by managing the categories of an attribute and selecting Import terms from SNOMED CT shown in Figure 1312. Available terms include those for body structure, specimen, clinical findings, or organism. Select multiple terms from SNOMED CT by holding Ctrl key on the keyboard while clicking the mouse to select. These terms will become new top level categories in your attribute. When terms are imported from SNOMED CT, the Term depth indicates the number of sublevels that will also be imported as subcategories in your attribute.

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To add a numeric attribute in the Manage attributes page, click the Add new attribute. In the dialog box (Figure 1413), type a Name for the attribute, select the Numeric radio button next to Attribute type, and then click the Add button. Some optional parameters for numeric attributes include the Minimum value, Maximum value, and Units. When done, click Add to return to the Manage attributes page. Repeat the process add more numeric attributes. When done, click Back to sample management table.

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In the Data tab, click Add a system-wide attribute button. In the dialog box that follows (Figure 1514), a drop down menu is located next to Add attribute where you can select the System-wide attribute you would like to add to the project. Once selected, it will be recognized automatically as either Categorical, system-wide or the Numeric attribute.

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After adding all the desired attributes to a project, the sample management table will show a new column for each attribute (Figure 1615). The columns will initially as "N/A", as the samples have not yet been categorized or assigned a value. To edit the table, click  . Assign the sample attributes by using a drop down for categorical attributes (controlled vocabulary) or typing with a keyboard for numeric attributes.

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Using a text editor, prepare a table containing the attributes. An example is shown in Figure 1716. There should only be one tab between columns with no extra tabs after the last column. In this particular example, the first column contains the filename and the text file is saved as Sampleinfo.txt.

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To upload sample attributes, click Assign sample attributes from a file in the Data tab. Then indicate where the attribute text file is stored and navigate to it. Partek Flow will parse the text file and present attributes that will be available for import (Figure 1817).

Select the attributes you want to import by clicking the Import check box. Imported attributes that do not currently exist in the project will create new project-specific attributes.

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• The first column is always the unique identifier and can refer only to File names or Sample names.
• If using Sample names in the first column, they must match the entries of the Sample name column in the Sample management table.
• If using File names in the first column, use the filenames shown in the fastq column of the expanded sample management table (see Figure 54) then add the extension .gz. All filenames must include the complete file extension (e.g., Samplename.fastq.gz).
• The header name of the first column of the table (top left cell of our text table) is irrelevant but should not be left blank. Whether the first column contains File names or Sample names will be chosen during the process.
• The last column cannot have empty values
• Missing data (blank cells) can only be handled if the attribute is numeric. If it is categorical, please put a character in it.

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In the Data tab, each sample can be renamed or deleted from the project by clicking the gear icon next to the sample name. The gear icon is readily visible upon mouse over (Figure 1918). Deleting a sample from a project does not delete the associated files, which will remain on the disk.

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