GC Project provides support for organizing and reporting on sets of data developed during GCxGC analyses. GC Project is invoked from the desktop icon, from the Microsoft Windows Programs menu, or from the GC Image bin folder.
The GC Project graphical user-interface (GUI) is pictured in Figure 1. At the top of the interface are the title bar, menu bar, and tool bar. The File menu has options for creating a new project interactively or with the New Project Wizard (described in a separate chapter); opening a project or a recent project; closing or saving an open project; starting GC Image; and exiting. The Actions menu has options for importing files into a project; auto-processing and processing runs; reviewing images, comparing images (described in Comparative Analysis and Visualization); opening the Compound Library; creating a consensus templates; and exporting calibration tables. The Compound Library, consensus templates, and calibration tables, as well as the options on the Reports menu are described in Reports. Buttons on the tool bar provide convenient access to the New Project Wizard; opening, saving, and closing a project; opening the Compound Library; importing files; and starting GC Image.
The lower-left pane contains the Project Tree that visualizes and provides access to the project components and some operations. The lower-right pane presents Component Information about the user-selected components and provides access to component operations.
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| Figure 1: The GC Project graphical user-interface (GUI). |
The File menu supports creating a project, saving a project, opening a previously saved project (from the .gcp file), opening a project from the Recent Projects sub-menu (which lists recently opened projects, closing a project (without saving), and exiting. The tool bar has corresponding buttons for creating, saving, opening, and closing projects.
The Project Tree presents subtrees for each of several components of a project:
Each of these components and the operations supported by GC Project are described here and in Reports.
To create a new project, click the New Project button on the tool bar or select from the File menu of GC Project. Then, specify the directory location and the project name. GC Project creates a new folder with the project name in the user-specified directory. In the project directory, GC Project creates a project file (.gcp extension) and several subdirectories (described below).
New projects also can be created with the GC Project Wizard. To launch the wizard, select New Project Wizard from the File menu. As described in GC Project Wizard, the wizard guides users through the steps necessary to create a complete project.
The Vial structure encapsulates basic data and metadata about the mixtures analyzed by GCxGC. For example, the ASTM D2887 simulated distillation analysis involves two mixtures:
Other standard methods, e.g., those using internal standards, involve multiple calibration mixtures with different amounts.
Just as the physical vial contains the actual chemical mixture, so the Vial data structure contains data and information about the mixture. The vial metadata includes creator, date, notes, and Composition Table. The Composition Table lists the known chemical compounds in the Vial mixture and the (relative or absolute) amounts. As described below, runs are associated with Vials, allowing processed chromatograms to reference the composition table of the associated vial.
GC Project supports several operations on vials:
The Project Tree pane (lower-left) of GC Project contains a Vials node, as pictured in Figure 1. If the node has a '+', then it can be expanded by clicking so that the vials are listed as leafs in the tree. If the node has a '-', then it can be collapsed so that the list of vials is not shown. If there is neither a '+' nor '-', then there are no vials in the project.
A user views the list of all vials in the project by clicking on the Vials node in the Project Tree. Then, the list of all vials is presented in the Component Information pane (lower-right), as in Figure 1.
One can start modifying the Vials table by clicking the "Edit" button (as shown in Figure 1). Then, the Vial Edit table is shown, as in Figure 2, with several controls. Vials can be added while in editing mode, but vials are only activated for the project when the user clicks "Apply Changes". These fields are shown in the Vial Edit table: Vial Name, Composition Table to import for each vial, Date, Author, Status, and Notes. The "Status" of the Vial indicates "editing" for vials that are not yet activated or "active". A vial in "editing status can be deleted, but once a vial is "active", it cannot be deleted. A vial with "editing" Status becomes "active" when the user clicks "Apply Changes".
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| Figure 2: New vials with CSV composition table files. |
There are several buttons on the Vial Edit table:
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| Figure 3: The Add Vial(s) popup dialog. |
As Vials are created, if there is a CSV-format composition table file in the project's Vials folder with the same name as the vial to be created (e.g., a file named Cal01.csv and a vial to be created named Cal01), then the Composition Table column in the Vial Edit table will be filled automatically with the matching composition table name. If a composition table with matching name is not present, then the user can manually select a composition table from the combo box in the Vial Edit table listing of CSV-format files in the Vials folder or select Browse inside the combo box to select a CSV-format composition table file located outside of the project. A composition table from outside the project is shown with the full path to its location.
Some fields in the Vial Edit table can be edited directly, even for active vials, including the Date, Analyst, and Note fields. The Apply Changes button saves the Vial Edit table and the Cancel button discards the Vial Edit table.
The typical process for creating a vial and importing its composition table follows. (The same process can be followed for creating multiple vials.)
Once a new vial is activated, it is added to the Existing Vials list and also is also added as a leaf node in the Project Tree under the Vials node. A user views the information about a specific vial by clicking on the Project Tree leaf node corresponding to the desired vial. Then, data and metadata for the vial, including Composition Table, creator, date, notes, and status, are presented in the Component Information pane, as in Figure 4.
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| Figure 4: A Vial node in the Project Tree. |
A Composition Table lists the known compounds in a Vial mixture and the (relative or absolute) amounts of those compounds. Compositions and amounts can be edited by individual vial or in a combined table.
When a vial is selected in the Vials tree (as shown in Figure 4), the Composition Table is shown with amounts in the Component Information pane. At the bottom of the Component Information pane are four buttons for manipulating the Composition Table for the selected vial:
GC Project can import composition files in comma-separated value (CSV) text format with each line formatted as "compound-name, amount". For example, GC Project could import a file with:
benzene, 0.09
2-hexanone, 9.99
Compound names containing commas should be enclosed in quote marks.
Clicking the Add Record button presents a popup dialog, pictured in Figure 5, in which the user directly enters the compound name and amount for the added Composition Table record.
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| Figure 5: The Add Record popup dialog to add a record to the composition table. |
GC Project also provides an interface for viewing and editing the combined composition and amount table for all vials, as shown in Figure 6. This interface has a row for each compound and columns for the compound name and for each vial. There also are controls to add a compound record (with amounts for each vial), delete a compound record, edit a compound record, or edit the entire table. Users also can specify the amount unit, which is used for reporting but not for computations.
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| Figure 6: A combined Amount Table for all vials. |
Instrument-control software uses sequence tables to perform injections, chromatography, and data acquisition. For GC Image, Sequence Tables provide information about runs, including source vials for runs, and are used in GC Project for Auto Processing. Figure 7 shows the Sequences branch of the Project Tree and Sequences information pane. The Sequences information pane has three buttons for creating, importing, and exporting sequence tables.
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| Figure 7: The Sequences branch in the Project Tree. |
To create a Sequence Table, click the "Create Table" button on the Sequence Table information pane. Then, the Add Sequence Table dialog, shown in Figure 8, presents four pre-populated fields that can be changed by the user:
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| Figure 8: The Add Sequence Table dialog. |
Clicking Cancel cancels sequence table creation. Clicking OK opens the Sequence Table Editor, shown in Figure 9. The Sequence Table has a row for each sample in the sequence and columns for Vial Position, Vail/Sample Name, Data File Name, Acquisition Method, LIMS Number, Modulation Cycle time (which might not be available in the data file), and Comments.
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| Figure 9: The Sequence Table Editor. |
Several editing operations can be performed in the Sequence Table Editor:
Figure 9 shows an example of a finished Sequence Table with an auto-generated data file name from using "Next Vial".
Once finished, click the "Done" button. The Sequence Table is created, as shown in Figure 10, and is selectable and editable by clicking the "Edit Table" button.
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| Figure 10: A Sequence Table created and ready for use. |
Two sequence table formats can be exported from GC Project:
Three different sequence table formats can be imported by GC Project:
The software supports importation of sequence tables in CSV format with a flexible CSV Importer. To import a Sequence Table in CSV Format:
The Runs node presents information about the raw chromatograms (i.e., each run of the instrument creates a single chromatogram). The raw data for all of the chromatograms are stored in the Runs subdirectory and each chromatogram in the Runs subdirectory is listed in the Project Tree under the Runs component, as illustrated in Figure 11.
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| Figure 11: The Runs node in the Project Tree. |
To fully incorporate a chromatogram into a project, the user must associate the run with a vial (created as described above). Each run is associated with a single vial, but a vial may have multiple runs from it. The color of the dot next to each chromatogram run in the Project Tree indicates whether or not an association has been made for that run. A red dot indicates that there is no vial association for the run and a green dot indicates there is a vial association.
Clicking on the Runs component of the Project Tree presents in the Component Information pane a table of runs that have been associated with a vial, as shown in Figure 11. Each associated run in the table has the data file of the chromatogram, the associated vial name, and a sequence number for the run. The sequence number is automatically assigned when the run is associated with the vial.
As pictured in Figure 11, the Component Information pane for Runs also contains a GUI for associating un-associated runs with specific vials. To make an association between a vial and one or more runs, select a vial from the list of vials, select a run(s) from the list of runs, and then click the Associate button. Then, the run(s) are removed from the list of un-associated runs and added to the table of associated runs (with vial name and sequence number), and the color of the dot(s) in the Project Tree are changed from red to green. To un-associate a run from a vial, select the run from the list of associated runs, then click the Un-associate button. The run is removed from the list of associated runs and added to the list of un-associated runs, and the color of the dot in the Project Tree is changed from green to red. The un-associate operation is not allowed if the chromatogram has been processed into an image which may have been used in a report.
Once run data files and vials are associated, the user can double click on the (green) run data file node in order to invoke the Process Runs dialog for processing the run as described below.
GC Project analyzes data in runs to produce processed images. Analysis typically utilizes various files, including GC Image configuration files, templates, and other types of files. The Processing subdirectory for the project, shown in Figure 12 is provided as a convenient location for files used for analysis.
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| Figure 12: The Processing node in the Project Tree. |
After associating a run with a vial, the user can initiate processing of the chromatogram. GC Image allows the user to designate a group of runs to be processed in an identical fashion. Choosing the Process Runs option on the Actions menu presents the dialog pictured in Figure 13. The dialog is similar to the import dialog described in Configuration Files, but the user can choose multiple runs to be processed. In the Process Runs dialog, the user may indicate that timing parameters available in the data file are to be used, but must supply information about the GCxGC data that is not available in the data file (e.g., modulation cycle time). The user may specify other import settings (such as interpolation or a limit on the number of MS intensities), a configuration file as described in Configuration Files, and processing actions (such as background removal, blob detection, and template matching) as described in File Input and Output. Each processed image is set automatically to reference the associated vial's composition/amount table and the user can specify that each image references a calibration file (as described in Reports). The user also can indicate that a Summary Report be generated automatically for each image. With Process Runs, as the specified runs are processed, the progress is reported in a Group Processing Log, which can be saved as a report and left open or closed after the last run of the group is processed.
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| Figure 13: The Process Runs dialog. |
To initiate processing of a single chromatogram, the user can simply double-click on the chromatogram in the Project Tree under Runs. The user is presented with the run selected in the Process Runs dialog for importing the chromatogram.
The Auto Process option on the Actions menu allows the user to process new runs as they are created in or added to the Runs folder. The software also can Auto Process linked runs from a data path specified in a Sequence Table. The menu option "Actions -> Auto Process" instantiates the Auto Process dialog, shown in Figure 14, which resembles the Process Runs dialog. The user indicates the settings that will be used for processing all runs. For example, if the vial is specified, then all new runs will be associated with the specified vial. The Start button initiates Auto Process, beginning with any un-associated runs in the Runs folder and then any new runs discovered by periodic polling of the Runs folder. If the runs are not associated with vials automatically, they must be associated manually before they are fully integrated into the project. Auto Process generates a report for all processed runs.
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| Figure 14: The Auto Process dialog. |
When a run is processed in GC Project, the resulting image is stored in the Images subdirectory. GC Project maintains an association between the image and the run. Multiple processed images may be created for a single run (e.g., to test different processing parameters), but each processed image is associated with a single run. The processed images are named with an image sequence number for the run. For example, Cal01_Run03_Img02 is the name for the second image created for the third run from the vial named Cal01. All of the images in the project are listed under the Images node in the Project Tree, as illustrated in Figure 15. Clicking on the Images node in the Project Tree presents in the Component Information pane a table of images in the project with the status of each.
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| Figure 15: The Images node in the Project Tree. |
Clicking on an image listed under the Images node in the Project Tree presents in the Component Information pane information about the specific image, such as its dimensions and an overview of the processing information, as shown in Figure 16. The Component Information pane for an image also provides buttons for viewing the image blob table and blob set table. Double-clicking on an image listed under the Images node in the Project Tree opens the image in GC Image.
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| Figure 16: An Image node in the Project Tree. |
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| Figure 17: The Review Images dialog. |
Existing images (i.e., image files that have been processed and analyzed with GC Image) can be imported into a project and renamed based on the Run-Vial association. To import previously processed images, select the Images branch of the Project Tree, then select "Actions -> Import Files" or click the Import Files button. In the dialog, select the files to be imported and their Vial-Run association. When the list is complete, click the "Import & Rename" button. Then, the project tree is updated with images that have been imported and renamed according to the Run-Vial association. Imported and renamed images do not replace existing images; instead, the image count in the file name is incremented. For example, if Cal01_Run01_Img01.gci exists, the imported image is renamed Cal01_Run01_Img02.gci.
The Overview in the Project Tree presents the hierarchy of vials, runs, and images, as pictured in Figure 18. A project may have one or more vials, each of which may have one or more runs, each of which may have one or more images. Clicking on the Overview node in the Project Tree presents in the Component Information pane a table of the vials in the project.
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| Figure 18: The Overview in the Project Tree. |
Clicking on a vial listed under the Overview node in the Project Tree presents in the Component Information pane information about the specific vial, such as its composition table, and a table of the runs from the vial.
Clicking on a run listed under an Overview->Vial node in the Project Tree presents in the Component Information pane information about the specific run, including a table of images for the run.
Clicking on an image listed under an Overview->Vial->Run node in the Project Tree presents in the Component Information pane information about the specific image.
Double-clicking on an image listed under an Overview->Vial->Run node in the Project Tree opens the image in GC Image.
Many analyses entail processing a set or batch of multiple runs. The U.S. Environmental Protection Agency (EPA) defines a batch as: "A group of samples which behave similarly with respect to the sampling or the testing procedures being employed and which are processed as a unit." [U.S. EPA, SW-846, Revision 2, 1996, p. ONE-23] GC Project provides tools for creating and managing batches of processed runs for subsequent use in analyses and reporting. Batches are a convenience in analysis and reporting because the same set of processed images, e.g., a set of calibration images, may be used repeatedly in performing analyses and generating reports. Once grouped in a batch, the set of images can be selected en masse for a report.
The Batch structure in GC Project contains a set of processed chromatograms. Each Batch defined for the project is listed under the Batches node of the Project Tree, as in Figure 19. Clicking on the Batches node of the Project Tree lists the table of batches in the Component Information pane.
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| Figure 19: The Batches node in the Project Tree. |
A user creates a new batch by clicking on the Add Batch button below the list of existing batches. GC Project presents a batch creation popup, pictured in Figure 20, that allows the user to specify the processed images in the batch. Once the processed images are selected, click OK to create the new batch. The new batch is added to Batches list in the Component Information pane and is added to the Project Tree under the Batches node.
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| Figure 20: The Add Batch popup dialog. |
Clicking on a batch under the Batches node of the Project Tree presents, in the Component Information pane, information about the batch, including the list of processed images, as illustrated in Figure 21 .
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| Figure 21: A Batch node in the Project Tree. |
GC Project uses batches for generating Calibration Tables, Consensus Templates, and various Reports.
GC Project allows users to create additional folders in a project. The project centrally manages those user-created folders and their contents under the “Others” node in the project tree. The “Others” node lists all miscellaneous folders directly under the project folder, as shown in Figure 22.
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| Figure 22: The Others in the Project Tree. |
In the Others component information panel, shown on the right in Figure 22, the folders are listed and two buttons allow users to add and delete folders.
Clicking on a folder node in the Others tree shows the files and folders inside the selected folder, as shown in Figure 23. Files under the folder can be opened by double clicking. New files can be dragged and dropped into a folder.
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| Figure 23: The Others folder file chooser. |
The Import Files operation provides a convenient mechanism for gathering files into a project. To use Import Files, select one of the following nodes: Vials, Runs, Processing, or Images. Then, select Actions -> Import Files or click the Import Files button. Next, choose the files to be imported. The imported files are then copied into the folder for the selected node. Typically, Composition Table files are copied into the Vials folder; raw chromatograms are copied (or linked) into the Runs folder; configuration files, templates, and other processing files are copied into the Processing folder; and processed chromatograms are copied into the Images folder.
GC Image™ Users' Guide © 2001–2010 by GC Image, LLC, and the University of Nebraska.