JRSO—LIMS Viewer (LIVE) User Guide
Introduction
LIMS Viewer (LIVE) is a Web-based application that allows users to retrieve sample information and analytical data from the Laboratory Information Management System (LIMS) database and display them in a graphical format. This tool is a replacement for the LIMSPeak viewer, as the technology behind the old program could no longer be supported.
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LIVE can be found on the ship on the applications page, or at web.ship.iodp.tamu.edu/LIVE. On shore, it can be found at web.iodp.tamu.edu/LIVE.
LIVE is optimized for use in the FireFox browser. For best results, use FireFox on either a Mac or PC.
The LIVE main screen is divided into control bar (top) and data display (bottom) areas (see below).
LIVE Control Bar
The main screen control area is divided into four sections, as shown in Figure 1.
Title Bar: The top blue bar (Fig. 1, outlined in black) is the title bar and controls data view functions:
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- Specifying only a top depth (in meters) retrieves data from the specified top depth to the bottom of the hole.
- Specifying only a bottom depth (in meters) retrieves data from the top of the hole to the depth specified.
Depth Scale Filter: The default query is CSF-A, and CSF-B is available for any data set. If a composite depth scale is available in LIMS for the selected hole, it will appear on the drop-down list. Depth scale filters may be useful if there are overlaps in cores or sections (indicated by darker shading in the recovery panel).
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BIO, CARB, CELL, CHNS, CLU, CNTMASSVOL, CONT_MASS, CUBENG, DIAT, DINO, DML, FORAM, FORAMB, FORAMP, H2, HS, ICP, IW, LOI MAD, MBIO, MSPH, NANNO, NOTESTS, OSTRA, PAL, PALY, PFT, PMAG, PP, RADS, RMS, SCRAPE, SED, SEM, SRA, STRX, TCH4, TOC, TS, TSB, TSS, VAC, VP, XRD, XRF
Results Display
Navigation and Control
Once data are retrieved, a number of methods of navigation for viewing data exist. In each case, navigation does not run another query but instead uses the data already retrieved. In this way, a user may zoom in to a region of interest and then zoom back out (to a maximum of the full scale of the originally-retrieved data; Unzoom) without having to wait for a database query to run.
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Figure 5. Depth columns and depth navigation bar (shaded area in first column).
Recovery Panel
The recovery panel is shown in Figure 7. The panel is divided into four column areas:
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The checkboxes Sect break and WR break on the title bar display horizontal lines across all data panels where section breaks occur or where whole-round samples (e.g., interstitial water or microbiology samples) were taken, respectively. Either or both checkboxes may be selected.
Panel Panel View Options
Data panels have scale bars on either the top or bottom or both horizontal axes. Components plotted against the top axis are shown in the header of the panel; those plotted against the bottom axis are shown in the panel footer.
The panel options window for each axis provides the capability to alter data and sample properties (Figure 8). Changes are shown in the panel immediately; Exit closes the window.
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If the panel to be changed is a sample panel, the Sample display options will enable, allowing the user to toggle area shading (fill area) or display text (display text button).
Advanced User Options
Users with appropriate privileges may log in to access the Panel Builder and Template Builder.
Panels can display data sets that may be analytical data, sample information, images, and/or lithology. Data types can be combined in a single panel if desired.
Templates are made up of several panels that plot side by side on the main results screen after the LIMS query. Related data sets can be viewed simultaneously for comparison or trend recognition, or several types of data can be viewed together as an overview for quality control.
Note: The Panel Builder and Template Builder windows appear in new tabs in the browser. If the user logs out of LIVE on the main screen, or closes its tab, the Panel Builder and Template Builder windows will be orphaned. They will appear to be functional, but will not allow the user to take any action.
Note: If the user plans to make a lot of panel and template changes, a good technique is to open LIVE in two different browsers (e.g., Firefox and Chrome), make and save changes on one, and observe the changes on the other. This prevents the user from having to log in repeatedly after refreshing the browser in order to access new templates, if any.
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After selecting an existing panel to edit or modify, change the panel name to ensure that panels already used in active templates remain as originally designed. Changing or deleting a panel in use in active templates may cause problems for other users! Proceed with care; DO NOT give a panel the same name as an existing panel.
Panel naming convention is optional but may reduce panel duplication: include at least component plotted + analysis code (if needed) + axis + instrument (if needed) + other information (if needed). Examples:
MS_WRMSL_top_MSPOINT_SHMSL_bottom RSC_AB_top_L_bottom SRANL_HI_top_OI_bottom PWB_yz_manual_top
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Figure 13 shows the image panel controls. The first control panel will show the full cropped section-half line-scan image aligned to both top and bottom depths of the interval where the image was taken. The second control panel will show the jpeg file of the close-up thumbnail image aligned at the top of the depth interval where it was collected.
*Note that only one choice can be made for these two fields, either depth-referenced or thumbnail. A panel cannot have both types.
Figure 13. Add image to panel.
Field/Control Name | Field/Control Description | Required? |
Axis | Select top or bottom axis for the horizontal scale label of this panel | Yes |
Depth-referenced image OR | Select the depth-referenced (section or section half) image to be displayed | Yes |
(*) | ||
Thumbnail image | Select the thumbnail image (closeup, micro image, SEM image, or thin section image) to be displayed | Yes |
(*) | ||
Component | Populated by selecting the image type, shows the plottable component(s) for that image type | Yes |
Selected | Displays the selected component to be added to the panel | NA |
Add | Adds the defined parameters to the list of data elements in the panel | NA |
Cancel | Aborts the operation without saving the parameters | NA |
Adding Lithology to a Panel
Figure 14 shows the add lithology to panel controls. This panel retrieves specific lithology components. This panel must be built for each expedition. The panel shown will plot the principal lithology component as a colored area block. In the following example tThe lithology is picked up from the Sediment tab in the 362_-macro DescLogik DESCLogik template. The label "Principal lithology" will appear on the bottom axis of the panel.
Important! This panel will only work for a specific expedition DESClogik template, and DESClogik tab! It must be changed before it will function for a different DESClogik template or tab.
Figure 14. Add lithology to panel.
Field/Control Name | Field/Control Description | Required? |
Axis | Select top or bottom axis for the horizontal scale label of this panel | Yes |
Template name | Select the expedition-specific |
DESCLogik template to be used for this panel; lithology is usually found in the macroscopic template for sediment cores. Clicking a template will populate the |
“Tab name” field (takes a few seconds) | Yes | |
Tab name | Select the tab name where the lithology parameters can be found; selecting a tab that does not contain any of the allowed lithology components will produce an error message warning the user | Yes |
Component | Populated by selecting a tab with the allowed components; select the lithology component to be plotted | Yes |
As Text Radio Button | Sets the default behavior for the panel to display/not display text labels | No |
As Area Radio Button | Sets the default behavior for the panel to display/not display as filled area plots | No |
Add | Adds the defined parameters to the list of data elements in the panel | NA |
Cancel | Aborts the operation without saving the parameters | NA |
Lithology Components:
lithology_before_principal; principal_lithology; lithology_after_principal; lithology_ab, lithology_abc, lithology_bc (a = lithology before principal, b = principal lithology, and c = lithology after principal)
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Warning! Changing or deleting a panel in use in active templates may cause problems for other users! Proceed with care.
Highlight a panel from the panel list on the Panel Builder main page and click Select Panel. The builder screen will populate with defined parameters for the selected panel (Figure 15). The name can be changed, data elements added or removed, default panel width changed, and min/max top and bottom axis scales set or (if left blank) set to autoscale.
Important: Rename the panel to avoid conflict with this existing panel being used in active templates.
This panel shows caliper P-wave velocities in the x, y, and z directions, both manual pick and autopicked, all on a single plot. Autopicked and manual pick x-direction measurements are shown on the top axis, and autopicked and manual pick y- and z-direction measurements are shown on the bottom axis. The data values will be shown as symbols, as they are discrete measurements, and top and bottom axis scales will automatically set to fit the data values in the sets plotted on each axis. As these components all share the same unit, they will be directly comparable plotted on the same axes.
Figure 15. Data elements in panel.
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To see newly created panels in the Template Builder, refresh the browser tab. New panels will not appear without doing so. Login will be maintained in this case—note that refreshing the main screen will cause automatic logout to occur.
Click Template Builder on the main screen to open a new tab for the Template Builder. The user will see version information, what account they are logged in as, and a list of templates with two controls: "New" and "Select template" (Figure 16).
Figure 16. Template builder - list of templates.
Creating a New Template
Click New on the Template Builder main screen to display the controls for building a template. Figure 17 shows the options available to build a template. Each number in blue corresponds to an entry in the corresponding table below.
Figure 17. Template builder "New" screen.
Template Builder fields and controls
No. | Field/Control Name | Field/Control Description |
1 | Template name | Text field for the template name; the name should conform to the template naming conventions (see below). |
2 | Data groups | User may filter the panel list by selecting a data group. Some panels have multiple data groups assigned, and these panels will show up in all applicable data groups. |
3 | Panel | Displays the panels available to add to the template; filterable by using data groups (2). User highlights a panel before moving to the next control. |
4 | Add panel | Adds the highlighted panel to the list of panels in the template (appends to end). |
5 | List of panels in template | List of the current panels in the template, in order of their display (left to right). |
6 | Reorder panels controls (up/down arrows) | These controls are used to move a highlighted panel up or down in the order in the list of panels in template. |
7 | Remove panel | Removes a highlighted panel from the list of panels in template. |
8 | Edit selected panel | Allows definition of initial panel width, minimum and maximum panel width, and whether panel width can be changed in the active template in LIVE. |
9 | Publish checkbox | Selecting this checkbox will make the template viewable to users without a login. Only authorized, logged-in users can see templates without this selection. |
10 | Save | Click this button to save the template and return to the base Template Builder screen; the user will be prompted if required information is missing. Note: Give the template a unique name before saving. |
11 | Cancel | Click to discard all changes and return to the base Template Builder screen |
12 | Delete template | Click to delete the template completely. Use with caution! |
Template naming conventions
Include enough information so users can tell what is in the template, for example:
LSIMG_COUL_RGB_RSC-L L MS_MSPGRA_MADPWLMSP GRA_MAD PWL_PWB_PWC (or maybe PWAVE_ALL) 349_LITH_WRND-GRA_NGR_RSC
Alternatively, templates used for routine QA/QC can be named for their function, for example:
BOX TIMELITHOLOGY 362 SPLIT COREREADY TO SPLITAnchor
Editing an Existing Template
An existing template can be modified and saved as a new template. Warning: rename the modified template before saving! The existing template below was built as a quality control check on whole-round data. The panels in the template are listed (note the panel names are not exactly like they were named in the Panel Builder, as the application adds additional information to the panel name. The five panels in this template include (1) magnetic susceptibility from WRMSL and STMSL, both plotted on the same axis (top), (2) GRA density from WRMSL and STMSL, both plotted on the same axis (top), PWL (by default, x- and y-directions only, (4) NGR plotted on the top axis, and (5) thermal conductivity plotted on the top axis. Note that both the panel names and the template names are clear enough to determine what they contain.
If we wanted to add the section-half image to this template, we would select Data group I_depth_referenced, select the panel that shows the cropped jpeg or tiff, and click Add panel. If we wanted the image to be the first panel shown, we would use the up arrow to move the image panel to the top of the list. Very important – we would rename the template something descriptive such as Whole-Round Data plus LSIMG.
Figure 18. Edit an existing template.
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Figure 19 shows a data query with section-half image (LSIMG) in the first 3 data panels: (1) with COUL-calcium carbonate overlain (orange open circles; note that the color of the data point or line matches the color of the corresponding header); (2) with RGB (labels on the bottom axis); (3) with L*.Panel 4 shows RSC L*a*b*, and panel 5 RGB data again, this time scaled to separate the red and green (top axis) from the blue (bottom axis). Panel 6 shows COUL calcium carbonate (bottom axis), same values as in the first panel, this time with data results value (text) next to each point. On all data panels, the magenta areas are duplicate samples or duplicate runs.
Figure 19. Control panel with data view.
Core overlap (darker shading) between 18H-CC and 19H-1 is shown on Figure 20. Note that the lithology panel shows overlapping lithology as well.
Figure 20. Core overlap between 18H-CC and 19H-1 on the CSF-A depth scale..
Changing the search query to depth scale CSF-B resolves the overlap (Figure 21).
Figure 21. No core overlap on the CSF-B depth scale.
This data query displays LSIMG, sample type as area intervals and text, and sample panels with request code and test list as text (Figure 22).
Figure 22. Sample type, request code, and test list.