µBio

1. Overview

The "µBio" application is a system to describe the mixing situation of the microorganism included in Sample that the embarkation researcher (microorganism researcher) gathered, and to preserve it in the data base. The data registered here is accumulated in the data base for the research. The data inspection system can inspect the accumulated data.

Flow of processing

The flow of the processing of this software is as follows.

1. Login
2. Expedition is selected.
3. The confidence lower detection limit value is registered with "Confidence Lower Detection Limit Editor".
4. The object function of data to which object Sample is selected, and registered with "Sample List Display" is selected.
5. The registered data is input, and it executes it registration.
6. "Sample List Display" is shut, and it ends the application.

2. Login

2.1. User authentication

After starting the application, the Login dialog (Fig. 2.1) will appear and prompt you to enter your username and password.

Fig. 2.1 Login dialog

After logging in, the menu dialog will open. If the entered username or/and password are invalid or if the user doesn't have permission to use this application, an error dialog (Fig. 2.2, Fig. 2.3) will appear and request that you login again.

Fig. 2.2 Login failure dialog - invalid username or password

Fig. 2.3 Login failure dialog - user doesn't have permission

2.2 Qualified User Role

Microbiologist can use all functions in this application.

2.3. Changing your password

To change your password, click the button at the bottom right of the Login dialog. The Change Password dialog will be displayed (Fig. 2.4).

Fig. 2.4 Change Password dialog

Type your login ID, your current password, a new password,and retype the new password. After filling all fields, click the "OK" button. When your password is accepted, the Login dialog will be activated. Otherwise an error dialog will be displayed.

3. Selecting Expedition

When your logging-in is succeeded, the "µBio Menu dialog " will be shown (Fig. 2.5). In this dialog, you can select edit object Expedition. Only Expedition that can be edited can be selected. (Editing only Current Expedition as a rule becomes possible in the shipboard. )

Fig. 3.1 µBio Menu dialog

To select Expedition,

1. Select expedition to edit.
2. Click "OK" button.

4. Selecting a Sample & a Function

When Expedition is selected, Sample List Display of object Expedition is displayed. (Fig. 4.1) The object sample and the function (kind of data that registers =) to register data are selected on this screen. Moreover, the confidence lower detection limit setting screen can be called.

Fig. 4.1 Sample List Display

In an initial display, the value of "confidence lower detection limit" that relates to the selected Expedition is displayed. (Fig.4.2)

Fig. 4.2 Sample List Display (Initial display)

confidence lower detection limit

In confidence lower detection limit, the following four are in the kind and each unit of data.

• Total Cell(/cm³)
• Total Cell(/g)
• Beads(/cm³)
• Beads(/g)

When the value has already been registered, the numerical value is displayed. When the value is not registered, it is displayed, "Undefined".

The confidence lower detection limit editor is displayed when the "Edit" button in the "confidence lower detection limit frame" is pushed, and the confidence lower detection limit value can be edited. ( 5. Editing Confidence Lower Detection Limit Data)

Information button

There is button next to confidence lower detection limit frame. Clicking on this button shows the Application Information Dialog. The user is requested to specify the web browser to use prior to display the document. This button is also in other some screens. The called one is always the same dialog even if pushed on which screen.

4.1. Selecting a Sample

To register data, Sample that first becomes an object is selected. To select Sample, it narrows it by Site and Hole. The narrowing condition is set in order of Site and Hole.

Site List:

Hole List:

Fig. 4.3 Site list

Fig. 4.4 Hole list

When Site and Hole are selected, the "Query" button is pushed. Then, it narrows by Site and Hole and the list of retrieved Sample is displayed on the screen. (Fig.4.5)

The following columns are displayed in the sample list.

• Sample : Expedition - Site - Hole - Section - Core
• Sample Information
• Description
• Preservation
• Cell Density
• PFC
• Beads

Sample that registers data is searched out from Sample List. The object line enters the state of the selection if the mouse is clicked on target Sample. (Fig.4.6)

Fig. 4.5 Sample List Display (sample list)

Fig. 4.6 Sample List Display (selecting a sample)

4.2. Selecting a Function

Four kinds of data groups can register in this application. Each registration function is as follows.

• Sample Preservation : The preservation method of Sample is registered.
• Biomass Analysis : The biomass measurement result is registered.
• PFC Test : The PFC Contamination test result is registered.
• Beads Test : The Contamination test result with a fluorescent bead and a fluorescence microscope is registered.

The button of a target function is pushed with Sample of the object selected to use the registration function.

Fig. 4.7 Sample List Display (selecting a function)

5. Editing Confidence Lower Detection Limit Data

The confidence lower detection limit value is registered on this screen. (Fig.5.1)

Fig. 5.1 Confidence Lower Detection Limit Editor

To edit values,

1. Inputs the confidence lower detection limit value respectively of Total Cell(/cm3,/g) and Beads(/cm3,/g).
   The multiplier mark is used for the setting of the value. Moreover, there are the following input limitations.
   • One place digit of one. 1st place after the decimal point. Two digits in total. (example: 1.0 and 1.8 etc.)
   • The multiplier value of ten is 4-10.
2. The "OK" button is pressed, and registered.

6. Editing Sample Preservation

The preservation method of the specified sample is registered on this screen. (Fig.6.1, Fig.6.2)

Fig. 6.1 Sample Preservation Editor

Fig. 6.2 Sample Preservation Editor

To edit values,

1. Inputs the description of the specified sample.
2. Selects the preservation method from the list.
3. The "OK" button is pressed, and registered.

7. Editing Total Cells

The biomass analysis result of the specified sample (ie. cell density, stain reagent, comment etc.) is registered on this screen. (Fig.7.1, Fig.7.2)

Fig. 7.1 Total Cells Editor

Fig. 7.2 Total Cells Editor

To edit values,

1. Inputs the cell density value
   If the cell density value is less than measuring limit, selects the "Below Detection Limit".
2. Selects the stain reagent from the stain reagent list.
   If the reagent is not in the list, selects the "Other" from the list and inputs the reagent into the right text field.
3. Inputs the comment.
4. The "OK" button is pressed, and registered.

8. Editing Microscope Images

The microscope image used for the biomass measurement is registered on this screen. (Fig.8.1)

Fig. 8.1 Microscope Image Editor

Please refer to "Common User Interface: Registering microphotographs" for the usage of the dialog.

9. Editing PFC Test Data

The result of the contamination test of PFC is registered on this screen. (Fig.9.1)

Fig. 9.1 PFC Test Editor

To edit values,

1. Inputs the result of the contamination test of PFC.
2. Inputs the comment.
3. The "OK" button is pressed, and registered.

10. Editing Beads Test Data

The result of the Contamination test with a fluorescent bead and a fluorescence microscope is registered on this screen. (Fig.10.1)

Fig. 10.1 Beads Test Editor

To edit values,

1. Inputs the beads density value.
   If the beads density value is less than measuring limit, selects the "Below Detection Limit". If the beads density value is more than measuring limit, selects the "Over Detection Limit".
2. Inputs the comment.
3. The "OK" button is pressed, and registered.