Overview
DESClogik is a core description software for core describers and micropaleontologists to enter observations. The software is configurable to meet different needs of different science parties. Configuring and editing the software is the responsibility of the Core Description Technician (you!).
As you're getting started make sure to read the Core Description S.O.P. for useful information on what (and how) you need to do at the beginning, middle, and end of the expedition.
Important Terminology
- Configuration Sheet (Config Sheet): This is an excel workbook that is the basis for DESClogik. These configuration sheets contain all the column information such as header, width, visibility, whether a column is free text or uses a pre-determined drop-down set of terms, and a unique definition for each column. Configuration sheets create the templates in DESClogik (see below).
- Template: A template is what the scientists are entering their data into in DESClogik. Templates are broken up into somewhat standardized groups: Macroscopic, microscopic, and one for each micropaleontology group sailing (e.g. nannofossils, forams, etc.). We'll discuss the difference between these templates later.
- Value lists: Value lists are groupings of similar terms. For example one value list we have is "principal_lithology_sediment_names" and inside that value list are terms that fall within this category such as "sand" and "clay". All terms used in DESClogik must be inside a value list.
- Sub Lists: A sublist is a subset of values from a value list that will be used on an expedition. In DESClogik sublists appear as a drop-down list of options for descriptive terms. For example "principal_lithology_sediment_names" value list could have thousands of values, so scientists will choose a smaller list of terms of only the principal lithologies they expect to see.
- Data Workbooks: These are exports from DESClogik that contain the descriptions uploaded by scientists.
What You Need
You will need to use the following software, server folders, and web based applications:
- 'All Things DESClogik' folder (VOL 1 > IODP_Share > All Things DESClogik): Contains previous expedition folders with all the configuration sheets and data workbooks from those expeditions, tutorials, and resources to give scientists to help them use the software.
- DESC Value List Manager: A web based application where value list and sublist excel workbooks are uploaded every time a change has been made to those sheets. http://eiger.ship.iodp.tamu.edu/apps/valuelistmanager/
- DESClogik: The description software users enter data into. Config Sheets are loaded into DESClogik, which generates the templates that users will use. It is an iterative process making edits to the config sheet, loading it into DESClogik, then making more edits.
Getting Started
General
In the first few days on the ship get these items done to ensure a smooth transition, but note deadlines can be pushed forward or back depending on length or portcall and transit. Other portcall activities take priority so work with your ALO and LO your priorities.
- Talk to the MCS' to get at least two email distribution groups together: ExpXXX Core Description and ExpXXX Micropaleontology.
- Talk to the EPM to get an idea what expeditions are similar to your current expedition.
- Propose those expeditions to your scientists and see if they have any other expedition ideas
Set up the Expedition Folder
Each expedition has its own folder in the "All Things DESClogik" folder. These folders contain the current value lists, configuration sheets, data exports, smear slide templates, Thin Section Reports, and logsheets. Open up recent expedition folders to get an idea of the structure previous techs have used.
1.Open up the "All Things DESClogik" folder VOL 1 > IODP_Share > All Things DESClogik. The most recent expedition is at the top of the list with an underscore before the name.
Figure X: The file structure
2. Create a new folder following the same format as previous expeditions: "_DESClogik_EXP999". Put an underscore at the beginning to make it easier to access during the expedition.
3. Open up the folder of the most recent expedition and copy the "Value Lists" folder into your new expedition folder. Taking the value list from the most recent expedition ensures you have the most updated set of terms.
4. Go back to the previous expedition folder and remove the underscore. Now the only expedition folder at the top is your current expedition.
Finding a Jump Off Point
The best way to get started is read the scientific prospectus and chat with the EPM to find an expedition that encountered similar material as what your current expedition anticipates. Keep in mind expeditions prior to 341 used a different system that cannot be opened in DESClogik.
1.Click on the DESClogik icon to open the software.
2. Login with your LIMS application username and password.
3. The main DESClogik screen opens.
5. Click the black T. A list of all previous expedition templates will appear in the right 'Groups' panel. The left panel shows all the templates used in that expedition. Double-click the template of interest.
6. The template loads into the main screen.
7. Check the 'All tabs' box.
8. Click the green 'Export' button. In the drop-down menu 'Include Classifications' is already checked. Check the box for 'Valuelists Instead of Data'. Then click 'Export...'
9. Save the file in your expedition folder in the 'All things DESClogik' folder.
10. Open up the file and add a key in each tab indicating the most useful way to make edits to the sheet. Note in the example below, it's asked that any additions be made in green, any deletions made in red, and any spelling changes in yellow. Save the workbook when the instructions are on every page.
11. Send an email to the appropriate distribution group with the workbook attached. For paleo groups, send to the few members in the particular discipline rather than the whole group. In the email mention that they all need to review and agree upon changes as a group. Include how they should make edits to the page and then email it back to you once they all agree. It will likely take a few iterations before everyone is satisfied. Make sure you get this back with enough time to make the changes before the first core on deck. If time is running out prioritize the Macroscopic workbook first, then microscopic, then the different paleo groups.
12. Now that the scientists are working on their changes let's go back to DESClogik and export the Configuration sheet.
13. Open up DESClogik and click on the 'Design' tab at the top of the screen
14. Select the black T and click on the appropriate template. After it loads select the green excel button and click 'Export'.
15. Direct yourself to your expedition folder inside "All Things DESClogik". If not already there, make a folder called "Configuration Sheets". Save the file in your new "Configuration" folder with a name such as "XXX_Macroscopic_Draft". At this stage give the sheet a temporary name as demonstrated in the previous sentence, we will explain why in later sections.
Making Edits
Overview
When the scientists have gone through the excel workbooks and send you an edited copy, we start making edits to the configuration excel workbook.
1.Go to the 'Configuration Sheets' Folder and open up the workbook that corresponds to the file you received.
2. The sheet opens up. There are three areas of note as illustrated in the different boxes in the image below.
Box 1: These first 5 lines of the workbook have primarily fixed values that either cannot be changed or often do not need to be changed. The sample type filters and test type filters can be added or removed but do so with caution. We will show you how to do this in later sections.
Box 2: This is where the action happens. Regardless of the config sheet opened the column layout will always be the same.
A. Header: This shows the header names as they display in DESClogik. Here the headers are laid out as rows but is transposed in DESClogik to
B. Text Orientation: Text orientation for the header can be changed between vertical and horizontal
C. Column Width: Can change the width of the entire column here. A known bug is that width changes will not take more than once to the same template name.
D. Visibility: Columns can be either 'visible' or 'hidden'. If visible it shows up in DESClogik and if hidden it does not. If a group doesn't want a column you can change its visibility to hidden, then if later they decide they do want it, you can change it back to 'visible', rather than remake the column.
E. Sub-list: The name of the sub-list that the config sheet points to to populate the dropdown menu. The name will be the same name as entered in the sub-list excel sheet. 'default' is used for free-text columns such as a comment column.
F. Check for overlaps: Can be set to 'yes' or 'no'. If set to yes will highlight rows that have overlapping descriptions in that particular column.
G. Formula: Shows any formula used in that column. Formulas cannot be entered here. They can only be entered in DESClogik.
H. Metadata Class: Applies to 'piece number lookup' and does not need to be edited.
I. EC: Stands for 'Entry Component'. This value corresponds to the names of each value list, although it is not always a direct match. The sub-list must be in the sub-list for the value list from the EC. This is the broadest term to describe the column. For a list of Entry Components that can be used in DESClogik follow this link.
J. QC1: Stands for 'Quality Component'. This value also corresponds to the value list terms. There can be multiple QCs, each one increases in number, i.e. QC2, QC3, etc.
K. QV1: Stands for 'Quality Value'. This value must be one of the terms from the value list used in QC. The QV is paired with the QC so if there are multiple QCs you must have the same number of QVs, i.e. QV2, QV3.
The EC, QCs, and QVs are used to create a unique definition for each column. The definition is key to data uploading and downloading successfully. If two or more columns have the same definition, even if they have different headers, data will inconsistently move back and forth between columns.
Box 3: The tabs at the bottom of the screen are the tabs that show up in DESClogik. Tabs can be added or removed from the workbook.
3. On another screen open up the edited sheet from the scientists.
Add and Remove Columns
1. Any columns marked for deletion, go to the corresponding row in the configuration sheet and either change the visibility column to 'hidden' or delete the row. If you delete it, first highlight the whole row, then clear contents, and then delete it. The cells and rows in these workbooks can get stuck on values, even if deleted, so the best way to avoid issues is clearing the contents before deleting.
2. If a column needs to be added, first check the sheet to make sure the column doesn't exist but listed as hidden.
3. Insert a row where the column should go. Fill in the header name. Enter in the text orientation, column width, visibility, and check for overlaps column. Leave the sublist column empty for now, we will re-visit this later.
4. Create an appropriate EC, QC, QV definition. You can use multiple QCs and QVs if necessary. You can also look for similar columns in other tabs or workbooks and copy and paste that definition.
Add and Remove Tabs
1. If you need to add a tab, make sure to copy the top seven lines from a previous tab. To delete a tab, clear the contents for the whole workbook then delete the tab.
Add and remove terms from a sub-list
If users want to add or remove terms from a sublist, we will need to make a new sublist rather than altering another expedition's list. In row 2 of the workbook given to the scientists the sublist name is listed. In the image below we see "drill_disturb_372" as the sublist for column "Drilling disturbance type". This sublist name is what you'll find listed in the configuration sheet in the sublist column.
We will use the Value List Builder macro excel workbook. Here we briefly go over what you need to do, for more in depth information refer to the Value List Builder Macro User Guide
Add Terms
1.Open the "Value List Builder.xlsm" located in Vol 1 > IODP_Share > _DESClogik_EXPxxx > Value Lists
2. If prompted, click "enable macros" and "trust this document". In the top left corner click the circled x to clear the form of previous search results.
3. In the sheet sent by the scientists copy the new terms for one column. Do this one column at a time as each column will have its own sublist, terms are located in different values, and easier to add values if they don't yet exist.
4. Copy all the wanted terms into the column labeled "Paste you Value List Below"
5. Click the magnifying glass in the top left corner of the workbook.
6. A prompt pops up. Enter your expedition number and click 'OK'.
7. A Value List Selection window pops up. Click in the Value List Category and select the appropriate category. Then select a value list from the next drop down. In Figure XX terms were added to the Lithology principal name, so to search I would select the category 'Lithology' and value list 'principal_lithology_sediment_names' since this is a sediment tab. Click Search. If you have no idea where to start or how this column should be defined , click Search All Value Lists.
8. Results populate the fields. Any results that are found will show up in the 'Closest Value Match Found in Value Lists' and corresponding definitions. Any terms that are not found in that value list show up in the 'Values not found' column. In the below example we have three terms that are not in our value list.
9. For the values that haven't been found, open up the appropriate value list, in this example the 'principal_lithology_sediment_names' list.
10. Copy the values from the 'not found' column from the Value List Builder and paste into the first column of the value list spreadsheet, with the reference and definition in the following columns. Click 'save' and close the spreadsheet.
11. Now double check the Value list builder and search again to make sure the terms show up.
12. Open up the corresponding sub list spreadsheet, in this example 'sublist_principal_lithology'. The subllist spreadsheets are in a 'sublists' folder inside the 'Value List' folder.
13. The spreadsheet opens up. This list contains all the sublists that have been used for expeditions with this value list. Note the top line is empty, the next line has the name of the sublist, and below are all the terms in the sublist.
14. Copy the formatting of the top two lines and paste in the next available column. Give the sublist a unique name, this can be done by incorporating the expedition number. Then copy all the terms from the value list builder from the 'Closest Value Match' column. This column has formatted the terms correctly. There have been errors using values that aren't formatted correctly. The newly created sublist is outlined in red below.
Now that we have added terms to our a value list and a sublist we need to update these worksheets in the database. If these are not updated the new values will not be recognized by DESClogik and throw errors.
15. Close the value list and sublist excel worksheets you were working on.
16. In your internet browser go to DESC Value List Manager. http://eiger.ship.iodp.tamu.edu/apps/valuelistmanager/ . You can access it from the shipboard iodp home page > Access LIMS applications >and under Web applications select DESC Value List Manager.
17. Click the login button in the top right corner. Login with your LIMS username and password. Now in the right corner you should see your username.
18. Click the Value List button on the left side of the screen. The window will slide out to the right. Click 'Choose File' and navigate to the value list you added terms to, in our example its the 'principal_lithology_sediment_names value list. Click Set Value-List (Excel). This file can take a few minutes to upload. When done a message will appear in the upper right-hand corner saying 'Server Response Success'.
19. Give it about 30 seconds and then click on the Value List button so the window retreats and then click on the Sub List button. Click Choose File and then navigate to the sublist file you updated, in our example 'sublist_principal_lithology. Then Click Set Sublist. This file can take a few minutes to upload. When done a message will appear in the upper right-hand corner saying 'Server Response Success'.
20. Open up the configuration sheet, if not already open. Find the column you were editing the sublist for. In our example its the Lithology Principal Name column.
21. Go to the sublist cell for that column. Click in cell and use the clear contents command.
22. Re-open the sublist excel worksheet you just updated. Navigate to your sublist and copy the name cell. Go back to your configuration sheet and paste using the 'values only' command.
23. Save the configuration sheet.
Delete Terms
If the scientists have no additions to a sublist and only deletions we still need to make a new sublist.
1.Open up the appropriate sublist excel spreadsheet. If you're not sure which sublist file your list is in, you can look at the configuration sheet and the corresponding EC value. In the below example I am deleting terms from the drill_disturb_372 sublist. Looking at the configuration sheet the EC for this column is 'structure' so I can find this sublist in the 'sublist_structure' excel file.
2. In the sublist excel worksheet, copy the formatting of the top two lines and paste in the next available column. Give the sublist a unique name, this can be done by incorporating the expedition number.
3. Copy the wanted values from the edited worksheet sent by the scientists and copy the values into into your new sublist column.
Software Introduction
You can access the software through the yellow spreadsheet icon located on the core description computers or through IODPLauncher. Open the software and login with your LIMS application software.
Spreadsheet Tool Ribbon
The main window opens up. Let's take a look at the main ribbon at the top of the screen.
At the top of the window there are three tabs: Spreadsheet Tools, Design, and Recovery. The software defaults to open on the Spreadsheet Tools tab. The Spreadsheet tab is the primary tab that scientists will use. The tools are outlined below:
- Template: How users select templates.
- Select Sample: allows users to find and add samples to describe
- Upload: Uploads data to the database
- Download: Downloads data into the spreadsheet for the selected samples.
- Clear: Removes data from the screen but does not delete or remove data from the database.
- All Tabs: Checkbox, when checked indicates that actions taken will apply to all the screens. Example: Box checked and click the 'Clear' button, data from all tabs will be cleared.
- Filters:
- Sort: Sorts data on the screen.
- Export: Allows users to export templates with data and valuelists into excel spreadsheets.