HOW TO...

Type in your username and password which has been set up for you or the defaults SYSTEM/SYSTEM. (It is an easy task to set up a new username and password on the system later - Control Panel | Accessories | Config | Users).

A licence window will then appear displaying the name and address of the licensee and a description of the version of the program being used. This is immediately followed by the StrataBugs Control Panel.

StrataBugs has eight main applications or sets of applications each represented by an icon on the Control Panel.

• Wells
• Samples
• Taxonomic Database (Taxa DB)
• Interpreted Geological Data (IGD)
• Charts
• Events
• Index
• Tools

If the on screen HELP or this guide do not provide answers to your queries, in the last resort ask for help from StrataData by email, phone or fax. If you have held a licence for more than 90 days you will not be entitled to receive assistance unless you have a StrataBugs maintenance agreement.

Each of the applications within StrataBugs deals with a different aspect of the data management process. You will use different parts of StrataBugs depending on the nature of the data or the results you are trying to achieve. Some users will never use some applications. For instance, if you are a data user you may never use the Samples application, the Concept keyboard or any of the Export applications. On the other hand if you are a data provider you will probably make great use of Samples and the StrataBugs Export application.

It will probably be best to experiment with StrataBugs for a while before you begin to add real data in order to familiarise yourself with the general principles and styles.

To familiarise yourself with StrataBugs try experimenting with the data from the dummy well StrataBugs-1 that is supplied with the program. You can add data to this well, edit, export, import and delete it to see how StrataBugs works.

When you are ready to enter new data for your first well or outcrop section you must first enter Well/Outcrop details using the Wells application.

Then you must enter samples for the new well using the Samples application. You can then record the occurrence of taxa in samples in wells and outcrop sections.

The default Taxonomic database contains several thousand assorted names of many different categories of fossils but you will probably need to add some more. You can do this before you start to record data or as you the need arises.

You should also create an overlay in the Taxonomic database so that a group of taxa can be used to record the occurrences of the taxa you find using a Concept keyboard.

If you want to enter interpreted geological data (biozones, chronostratigraphy, etc.) create schemes of terms in the IGD application and then assign these pre-defined terms to intervals in your well.

When you want to look at the data you have entered, in the Charts application you should create a chart, which can be viewed on screen or plotted.

It is quite a good idea to import data using one of the Import programs so that you have some data to start work with from the outset. Imported data can be in a variety of formats from a number of different programs including other StrataBugs systems.

If you want to an overview the data you have entered you can do this using Index. From here you can also Export data in a variety of formats.

Familiarise yourself with the various conventions, terms and commands used in StrataBugs. There is a separate section about this (see Conventions, terms and commands)

To add a well (or outcrop) section open the Wells application and enter information about the section in the tabbed dialogs. Fields highlighted in red are mandatory, other fields can be filled in at a later date or as required.

If you intend to record fossil occurrence data semi-quantitatively you must select an abundance scheme. Each abundance scheme is a set of semi-quantitative terms expressing relative abundance each of which has an equivalent numerical range. To add, edit, select or show the usage of an abundance scheme select File | Abundance Schemes.

If you have TVD and TWT ASCII files which you wish to use with StrataBugs you import the files in this application.

To add a sample depth and type choose Sample | Add.... The Add Sample dialog box will appear.

Enter a new sample depth in the Depth field. If a sample has a range of depths (e.g. cuttings samples). StrataBugs allows you to enter either a depth range or single depth for each sample.

Note: You should be aware of the different ways in which sample depths are used in order to understand how StrataBugs interprets the depth values you enter. Cuttings samples collected every 5m for example will be labelled with a depth range 1200m - 1205m, 1205m-1210m, and so on. Each sample can be referred to either by the depth range, or by either the top or base depth. Base depth is more usual, but confusingly some workers use the top depth! Bear this in mind when importing data from other users.

For well samples, select the sample type from the drop-down list box on the Type field. The default sample type is CU (=cuttings). In addition you may record SC (=sidewall core), CO (=conventional core) and OC (=outcrop) samples.

For outcrop samples you may use positive and negative numbers to record vertical depth/elevation above or below a datum. You may also use the Depth field to record the order of samples from a stratigraphic section or traverse, substituting artificial numbers for depths/elevations. The "depths/elevations" need not be displayed on charts and the may be edited later to revise sample order if required.

How to record fossil occurrence data in a sample

You can enter the abundance of fossils species in individual samples in well or outcrop sections. You must first select the abundance scheme for the well before you start recording (logging) data (see File | Abundance Schemes in the Wells application).

Select a sample (see How to add samples). Then select Sample | Add/edit taxon occurrences to display the Data dialog.

Select Taxon | Picklist to display a blank Picklist. Populate the Picklist with taxon names from Groups, Wells or from the database (Picklist | Insert...). To do this select Picklist | Insert... or use shortcut buttons on the Picklist. If you have previously entered data from a section which yielded fossil assemblages similar to those which you expect to encounter in the current well/outcrop you may find it advantageous to build a picklist based on the taxa from the earlier section.

Select a taxon name from the Picklist, select an abundance (semi-quantitative) or count (quantitative), then any qualifiers (?, cf., etc) then push Add to sample button. The name, abundance and qualifiers will appear in the Data dialog. If you want to add a taxon qualified with cf. of aff. or you want to add a unspeciated genus (spp.) you may do so "on the fly".

If you prefer to use a "Concept" keyboard to enter records you will first need to learn how to connect and set up your Concept keyboard and how to create an overlay bearing the names of the taxa you expect to record.

Note: Methods of recording fossils: Whenever possible, use numerical counts as this gives greatest flexibility when displaying your data. There are a number of calculations, which can be made from numerical data when you design your charts. Calculations can be based on the taxa displayed in independent panels on a chart.

You may for instance calculate Percentage abundances and explicitly include or exclude individuals or groups of taxa. A special case is "outside the count" a method favoured by many palynologists. This method allows rare taxa to be recorded outside the statistical cut-off for a standard count. Taxa recorded in this way can be displayed on charts but do not feature in any calculations. To do this set up an Abundance scheme including the abbreviation "+" for "outside the count". You must switch off Refresh window data and Link abundance and Link counts (in Picklist | Options) so that no counts are assigned to any "outside the count" taxa.

A variant of this method is to count up to (for example) 200 palynomorphs of all types, and then to count until (for example) 200 dinocysts have been found. In this case the recommended procedure is to record "dinocysts" as a single taxon for the purposes of the initial count. This will enable you to display all palynomorphs in one panel as % based on 200 counts and all dinocysts in another panel as % also based on 200 counts.

You can enter geological interpretations (Biozones, Lithostratigraphy, Sequences, Chronostratigraphy and Palaeoenvironments) so that these can be displayed on a chart later. You can also enter graphic Lithology directly onto a chart and pick up ASCII log files for display.

Recording IGD is a two-stage procedure.

• Create IGD Schemes and Units

  The first part of the procedure is to define the IGD schemes and their component units. To do this select the correct scheme from the Schemes menu, and then add Units to the Scheme. You need only define a scheme once; however, it can be edited later as you wish.

  Refer to the on screen help for instructions on how to record each type of data.

• Assign Schemes and Units to Sections

First select the IGD type and version (File | Open | IGD Window) and then assign the selected unit name to an interval ( Interval | Add). If you wish you can edit the text to an informal term in the unit name fields. The informal term will be displayed whilst the selected unit will be stored in the database.

It is possible to omit the first step of this procedure (i.e. not to create Schemes) but this will result in all unit names being informal terms. This will prevent you from drawing correlation lines at a later stage.

If you enter IGD terms from low in a hierachy (eg. member) you can choose to automatically fill higher levels (eg. Formation).

To display a Scheme that you have added select File | Open | Scheme viewer. This will enable you to select the scheme and various display parameters and to view an entire scheme on screen or to plot a hardcopy.

To enter interpreted Lithology you use the "drag and drop" features in the Charts application to select main lithotypes, qualifiers, accessories and stringers from graphical palettes, and to draw a grain size profile..

To set up and use a Concept keyboard there are three main steps:

Connect and set up your Concept keyboard

• Connecting to a PC

Plug one end of the cable supplied with the keyboard into the board and the other into a spare serial (=COM) port on your PC.

You may need to reset the address of the port to which the Concept keyboard is attached. To do this use a text editor to edit the line in the SBUGS.INI file which begins "Keypad comms=" so that the COM port listed is the one your Concept Keyboard is plugged into. Do not modify the other items on this line.

Keypad type=2

Keypad comms=COM3:4800,n,8,1

• Connecting to Unix workstations on Solaris.
The Concept Keyboard may only be used in a Unix environment on the host node. If you are displaying X-windows onto another X server then the concept Keyboard may not be used.

Attach the Concept keyboard to one of the 25-pin ports on the back of the system unit. These are usually marked A or B. StrataBugs will connect to port A by default. If you are using port B then set the following environment variable in your login, or startup, script:

setenv STUGSCK /dev/ttyb

If you are using one of the older keyboards (with the blue metal surround), you must also set the keyboard type as follows:

setenv STUGCKTYPE 1

The default, type 2, is the Concept Universal range of keyboards.

Creating an overlay is a three-step procedure in the Taxonomic database application:
• First create a Group (Group | Edit) and highlight the taxa you want to add to the overlay.
• Then Open a blank overlay (Taxon | Overlays...)
• Next "insert" the taxon names onto the blank overlay (List | Insert | selection into Overlay) either horizontally or vertically. When all the names you require have been added to an overlay, select Overlay | Save, enter a unique name for the overlay and (optionally) a description.
• Print an overlay

  When Overlay | Print overlay is selected the Overlay menu item on the menu bar is replaced by the Overlay Print menu.

  To print an overlay from the Overlay Print menu you must first select the abundance scheme which is to appear on the overlay, set the paper margins so that the overlay will fit on the Concept keyboard properly and select the correct printer/plotter.

  Select an Abundance Scheme for the overlay (Overlay Print | Abundance Scheme...).

  Preview the overlay on screen and change the paper margins if required (Overlay Print | Margins...). Enter values (in mm) to increase the width of the Left Margin and the Top Margin.

  To print the Overlay select Overlay Print | Print.... Select a printer and push Print... to send the overlay to the printer.

The Taxonomic database application holds information about fossil taxa, their names, distributions in wells and outcrops and their various attributes. Menus enable you to add new taxa to the database, create new categories, groups and sets, and allocate taxa to them. In addition, you may link synonyms to preferred taxon names, interrogate the database for taxon occurrence data and produce reports on species associations.

Note: The default taxon database provided with StrataBugs contains a fairly random selection of several thousand taxa belonging to numerous categories. This is intended to help you start to build your own database. Taxa in the dinocysts category have been audited by John E. Williams and are consistent with the latest edition of the Lentin and Williams catalogue. You are warned that some of the names in other categories may not be correct. StrataData does not accept any responsibility for the accuracy or otherwise of the data supplied. If you require a bespoke database from the outset please consult StrataData.

TAXA: To add a new name to the database choose the Taxonomic database application icon on from the StrataBugs Control panel. This dialog displays the name of the Current (= last selected) taxon. Then choose Taxon | Add.... Select a Category from the drop down list and then type in the name of the new taxon. Taxonomic names are standardised and each element recorded in a separate field to reduce the risk of spelling variations of the same name and to aid database retrievals. Make sure you enter the various elements of the new name in the correct fields. You can add qualifiers, author's names and year of publication if you wish. There are short cuts for creating new names. For instance, type in the first few letters of the Genus name and push the Genera... button to bring up a list of genera. Select one, and then edit it to create the new name. Another way is to select a name (Taxon Select taxa...), push Apply to make it the current taxon then edit the existing name to create the new name.

There are short cuts for creating new names. For instance, type in the first few letters of the Genus name and push the Genera... button to bring up a list of genera. Select one, and then edit it to create the new name. Another way is to select a name (Taxon Select taxa...), push Apply to make it the current taxon then edit the existing name to create the new name.

Note: A taxon is a species with a formal Linnean binomen (e.g. Ammonia beccarii), an informal code (e.g. Ostracod sp.1) or a convenient term for a group of indistinguishable species (e.g. rotaliform foraminifera or Ammonia spp.). In StrataBugs all taxa are assigned to categories for convenience (e.g. dinocysts, planktonic foraminifera, diatoms, etc.) to assist in searching the database. Taxa can also be displayed by Category on charts.

SYNONYMS: Preferred names and their junior synonyms can also be recorded. There is no formal synonymy imposed on the database; instead preferred names may be linked by the user to other names referring to the same taxonomic concept. To add a synonym first select a preferred taxon name (Taxon | Select) and then select Taxon | Synonymy... and then select another name to add to the list of junior synonyms. It is possible to have more than one synonym scheme. You may wish to do this if, for example you deal with spore names and botanical names and with to set up different preferred names for different projects.

CATEGORIES: The taxonomic names in StrataBugs taxonomic database are organised in Categories. Each category contains a number of taxa which you may wish to group together for the purposes of searching the database or displaying together on charts. Every taxon must belong to a category but can only belong to one. You can add a new category or re-assign taxa to different categories if you wish (Taxon | Categories... | Add...), but in general we advise against this and suggest you use Groups instead (see below).

GROUPS AND SETS: In addition, you may use the Taxonomic database application to assemble taxa in informal Groups. You can then use these groups to organise your data and plot them on charts, design overlays, etc. Groups are distinguished from Categories in that a Group can contain any taxa and any taxon can belong to any number of Groups. To add a new group select Group | Add... and then select List | Insert to select taxa from a number of sources to add to the group. Groups themselves may be grouped in Sets. To add a new Set select Group | Sets and then add groups one at a time to make a new Set.

Note: Currently auto-correlation will work only with chronostratigraphy, Lithostratigraphy, Biozones and Sequences IGD types. In addition, all the IGD units that you may wish to correlate must belong to a Scheme.

• Create a multiwell chart

  Insert panels one at a time for one well at a time or insert a template for a number of different wells. Separate each group of panels representing data from a well by a blank panel.

• Select Data mode

  Click right once and a menu appears. Select Data mode.

• Select the IGD unit

  Select the IGD unit you wish to correlate in any of the wells and click left once to highlight it (unit is marked out by a dotted line).

• Select the IGD boundary

  Click right once and a menu appears giving you the choice of Correlate top or Correlate base of the selected unit.

• Select the line type

  Directly you make this selection a dialog will appear from which you may select the colour, thickness and style of the correlation line and select any line as the datum for the display.

  Note: The correlation will only work if the selected IGD units are assigned to a scheme and present in more than one well. If the selected units is in one well only a line will be drawn across the width of the panels represented the well. If an IGD unit is absent from an intervening well the correlation lines will extend fractionally beyond the limits of the panels representing a well. All correlation lines may subsequently be deleted or their attributes changed.

• Save the Chart

  Note: If after you have saved the chart the data that the chart is based on is changed, the chart will be redrawn correctly next time it is opened.

The procedure for Events is as follows:

• Create a multiwell chart as above.
• Select an Event (View | Correlation lines)

  Note: The correlation line will only be drawn if the selected event occurs in at least one of the wells displayed.

• Save the Chart in the normal way.

The procedure is as follows:

• Enter sample ages

  To convert a depth scale display to an age scale display you must enter Sample ages (actual or estimated) for as many samples as possible in each of your wells. It is imperative that you enter ages for samples (usually "log" samples) which define unconformities or ?unconformities.

• Create a multiwell chart in the normal way.

• Draw correlation lines if you wish at this stage or later. You must ensure that you correlate tops and bases of successive unconformable stratigraphic units in order for the time gaps at unconformities are displayed. For maximum visual effect select "Inherited" as the line type.

• In Charts select Chart | Properties and then select Absolute age as the scale type.

• Save the Chart in the normal way.

Note: you cannot edit a chart while it displayed on an age scale; you must revert to a depth scale in order to do this.

How to do graphic correlation

• In Events enter a composite standard section. You can create a composite standard from scratch or use a well/outcrop section to generate a compositestandard which you can then edit.

• In Events generate events for the well/outcrop section you wish to compare with the composite standard.

• In Charts select Insert | Events and select the well/outcrop section, events and composite standard and display the event graph.

• Using the drawing tool position a line of correlation (LOC) observing or ignoring the events that you wish.

• Save the chart in the normal way.

• Plot the chart in the normal way if you wish.

Note: It is not currently possible to dynamically extend ranges of taxa or modify the composite section.

Hint: For users unfamiliar with the Graphic Correlation method please refer to SEPM Special Publication No. 53 Graphic Correlation (Eds Mann and Lane, 1995) for further information.

How to create a stratigraphic range chart

The procedure is as follows:

• In IGD select File | Open | Scheme viewer....

• Select View | Properties... and then Setup Taxon Ranges by selelcting the Plot taxon range data checkbox and using the ellipsis (...) button.

You will then be able to display the stratigraphic ranges against the selected Scheme.

How to draw graphic lithologies and a grainsize profile

Main Lithologies, Stringers/Accessories/Qualifiers and a Grainsize Profile can all be drawn interactively in Charts. Main lithologies can be entered (not recommended) and edited in IGD.

• Open Charts

• Insert a Lithology panel ensuring that Display lithologies as text checkbox is deselected and Display grainsize profile check box is selected.

• Switch to Data mode

To insert Lithology:

• Open the Lithology pallette

• Select Main from the Lithotype menu

• Highlight a pattern on the pallette

• Position, click and drag the interval to be filled in the column (it's best to drag towards an existing filled section).

• Repeat until you have entered all the main lithology types for your section.

To insert Stringers, Accessories and Qualifiers:

• Select the appropriate pallette from the Lithotype menu

• Drag and drop them into position

• Position the cursor (cross hair) at a starting position

• Drag it to draw a profile or edit an existing one.

• The profile will fill with the background colour of the main lithologies.

• Clean up logs

  If your logs are LAS format StrataBugs should read the files without a problem. However, some log files (including some LAS files) contain data usually in the form of headers and footers which StrataBugs cannot read. In these cases it is best to make a copy of the log file and remove this extraneous information. This can easily be accomplished using Excel or a similar program. Ensure that the first column on the left contains the log depths and is titled "DEPTH". Other columns can contain values for one or more logs and should be individually titled. These columns must be equally space-, comma- or tab-delimited. Make sure that the column tiles are separated in the same way as the data! StrataBugs has a dictionary of terms which it will automatically recognise and simplify the selection process later on.

  When you have completed this clean up process save the file as an ASCII text file.

• Set default log folder

  To simplify the procedure of locating well logs put them in a folder and set this as the default.

• Rename log files

  If you name the log file using the well code for the filename and the extension "txt" or "asc", StrataBugs will automatically recognise the file and open it. Of course this will only work if all your values are in a single multi trace file. You can combine data from a number of files to make a single multitrace file if you wish.

• Select wireline logs

  If you have completed the above process you should be able to open the file and select the log trace to plot in the Wireline log application.

• Register the section as an outcrop in the Wells application.
• Enter all the samples as Outcrops (OC) in the Samples application. Record sample "heights" as opposed to depths (wells). Use a negative number for the base of the section if required. If you need to use false numbers to order the samples correctly do so. You can enter a sample label (e.g. the sample collection number or location) as well if you wish and display this on a chart instead of the sample "height".
• Select the highest sample (largest positive number) as the top sample in Charts. When the symbolic sample types option (Panel | Insert | Biostratigraphy | Options tab) is switched OFF a sample label is plotted. When the option is switched ON samples are displayed as depths/heights.

• Database overview

One main function of the Index is to provide an overview of the data available in the database for a given selection of wells. This will quickly enable you to check if you have certain types of data for specific wells or to check on individual data items. To do this double click on any cell to "drill down" to view individual data items.

• Report generator

The second main function of the Index enables you to generate the basis of a wordprocessor report document using the Reporter feature. When the data matrix is displayed you can generate a report on the data types in the wells you have selected.

• Export and Import data

The third main function is to provide a means of selecting well data for export to other StrataBugs users or in other formats. (See How to export data).

There are four main steps in using Events:

• Create a Project
• Select the Sections to include in the Project
• Generate Events for each Section in turn
• Add, edit and delete Events to each section in turn

• Post the events in a Comments panel on a chart
• Post the events in an Events panel on a chart
• Graph wells against a composite standard section
• Export the events in GraphCor or RASC/CASC file formats for use by these programs