Does StrataBugs run on Windows 11?

We are getting asked increasingly if StrataBugs is compatible with Windows 11. The chances are that if you’re in the market for a new PC, then it will come pre-installed with Windows 11, or be eligible for a Windows 11 upgrade. You may or may not welcome the new look and feel, but the good news is that we have found no compatibility issues with any version of StrataBugs.

We’ve only tested back as far as v2.1, but if you’re running an older version, why? Well, if you really have to, it will probably still run OK.

The new, more rounded window style, and slimmer scroll bars carries into the application and so far we’ve not spotted any functional problems. It’s up to you to decide whether to run with it, but don’t let StrataBugs stand in your way.

Bug in recalibrating sequence schemes

All types of schemes are scaled using abolute ages, which is why we tie biozone, sequence and composite standards to a chronostratigraphic scheme. The chronostrat scheme gives a reference to the age scale used in those related schemes. What happens when there is a new timescale published, like GTS2020?

Moving the boundary ages in a chronostratigraphic scheme can have basically two effects on the schemes which relate to it. Either the boundaries and events in the previous scheme move with the new boundary changes, or, zones and events find themselves in different chronostratigraphic units as a result of the change.

Recalibrating

There has long been an option in the Schemes and Interpretations module to Recalibrate schemes, and this option makes the assumption that the former of the two conditions is always true: that if a chronostratigraphic unit changes its boundary age, then all the related content in linked schemes will change accordingly, and a new scheme can be saved where the boundary ages align with the new version of the timescale.

This works pretty well as a first pass way to create new versions of your schemes. however, for sequence schemes we’ve recently been alterted to a bug whereby the surfaces of the new scheme are not created: instead, the surfaces of the original scheme are updated. This of course isn’t the desired result!

The bug has been corrected in all current releases: v2.1.1, v2.1.1-14, and the test v3.0. Until you have updated to the latest version after 24 Mar 2022, do not use the recalibration tool for sequence schemes.

If you have previously done this and not spotted the resulting erroneous surface ages, then you can correct back to the original values by re-importing an XML/SBG file containing the original scheme, and during the import process use the “Update Surfaces” button to change the surface ages back to the original values. Contact us if you need further help.

No well data are affected by this.

StrataBugs 3.0 pre-release available

We have made available a pre-release version of StrataBugs 3.0 to allow interested users to help us test the system ready for release. Many of you have have previously expressed an interest in testing the new features, but we also need to make sure the existing functionality is unaffected with all the changes we have made.

If you are a StrataBugs user and entitled to a v3.0 licence, you can download the test release. Some of you will already have a v3.0 licence, others might need to contact us to get an updated licence file.

In this phase, we want to ensure that the changes to the database (the data model) do not require further changes before the full release, so we cannot guarantee that the database structure will stay the same as the final release. We therefore ask that any data you wish to work on are copied out of, or back into your existing 2.1.1 database, so that your database can be converted again when we provide the full production release.

To get started with v3.0 go to the download page and follow the instructions. Open the Help, and the learning trail for v3.0 to see a brief description of the new features. Currently we do not have a download bundle for Mac users, this will be available shortly.

The learning trail and the rest of the documentation still require further work, most of the help still relates to v2.1.1.

During the pre-release phase we will be making incremental update releases on a regular basis. Once we have reached the point of a production release, we will fix the data model for v3.0 but the applications will continue to be updated as part of our continuous product development. This means that once released, you will be able to convert your database to v3.0 and it will not need further conversion until we release v3.1.

Thank you for your patience.

 

 

Should groups contain only unique taxa?

Taxon groups in StrataBugs can contain any number of species (or genera, since v2.1). Groups can be added to a Group Set, which allows the relative proportion of the taxa in each group to be plotted, often in the form of compact “closure” diagrams that show stratigraphic or environmental trends. So far so good. We’ve pretty much assumed that, up until now, a Group Set will contain an exclusive set of taxa; i.e. each taxon will only occur in one group, when that group belongs to a Set. Indeed, when you create or edit a Set in the Taxonomic Database module, it warns you if there is any duplication between the groups, and allows you to see the duplicates:

 

But what happens when a taxon belongs to more than one group in the Set? What if you have groups that reflect broad environmental conditions, and some taxa are present in a range of environments which spread across more than one group? To display these groups as a relative abundance curve would be to double count the abundance of taxa in each group. But to include them in some groups and exclude them from others seems arbitrary. Up until now, the latter is what has happened in the v2.1 charts, and this has been inconsistent with the previous behaviour in the “legacy” charts. In the “legacy” charts, each taxon was added to the total for each group, so if a Group Set was plotted with relative group abundance, those groups with duplicate taxa would be more heavily weighted compared to the other groups. In the v2.1 charts, the taxon is only counted once – but this has the distorting effect of ignoring the influence of the taxon in any subsequent group it might appear in.

I think a better solution exists than either of these scenarios. If a taxon exists in more than one group, then perhaps the weighting of that taxon’s abundance should reflect the number of groups that it is spread between. So if it occurs in two groups, then 50% of the count gets allocated to each group. We have just updated the v2.1.1 (and v2.1.1-14) release to reflect this new thinking.

Let’s look at a simple example to illustrate the change. Suppose we have two groups; Group 1 and Group 2. Group 1 contains one taxon (Ammonia spp.); Group 2 contains 2 taxa, Ammonia spp. again, and Elphidium spp. Both taxa are recorded in an analysis, each with a count of 10 specimens. The total count is 20 specimens. Let’s start by plotting this in the legacy chart application:

The first panels, Group 1 and Group 2 plot as expected: an abundance of 10 for each specimen. No problem there. In the third panel, showing the Group Set, the duplicate taxon in Group 2 is counted twice, so although the panel looks reasonable, the total count displayed here is 30 – whereas the true total count is only 20. The fourth panel, the relative abundance of the groups within the Set, also looks quite reasonable, but the proportions don’t correctly reflect the proportions of the contents of the groups.

Now we plot the same data in the unmodified v2.1 charts:

Panel 1 shows the individual taxon abundance; Panel 2 shows the abundance of each taxon as % of the total. Panels 3 and 4 have inner panels for each group, and show the count of individual taxa in the group and the group totals respectively.  Ammonia spp. contributes to the count in both groups. The inner panels in Panel 5 each show the Group Set, divided by its constituent groups. Now we see an equal count (and % distribution) of Groups 1 and 2, because Ammonia has been counted in Group 1, and isn’t counted again for Group 2. This is different to the “legacy” chart above, but still does not accurately reflect the group proportions.

Worse, when we rearrange the Set’s group order, so that Group 2 is now plotted first, we see Group 1 disappearing completely in Panel 5:

In the modified version which is now released, we divide the abundance between split groups, so we get this:

Panels 1-4 are the identical, but Panel 5, which shows the Group Set as a whole, has the 10 counts of Ammonia split between Groups 1 and 2. This means the total of the absolute abundances is (correctly) 20, and Group 1 only has 25% of the weight (as opposed to 33% in the legacy charts, and 50% – 0% in the previous version). The proportions remain the same when the groups are reordered. This also highlights the subtle but important distinction between plotting separate inner panels for each group (as in 3 and 4) compared to separate tracks for each group (as in each inner panel in Panel 5).

 

Finally, a real world example. This Group Set contains several hundred species which are ranged across different water depths. The left panel reflects unique group assignments: taxa ranging across environments are assigned to a group which exclusively contains taxa of the same range. It is difficult to get the group ordering right, with overlapping ranges, and the colour assignments can subtly affect the visual result. In the second panel, where there are fewer groups but taxa can occur in multiple groups, the deeper water depths are under represented.

 

When we display the same panels with the modified version, we see a more even spread across the main groups:

 

This issue only affects you if you use overlapping groups, so may not be a big deal, but perhaps some explanation of what’s going on here is useful, and it can be an opportunity to more easily group taxa for displays of this kind.

Your head’s probably spinning by now and you probably wish you’d never started reading this, but if you’ve lasted out until the end, and feel the urge to comment, we’d welcome any feedback.

 

Saving sessions, and clicks

Those of you that typically use the “Restore Session” option when reopening the Samples & Interpretations module will have noticed that although the previous sessions wells/outcrops and tabs are restored, it didn’t reinstate the previous tab selections. This hasn’t seemed to us to be a very big deal, as we assumed that most people, most of the time, tend to work more intensively on fewer wells, so the task of clicking on a few tabs to get back to the block template you were last viewing, seems trivial.

The assumption doesn’t hold true for larger field review studies, or for shallow borehole geotechnical work which typically involves tens of boreholes (the usual scenario for BioChron). In these cases, being able to reopen your session with the same tabs open can save a lot of clicks. If this applies to you, then an update to the latest release of v2.1.1 or v2.1.1-14 is all you need to do.

If you do restore a session but get an error message pop up during the restore, then copy this to us (as always) with a simple screen shot, but don’t worry unduly because an error in this phase is unlikely to need anything other than a few extra clicks to get back to where you were.

 

 

GNATTS off to BP

Note: if you’re receiving this for the first time, you’ve just been added to our blog list. You can unsubscribe if you’d rather not receive these, but we hope you’ll find the occasional post interesting.

Waiting for a timescale is like waiting for a bus in the rain. You wait for ages, then two come along at once. We are pleased to be able to share with you a data pack of schemes based on the BP Gulf of Mexico Neogene Astronomically Tuned Time Scale (GNATTS) published in 2019. The full background and reasoning for the scale are available under open access here:

Bergen, J. A., Truax III, S., de Kaenel, E., Blair, S. A., Browning, E., Lundquist, J., Boesiger, T. M., Bolivar, M. & Clark, K. (2019). BP Gulf of Mexico Neogene Astronomically-Tuned Time Scale (BP GNATTS). GSA Bulletin, 131 (11-12): 1871-1888.

GSA Bulletin; November/December 2019; v. 131; no. 11/12; p. 1871–1888; https://doi.org/10.1130/B35062.1; 7 figures; 7 tables; Data Repository item 2018407; published online 16 April 2019.

Data are available at http:// www .geosociety .org /datarepository /2018 or by request to editing@ geosociety .org.

We have taken all the zonation schemes and events, and turned them into an updated set of biozone schemes and composite standards, which are linked to corresponding named taxa. You can download the entire set of schemes which make up this chart and import them and reconstruct this chart if you wish. Alternatively you can just import selected schemes.

 

If you download the entire data pack you can import/match the linked taxa against your own data. A word of warning: the vertical scaling is based on GTS2012/2016 ages except that the Gelasian is included in Pliocene, making the Pliocene/Pleistocene boundary younger when compared to those published schemes (and indeed the standards ICS chart).

You’ll need StrataBugs 2.1 to read this file, preferably v2.1.1. use Help | About to find out which version you’re running, and contact us if you need help upgrading.

The Nannofossil events are differentiated on the basis of size, and this has been carried through to the taxonomy, to create separate species for the different size fractions. The µ symbol (for micron) is implicit in these taxon names: this is to follow the convention of the published chart, but also there is a quirk that a name search in StrataBugs will not pick up taxon names which include the µ symbol, because of the inconsistent way the uppercase character is handled in SQL.

Thanks to Todd Boesiger for supplying the initial data, and to Eric de Kaenel for all his checking and comments, much appreciated.

 

 

 

 

 

 

 

Time for a new timescale

Happy new year and happy new timescale! With the publication of the new Gradstein, Ogg, Schmitz & Ogg Geologic Time Scale 2020, we have a StrataBugs friendly encoding of the new units with their updated ages and colours, which is available to download from our Schemes page. Download the .SBG file, then open Schemes & Interpretations, select Stratigraphic schemes, and press Read… to read it – then press Add Scheme to add it to your database. It will then be available for use in any charts or with well data, or just to compare against previous versions, or your favourite biozone schemes. Please let us know if you spot any errors. Note that the substages in the Cretaceous, Jurassic and Triassic are informal and illustrative. We have not recalibrated any of the “Standard” biozone schemes yet – there is a re-calibration tool in StrataBugs which allows you to do this if you wish, but this is only intended as a starting point, the final schemes should be thoroughly checked!

Note that the timescale which is available from the International Commission on Stratigraphy website, although called the 2020/v3 revision, is actually based on the previous GTS2012 timescale, so don’t get confused! We have called the previous version of this timescale “ICS” to avoid this.

 

GTS2016 Calibrated Transgressive/Regressive cycle sequence scheme

We’ve recently added a new calibration of the SEPM global sequence scheme for the GTS2016 time scale, featuring the terminology used in the latest version. This is available on our scheme resources page. These schemes can be simply downloaded from here and imported into your database in the Schemes and Interpretations module.

Thanks to Jake Jacovides from Millennia for preparing this version of the scheme.

If you have schemes you’d like to see, or to contribute, please get in touch, and let us know if you spot any errors.

 

Exporting for multivariate analysis

So, you have a bunch of analyses in your StrataBugs database that have, of course, been nicely QC’d and you want to do some statistical analysis. Apart from the built in clustering offered through the taxon panel, we don’t do a lot of exploratory stats like Q/R mode cluster analysis, Principal Components etc. So, you have to export the data. Up until recently, you can only export one well at a time through the “Save As” mechanism on the Analyses tab in Samples & Interpretations. This is all well and good, but what if you need to combine data from more than one well? If you export into multiple spreadsheets, then unless the fauna/flora are identical, you’re going to end up with having to manually paste in each spreadsheet carefully, so the columns all line up correctly. Major headache.

Fortunately there’s now a Multi-well sample analysis export built into Organiser, and Lawrence Febo has kindly shared this simple graphic to explain the export steps … thanks Lawrence, and enjoy …

StrataBugs and Java updates

Here at StrataData towers we’ve been working to prepare for the next major release of StrataBugs, which will likely to be called v3.0 and involve some database updates. It’s also going to be built on the latest version of Java. Things have been happening in the Java world. Many of you will have noticed that Oracle have stopped freely licencing Java except for personal use: you are now required to buy (for a nominal fee) a licence for Java itself before you can run any Java-based software. Fear not, however, as there are open source builds of Java available to download with no licensing restrictions. The current version of StrataBugs, version 2.1.1, will require version 7 or 8 of java, and there are various builds available for you to use. To simplify, we have created a downloadable bundle of StrataBugs with the Azul Zulu version of Java 8; with this you can run StrataBugs without having to “install” Java on your machine. This means that you will also not be pestered about Java updates.

We have also made available an intermediate version between v2.1.1 and v3.0, which we’re calling v2.1.1-14, which uses the latest Java 14. In this case, a tailored version of Java 14 is bundled with the download. It is fully compatible with your v2.1/v2.1.1 database, and can be used in place of your existing installation. The advantage of using Java 14 is that it responds to screen sizing better. High resolution “4k” screens are becoming more common – if you look at your Windows display properties, and it shows that your fonts etc. are displayed at 200% or 250%, then you’re likely to be running a 4k screen. In its default setting, StrataBugs will be unusable, as the contents of the windows will “outgrow” the window borders. With Java 8 there is a workaround to this: but it does look slightly pixelated. With Java 14, scaling works correctly and the windows and dialogs are sharp.

You can download this new version but you will need a licence update to run it: we are only releasing this version to current (2020) maintenance holders.

Get in touch with support@stratadata.co.uk if you want more information, or for any other StrataBugs queries.