The Agile toolbox

Some new businesses go out and raise millions in capital before they do anything else. Not us — we only do what we can afford. Money makes you lazy. It's technical consulting on a shoestring!

If you're on a budget, open source is your best friend. More than this, it's important an open toolbox is less dependent on hardware and less tied to workflows. Better yet, avoiding large technology investments helps us avoid vendor lock-in, and the resulting data lock-in, keeping us more agile. And there are two more important things about open source: 

• You know exactly what the software does, because you can read the source code
• You can change what the software does, becase you can change the source code

Anyone who has waited 18 months for a software vendor to fix a bug or add a feature, then 18 more months for their organization to upgrade the software, knows why these are good things.

So what do we use?

In the light of all this, people often ask us what software we use to get our work done.

Hardware  Matt is usually on a dual-screen Apple iMac running OS X 10.6, while Evan is on a Samsung Q laptop (with a sweet solid-state drive) running Windows. Our plan, insofar as we have a plan, is to move to Mac Pro as soon as the new ones come out in the next month or two. Pure Linux is tempting, but Macs are just so... nice.

Geoscience interpretation  dGB OpendTect, GeoCraft, Quantum GIS (above). The main thing we lack is a log visualization and interpretation tool. Beyond this, we don't use them much yet but Madagascar and GMT are plugged right into OpendTect. For getting started on stratigraphic charts, we use TimeScale Creator. 

A quick aside, for context: when I sold Landmark's GeoProbe seismic interpretation tool, back in 2003 or so, the list price was USD140 000 per user, choke, plus USD25k per year in maintenance. GeoProbe is very powerful now (and I have no idea what it costs), but OpendTect is a much better tool that that early edition was. And it's free (as in speech, and as in beer).

Geekery, data mining, analysis  Our core tools for data mining are Excel, Spotfire Silver (an amazing but proprietary tool), MATLAB and/or GNU Octave, random Python. We use Gephi for network analysis, FIJI for image analysis, and we have recently discovered VISAT for remote sensing images. All our mobile app development has been in MIT AppInventor so far, but we're playing with the PhoneGap framework in Eclipse too. 

Writing and drawing  Google Docs for words, Inkscape for vector art and composites, GIMP for rasters, iMovie for video, Adobe InDesign for page layout. And yeah, we use Microsoft Office and OpenOffice.org too — sometimes it's just easier that way. For managing references, Mendeley is another recent discovery — it is 100% awesome. If you only look at one tool in this post, look at this.

Collaboration  We collaborate with each other and with clients via Skype, Dropbox, Google+ Hangouts, and various other Google tools (for calendars, etc). We also use wikis (especially SubSurfWiki) for asynchronous collaboration and documentation. As for social media, we try to maintain some presence in Google+, Facebook, and LinkedIn, but our main channel is Twitter.

Web  This website is hosted by Squarespace for reliability and reduced maintenance. The MediaWiki instances we maintain (both public and private) are on MediaWiki's open source platform, running on Amazon's Elastic Compute servers for flexibility. An EC2 instance is basically an online Linux box, running Ubuntu and Bitnami's software stack, plus some custom bits and pieces. We are launching another website soon, running WordPress on Amazon EC2. Hover provides our domain names — an awesome Canadian company.

Administrative tools  Every business has some business tools. We use Tick to track our time — it's very useful when working on multiple projects, subscontractors, etc. For accounting we recently found Wave, and it is the best thing ever. If you have a small business, please check it out — after headaches with several other products, it's the best bean-counting tool I've ever used.

If you have a geeky geo-toolbox of your own, we'd love to hear about it. What tools, open or proprietary, couldn't you live without?

Update on 2012-09-13 13:26 by Matt Hall

Just heard about this awesome list by John Stevenson, a postdoc at Edinburgh University, UK. Thanks to Jon Tennant, aka @protohedgehog, for the tip. Don't know how I missed that...

Checklists for everyone

Avoidable failures are common and persistent, not to mention demoralizing and frustrating, across many fields — from medicine to finance, business to government. And the reason is increasingly evident: the volume and complexity of what we know has exceeded our individual ability to deliver its benefits correctly, safely, or reliably. Knowledge has both saved and burdened us.

I first learned about Atul Gawande from Bill Murphy's talk at the 1IWRP conference last August, where he offered the surgeon's research model for all imperfect sciences; casting the spectrum of problems in a simple–complicated–complex ternary space. In The Checklist Manifesto, Gawande writes about a topic that is relevant to all all geoscience: the problem of extreme complexity. And I have been batting around the related ideas of cookbooks, flowcharts, recipes, and to-do lists for maximizing professional excellence ever since. After all, it is challenging and takes a great deal of wisdom to cut through the chaff, and reduce a problem to its irreducible and essential bits. Then I finally read this book.

The creation of the now heralded 19-item surgical checklist found its roots in three places — the aviation industry, restaurant kitchens, and building construction:

Thinking about averting plane crashes in 1935, or stopping infections in central lines in 2003, or rescuing drowning victims today, I realized that the key problem in each instance was essentially a simple one, despite the number of contributing factors. One needed only to focus attention on the rudder and elevator controls in the first case, to maintain sterility in the second, and to be prepared for cardiac bypass in the third. All were amenable, as a result, to what engineers call "forcing functions": relatively straightforward solutions that force the necessary behavior — solutions like checklists.

What is amazing is that it took more than two years, and a global project sponsored by the World Health Organization, to devise such a seemingly simple piece of paper. But what a change it has had. Major complications fell by 36%, and deaths fells by 47%. Would you adopt a technology that had a 36% improvement in outcomes, or a 36% reduction in complications? Most would without batting an eye.

But the checklist paradigm is not without skeptics. There is resistance to the introduction of the checklist because it threatens our autonomy as professionals, our ego and intelligence that we have trained hard to attain. An individual must surrender being the virtuoso. It enables teamwork and communication, which engages subordinates and empowers them at crucial points in the activity. The secret is that a checklist, done right, is more than just tick marks on a piece of paper — it is a vehicle for delivering behavioural change.

I can imagine huge potential for checklists in the problems we face in petroleum geoscience. But what would such checklists look like? Do you know of any in use today?

Update on 2012-07-06 13:16 by Evan Bianco

<img src="https://docs.google.com/drawings/pub?id=1obXW2658bqCNt6OpOzSU_vhfEdDKPHH467cqIDdpCoE&w=480&h=360">

Update on 2012-07-06 13:17 by Evan Bianco

News of the month

A few bits of news about geology, geophysics, and technology in the hydrocarbon and energy realm. Do drop us a line if you hear of something you think we ought to cover.

All your sequence strat

The SEPM, which today calls itself the Society for Sedimentary Geology (not the Society of Economic Palaeontologists and Mineralogists, which is where the name comes from, IIRC), has upgraded its website. It looks pretty great (nudge nudge, AAPG!). The awesome SEPM Strata, a resource for teaching and learning sequence stratigraphy, also got a facelift. 

Hat-tip to Brian Romans for this one.

Giant sand volcano

Helge Løseth of Statoil, whom we wrote about last week in connection with the Source Rocks from Seismic workflow, was recently in the news again. This time he and his exploration team were describing the Pleistocene extrusion of more than 10 km³ of sand onto the sea-floor in the northern North Sea, enough to bury Manhattan in 160 m of sand.

The results are reported in Løseth, H, N Rodrigues, and P Cobbold (2012) and build on earlier work by the same team (Rodrigues et al. 2009). 

Tape? There's still tape??

Yes, there's still tape. This story just caught my eye because I had no idea people were still using tape. It turns out that the next generation of tape, Ultrium LTO-6, will be along in the second half of 2012. The specs are pretty amazing: 8 TB (!) of compressed data, and about 200 MB/s (that's megabytes) transfer rates. The current generation of cartridges, LTO-5, cost about $60 and hold 3 TB — a similar-performing hard drive will set you back more than double that. 

The coolest cluster

Physics enables geophysics in lots of cool ways. CGGVeritas is using a 600 kW Green Revolution Cooling CarnotJet liquid cooling system to refrigerate 24 cluster racks in GRC's largest installation to date. In the video below, you can see an older 100 kW system. The company claims that these systems, in which the 40°C racks sit bathed in non-conductive oil, reduce the cost of cooling a supercomputer by about 90%... pretty amazing.

Awesomer still, this server is using Supermicro's SuperServer GPU-accelerated servers. GPUs, or graphics processing units, have massively parallel architectures (over 1000 cores per server), and can perform some operations much faster than ordinary CPUs, which are engineered to perform 'executive' functions as well as just math.

This regular news feature is for information only. We aren't connected with any of these organizations, and don't necessarily endorse their products or services. The cartridge image is licensed CC-BY-SA by Wikimedia Commons user andy_hazelbury. The CarnotJet image is from grcooling.com and thought to be fair use.

How big is that volume?

Sometimes you need to know how much space you need for a seismic volume. One of my machines only has 4GB of RAM, so if I don't want to run out of memory, I need to know how big a volume will be. Or your IT department might want help figuring out how much disk to buy next year.

Fortunately, since all seismic data is digital these days, it's easy to figure out how much space we will need. We simply count the samples in the volume, then account for the bit-depth. So, for example, if a 3D volume has 400 inlines and 300 traces per line, then it has 120 000 traces in total. If each trace is 6 seconds long, and the sample interval is 2 ms, then each trace has 6000/2 = 3000 samples (3001 actually, but let's not worry too much about that), so that's about 360 million samples. for a 32-bit volume, each sample requires 32/8 = 4 bytes, so we're at... a big number.  To convert to kilobytes, divide by 2¹⁰, or 1024, then do it again for MB and again for GB.

It's worth noting that some seismic interpretation tools have proprietary compressed formats available for seismic data, Landmark's 'brick' format for example. This optionally applies a JPEG-like compression to reduce the file size, as well as making some sections display faster because of the way the compressed file is organized. The amount of compression depends on the frequency content of the data, and the compression is lossy, however, meaning that some of the original data is irretrievably lost in the process. If you do use such a file for visualization and interpretation, you may want to use a full bit-depth, full-fidelity file for attribute analysis. 

Do you have any tricks for managing large datasets? We'd love to hear them!

Polarity cartoons

...it is good practice to state polarity explicitly in discussions of seismic data, with some phrase such as: 'increase in impedance downwards gives rise to a red (or blue, or black) loop.'

Bacon, Simm & Redshaw (2003), 3D Seismic Interpretation, Cambridge

Good practice, but what a mouthful. And perhaps because it is such a cumbersome convention, it is often ignored, assumed, or skipped. We'd like to change that. Polarity is important, everyone needs to know what the wiggles (or colours) of seismic data mean.

Two important things

    Click the image to find your favorite colorbarSeismic data is about contrasts. The data are an abstraction of geological contrasts in the earth. To connect the data to the geology, there are two important things you need to know about your data:

1. What do the colours mean in terms of digits?

2. What do the digits mean in terms of impedance?

So whenever you show seismic to someone, you need to answers these questions for them. Show the colourbar, and the sign of the digits (the magnitude of the digits is not very important; amplitude are relative). Show the relationship between the sign of the digits and impedance.

Really useful

To help you show these things, we have created a table of polarity cartoons for some common colour scales.

1. Decide if you want to use the American–Canadian convention of a downwards increase in impedance resulting in a positive amplitude, or the opposite European–Australian convention. Sometimes people talk about SEG Normal polarity — the de facto SEG standard is the American convention.

2. Choose whether you want to show a high impedance layer sandwiched between low impedance ones, or vice versa. To make this decision, inspect your well ties or plot impedance against lithology. For example, if your sands are relatively fast and dense, you may want to choose the hard layer option.

3. Select a colourmap that matches your displays. If you need another, you can download and edit the SVG file, or email us and we'll add it for you.

4. Right-click on a thumbnail, copy it to your clipboard, and paste it into the corner of your section or timeslice in PowerPoint, Word, or wherever. If the thumbnail is too small or pixelated, click the thumbnail for higher resolution.

With so many options to choose from, we hope this little tool can help make your seismic discussions a little more transparent. What's more, if you see a seismic section without a legend like this, then are you sure the presenter knows about the polarity of their data? Perhaps they do, but it is an oversight to assume that you should know as well. 

What do you make your audience assume?

---

UPDATE [2020] — we built a small web app to serve up fresh polarity cartoons, whenever you need them! Check it out.

Source rocks from seismic

A couple of years ago, Statoil's head of exploration research, Ole Martinsen, told AAPG Explorer magazine about a new seismic analysis method. Not just another way to discriminate between sand and shale, or water and gas, this was a way to assess source rock potential. Very useful in under-explored basins, and Statoil developed it for that purpose, but only the very last sentence of the Explorer article hints at its real utility today: shale gas exploration.

Calling the method Source Rocks from Seismic, Martinsen was cagey about details, but the article made it clear that it's not rocket surgery: “We’re using technology that would normally be used, say, to predict sandstone and fluid content in sandstone,” said Marita Gading, a Statoil researcher. Last October Helge Løseth, along with Gading and others, published a complete account of the method (Løseth et al, 2011).

Because they are actively generating hydrocarbons, source rocks are usually overpressured. Geophysicists have used this fact to explore for overpressured zones and even shale before. For example, Mukerji et al (2002) outlined the rock physics basis for low velocities in overpressured zones. Applying the physics to shales, Liu et al (2007) suggested a three-step process for evaluating source rock potential in new basins: 1 Sequence stratigraphic interpretation; 2 Seismic velocity analysis to determine source rock thickness; 3 Source rock maturity prediction from seismic. Their method is also a little hazy, but the point is that people are looking for ways to get at source rock potential via seismic data. 

The Løseth et al article was exciting to see because it was the first explanation of the method that Statoil had offered. This was exciting enough that the publication was even covered by Greenwire, by Paul Voosen (@voooos on Twitter). It turns out to be fairly straightforward: acoustic impedance (AI) is inversely and non-linearly correlated with total organic carbon (TOC) in shales, though the relationship is rather noisy in the paper's examples (Kimmeridge Clay and Hekkingen Shale). This means that an AI inversion can be transformed to TOC, if the local relationship is known—local calibration is a must. This is similar to how companies estimate bitumen potential in the Athabasca oil sands (e.g. Dumitrescu 2009). 

Figure 6 from Løseth et al (2011). A Seismic section. B Acoustic impedance. C Inverted seismic section where source rock interval is converted to total organic carbon (TOC) percent. Seismically derived TOC percent values in source rock intervals can be imported to basin modeling software to evaluate hydrocarbon generation potential of a basin. Click for full size..The result is that thick rich source rocks tend to have strong negative amplitude at the top, at least in subsiding mud-rich basins like the North Sea and the Gulf of Mexico. Of course, amplitudes also depend on stratigraphy, tuning, and so on. The authors expect amplitudes to dim with offset, because of elastic and anisotropic effects, giving a Class 4 AVO response.

This is a nice piece of work and should find application worldwide. There's a twist though: if you're interested in trying it out yourself, you might be interested to know that it is patent-pending: 

WO/2011/026996
INVENTORS:  Løseth,  H;  Wensaas, L; Gading, M; Duffaut, K; Springer, HM
Method of assessing hydrocarbon source rock candidate
A method of assessing a hydrocarbon source rock candidate uses seismic data for a region of the Earth. The data are analysed to determine the presence, thickness and lateral extent of candidate source rock based on the knowledge of the seismic behaviour of hydrocarbon source rocks. An estimate is provided of the organic content of the candidate source rock from acoustic impedance. An estimate of the hydrocarbon generation potential of the candidate source rock is then provided from the thickness and lateral extent of the candidate source rock and from the estimate of the organic content.

References

Dumitrescu, C (2009). Case study of a heavy oil reservoir interpretation using Vp/Vs ratio and other seismic attributes. Proceedings of SEG Annual Meeting, Houston. Abstract is online. 

Liu, Z, M Chang, Y Zhang, Y Li, and H Shen (2007). Method of early prediction on source rocks in basins with low exploration activity. Earth Science Frontiers 14 (4), p 159–167. DOI 10.1016/S1872-5791(07)60031-1

Løseth, H, L Wensaas, M Gading, K Duffaut, and M Springer (2011). Can hydrocarbon source rocks be identified on seismic data? Geology 39 (12) p 1167–1170. First published online 21 October 2011. DOI 10.1130/​G32328.1

Mukerji, T, Dutta, M Prasad, J Dvorkin (2002). Seismic detection and estimation of overpressures. CSEG Recorder, September 2002. Part 1 and Part 2 (Dutta et al, same issue). 

The figure is reproduced from Løseth et al (2011) according to The Geological Society of America's fair use guidelines. Thank you GSA! The flaming Kimmeridge Clay photograph is public domain.