November 30, 2018

I’m dreaming of a blueschist Christmas

November 30, 2018/ Matt Hall

The festive season is speeding towards us at the terrifying rate of 3600 seconds per hour. Have you thought about what kind of geoscientific wonders to make or buy for the most awesome kids and/or grownups in your life yet? I hope not, because otherwise this post is pretty redundant… If you have, I’m sure you can think of <AHEM> at least one more earth scientist in your life you’d like to bring a smile to this winter.

I mean, here’s a bargain to start you off: a hammer and chisel for under USD 15 — an amazing deal. The fact that they are, unbelievably, made of chocolate only adds to the uses you could put them to.

If your geoscientist is on a diet or does their fieldwork in a warm country, then obviously these chocolate tools won’t work. You could always get some metal ones instead (UK supplier, US supplier).

Before you start smashing things to bits with a hammer, especially one that melts at 34°C, it’s sometimes nice to know how hard they are. Tapping them with a chocolate bar or scratching them with your fingernail are time-tested methods, but the true geologist whips out a hardness pick.

I have never actually seen one of these (I’m not a true geologist) so the chances of your geoscientist having one, especially one as nice as this, are minuscule. USD 90 at geology.com.

Hammers can be used around the house too, of course, for knocking in nails or sampling interesting countertops. If your geoscientist is houseproud, how about some of Jane Hunter’s beautiful textile artworks, many of which explore geological and geomorphological themes, especially Scottish ones. The excerpt shown here is from Faults and Folds (ca. USD 1000); there are lots of others.

If textiles aren’t your thing, these hydrology maps from Muir Way are pretty cool too. From USD 80 each.

Topographic maps are somehow more satisfying when they are three-dimensional. So these beautiful little wooden maps from ElevatedWoodworking on Etsy, which seem too cheap to be true, look perfect.

There’s plenty more for geoscientists on Etsy, if you can look past the crass puns slapped clumsily onto mugs and T-shirts. For example, if geostatistics get you going, start at NausicaaDistribution and keep clicking. My favourites: the Chisquareatops shirt and the MCMC Hammer cross-stitch pattern.

I like statistics. Sometimes, not very often, people ask my where my online handle kwinkunks comes from. It’s a phonetic spelling of one of my favourite words, quincunx, which has a couple of meanings, but the most interesting one is a synonym for a Galton board or bean machine. Galton boards are awesome! Demonstrate the central limit theorem right on your desktop! From USD 10: a cheap one, and an expensive one.

Oh, and there’s a really lovely/expensive one from Lightning Calculator if your geoscientist is the sort of person who likes to have the best of everything. It costs USD 1190 and it looks fantastic.

Let’s get back to rocks. You can actually just give a rock to a geologist, and they’ll be happy. You just might not see much of them over the holiday, as they disappear off to look at it.

If your geologist has worked in the North Sea in their career, they will definitely, 100% enjoy these amazing things. Henk Kombrink and Kirstie Wright are distributing chunks of actual North Sea core. The best part is that you can choose the well and formation the rock comes from! We gave some resinated core slabs away as prizes at the hackathons this month, and the winners loved them.

Traditionally, I mention some books. Not that I read books anymore (reasons). If I did read books, these are the ones I’d read:

Timefulness: How Thinking Like a Geologist Can Help Save the World, by Marcia Bjornerud, Princeton University Press. (Who doesn’t want to save the world?)
The Writer’s Map: An Atlas of Imaginary Lands, by Huw Lewis-Jones (ed), University of Chicago Press. (I like maps.)
Beyond Weird: Why Everything You Know About Quantum Physics is Different, by Philip Ball. University of Chicago Press. (Not geoscience, but I’ve enjoyed Philip Ball’s books before.)

That’s it for this year! I hope there’s something here to brighten your geoscientist’s day. Have fun shopping!

PS In case there’s not enough here to choose from, you can trawl through the posts from previous years too:

Unlike most images on agilescientific.com, the ones in this post are not my property and are not open access. They are the copyright of their respective owners, and I’m using them here in accordance with typical Fair Use terms. If owners object, please let me know.

November 28, 2018

The Scottish hackathon

November 28, 2018/ Matt Hall

On 16−18 November the UK Oil & Gas Authority (OGA) hosted its first hackathon, with Agile providing the format and technical support. This followed a week of training the OGA provided — again, through Agile — back in September. The theme for the hackathon was ‘machine learning’, and I’m pretty sure it was the first ever geoscience hackathon in the UK.

Thirty-seven digital geoscientists participated in the event at Robert Gordon University; most of them appear below. Many of them had not coded at all before the bootcamp on Friday, so a lot of people were well outside their comfort zones when we sat down on Saturday. Kudos to everyone!

The projects included the usual mix of seismic-based tasks, automated well log picking, a bit of natural language processing, some geospatial processing, and seals (of the mammalian variety). Here’s a rundown of what people got up to:

Counting seals on Scottish islands

Seal Team 6: Julien Moreau, James Mullins, Alex Schaaf, Balazs Kertesz, Hassan Tolba, Tom Buckley.

Project: Julien arrived with a cool dataset: over 6000 seals located on two large TIFFs images of Linga Holm, an island off Stronsay in the Orkneys. The challenge: locate the seals automatically. The team came up with a pipeline to generate HOG descriptors, train a support vector machine on about 20,000 labelled image tiles, then scan the large TIFFs to try to identify seals. Shown here is the output of one such scan, with a few false positive and false negatives. GitHub repo.

This project won the Most Impact award.

Automatic classification of seismic sections

Team Seis Class: Jo Bagguley, Laura Bardsley, Chio Martinez, Peter Rowbotham, Mike Atkins, Niall Rowantree, James Beckwith.

Project: Can you tell if a section has been spectrally whitened? Or AGC’d? This team set out to attempt to teach a neural network the difference. As a first step, they reduced it to a binary classification problem, and showed 110 ‘final’ and 110 ‘raw’ lines from the OGA ESP 2D 2016 dataset to a convolutional neural net. The AI achieved an accuracy of 98% on this task. GitHub repro.

This project won recognition for a Job Well Done.

Why do get blocks relinquished?

Team Relinquishment Surprise: Tanya Knowles, Obiamaka Agbaneje, Kachalla Aliyuda, Daniel Camacho, David Wilkinson (not pictured).

Project: Recognizing the vast trove of latent information locked up in the several thousand reports submitted to the OGA. Despite focusing on relinquishment, they quickly discovered that most of the task is to cope with the heterogeneity of the dataset, but they did manage to extract term frequencies from the various Conclusions sections, and made an ArcGIS web app to map them.

Recognizing reflection styles on seismic

Team What’s My Seismic? Quentin Corlay, Tony Hallam, Ramy Abdallah, Zhihua Cui, Elia Gubbala, Amechi Halim.

Project: The team wanted to detect the presence of various seismic facies in a small segment of seismic data (with a view to later interpreting entire datasets). They quickly generated a training dataset, then explored three classifiers: XGBoost, Google’s AutoML, and a CNN. All of the methods gave reasonable results and were promising enough that the team vowed to continue investigating the problem. Project website. GitHub repo.

This project won the Best Execution award.

Stretchy-squeezey well log correlation

Team Dynamic Depth Warping: Jacqueline Booth, Sarah Weihmann, Khaled Muhammad, Sadiq Sani, Rahman Mukras, Trent Piaralall, Julio Rodriguez.

Project: Making picks and correlations in wireline data is hard, partly because the stratigraphic signal changes spatially — thinning and thickening, and with missing or extra sections. To try to cope with this, the team applied a dynamic time (well, depth) warping algorithm to the logs, then looking for similar sections in adjacent wells. The image shows a target GR log (left) with the 5 most similar sections. Two, maybe four, of them seem reasonable. Next the team planned to incorporate more logs, and attach probabilities to the correlations. Early results looked promising. GitHub repo.

Making lithostrat picks

Team Marker Maker: Nick Hayward, Frédéric Ramon, Can Yang, Peter Crafts, Malcolm Gall

Project: The team took on the task of sorting out lithostratigraphic well tops in a mature basin. But there are speedbumps on the road to glory, e.g. recognizing which picks are lithological (as opposed to chronological), and which pick names are equivalent. The team spent time on various subproblems, but there’s a long road ahead.

This project won recognition for a Job Well Done.

Alongside these projects, Rob and I floated around trying to help, and James Beckwith hacked on a cool project of his own for a while — Paint By Seismic, a look at unsupervised classification on seismic sections. In between generating attributes and clustering, he somehow managed to help and mentor most of the other teams — thanks James!

Thank you!

Thank you to The OGA for these events, and in particular to Jo Bagguley, whose organizational skills I much appreciated over the last few weeks (as my own skills gradually fell apart). The OGA’s own Nick Richardson, the OGTC’s Gillian White, and Robert Gordon Universty’s Eyad Elyan acted as judges.

These organizations contributed to the success of these events — please say Thank You to them when you can!

I’ll leave you with some more photos from the event. Enjoy!

November 06, 2018

TRANSFORM 2019

November 06, 2018/ Matt Hall

Yesterday I announced that we’re hatching a new plan. The next thing. Today I want to tell you about it.

The project has the codename TRANSFORM. I like the notion of transforms: functions that move you from one domain to another. Fourier transforms. Wavelet transforms. Digital subsurface transforms. Examples:

The transformative effect of open source software on subsurface science. Open source accelerates our work!
The transformative effect of collaborative, participatory events on the community. We can make new things!
The transformative effect of training on ourselves and our peers. Lots of us have new superpowers!

Together, we’ve built the foundation for a new, open software platform.

A domain shift

We think it’s time to refocus the hackathons as sprints — purposefully producing a sustainable, long-lasting, high quality, open source software stack that we can all use and combine into new tools, whether open or proprietary, free or commercial.

We think it’s time to bring a full-featured unconference into the mix. The half-day ‘unsessions’ open too many paths, and leave too few explored. We need more time — to share research, plan software projects, and write code.

Together, we can launch a new era in scientific computing for the subsurface.

At the core of this new era core is a new open-source software stack, created, maintained, and implemented by a community of scientists and organizations passionate about its potential.

Sign up!

Here’s the plan. We’re hosting an unconference from 5 to 11 May 2019, with full days from Monday to Friday. The event will take place at the Château de Rosay, near Rouen, France. It will be fully residential and fully catered. We have room for about 45 participants.

The goal is to lay down a road map for designing, funding, and building an open source software stack for subsurface. In the coming days and weeks, we will formulate the plan for the week, with input from the Software Underground. We want to hear from you. Propose a session! Host a sprint! Offer a bounty! There are lots of ways to get involved.

Map data: GeoBasis-DE / BKG / Google, photo: Chateauform. Click to enlarge.

If you want to be part of this effort, as a developer, an end-user, or a sponsor, then we invite you to join us.

The unconference fee will be EUR 1000, and accommodation and food will be EUR 1500. The student fees will be EUR 240 and EUR 360. There will be at least 5 bursaries of EUR 1000 available.

For the time being, we will be accepting early commitments, with a deposit of EUR 400 to secure a place (students wishing to register now should get in touch). Soon, you will be able to sign up online… we are working on a smooth process. In the meantime, click here to register your interest, share ideas for content, or sign up by paying a deposit.

Thanks for reading. We look forward to figuring this out together.

I’m delighted to be able to announce that we already have support from Dell EMC. Thanks as ever to David Holmes for his willingness to fund experiments!

In the US or Canada? Don’t despair! There will be a North American edition in Quebec in late September.

November 05, 2018

The next thing

November 05, 2018/ Matt Hall

Over the last several years, Agile has been testing some of the new ways of collaborating, centered on digital connections:

It all started with this blog, which started in 2010 with my move from Calgary to Nova Scotia. It’s become a central part of my professional life, but we’re all about collaboration and blogs are almost entirely one-way, so…
In 2011 we launched SubSurfWiki. It didn’t really catch on, although it was a good basis for some other experiments and I still use it sometimes. Still, we realized we had to do more to connect the community, so…
In 2012 we launched our 52 Things collaborative, open access book series. There are well over 5000 of these out in the wild now, but it made us crave a real-life, face-to-face collaboration, so…
In 2013 we held the first ‘unsession’, a mini-unconference, at the Canada GeoConvention. Over 50 people came to chat about unsolved problems. We realized we needed a way to actually work on problems, so…
Later that year, we followed up with the first geoscience hackathon. Around 15 or so of us gathered in Houston for a weekend of coding and tacos. We realized that the community needed more coding skills, so…
In 2014 we started teaching a one-day Python course aimed squarely at geoscientists. We only teach with subsurface data and algorithms, and the course is now 5 days long. We now needed a way to connect all these new hackers and coders, so…
In 2014, together with Duncan Child, we also launched Software Underground, a chat room for discussing topics related to the earth and computers. Initially it was a Google Group but in 2015 we relaunched it as an open Slack team. We wanted to double down on scientific computing, so…
In 2015 and 2016 we launched a new web app, Pick This (returning soon!), and grew our bruges and welly open source Python projects. We also started building more machine learning projects, and getting really good at it.

Growing and honing

We have spent the recent years growing and honing these projects. The blog gets about 10,000 readers a month. The sixth 52 Things book is on its way. We held two public unsessions this year. The hackathons have now grown to 60 or so hackers, and have had about 400 participants in total, and five of them this year already (plus three to come!). We have also taught Python to 400 geoscientists, including 250 this year alone. And the Software Underground has over 1000 members.

In short, geoscience has gone digital, and we at Agile are grateful and excited to be part of it. At no point in my career have I been more optimistic and energized than I am right now.

So it’s time for the next thing.

The next thing is starting with a new kind of event. The first one is 5 to 11 May 2019, and it’s happening in France. I’ll tell you all about it tomorrow.

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