News from the Underground

In the seemingly random content factory that is the Software Underground community, there has been a heavy sampling this past week around openness. What is open source? What is open data? What are good practices? and, How does this affect me? Here’s a collection of those conversations and more.

The Geothermal Hackathon — happened last week immediately following the World Geothermal Congress Geoscience virtual event. You can read about the things that people built leveraging open data sets and be sure to connect with these creators in the #geothermal channel.

The complicated world of open source — Spilling over from an SPE workshop on Open Software, is perhaps the longest thread in Swung history about what actually constitutes open source software, why it can be so confusing, and what the implications are for scientists and technologists. Matt followed up with a number of suggestions how technical societies can support openness, and also created a poll to measure the degree of confusion around open source. Conclusion: it depends.

A checklist for open scientific software — Yes, open source is complicated, especially for newcomers, so it seems fit for relatively straightforward tools to guide behaviours. Matt shared a so-called best-practice checklist for open scientific software, which quickly underwent a handful of revisions after some supportive feedback. It is meant to be more than just tick marks on a piece of paper but that it can be a vehicle for delivering behavioural change.

Big Borehole Dig – Steph shared a cool project launched by the British Geologic survey welcoming scientists and citizen scientists alike to digitize their vast collection of historic logs into a standard digital format. It’s the ‘ol PDF to actually-digital transformation challenge and this one is a tall order. But just imagine the data science possibilities from 1.4 M boreholes!

Tools and tactics – people are getting help on to tricky technical questions in the #python channel on a variety of topics including: dealing with very large tabular data with Vaex, how to constrain solutions to non-linear problems with scipy.optimize, and fixing missing data values in rasters with rasterio.

Vedo – in the visualization awesomness category, the winner goes to a post that Dieter made in the #viz channel about the Vedo project, whose gallery will incite all the feels of a kid in candy store for those working in 3D. Notably, the first tile in the gallery is a demo geo-model shared by Richard Scott. Check out his scene here before you get on with the rest of your day.

Vedo – a python module for scientific analysis and visualization of 3D objects.

News from the Underground

The reverberations from TRANSFORM 2021 have started to dampen, so we’re back with our weekly round-ups.

Badges of honour — Did you know that you can slap a Software Underground badge on your projects and webpages? These badges aren’t just for showing off either. They can links to other places, for instance to your project’s channel in the Swung Slack, if it has one.

Geothermal Hackathon 2021 — is taking place at the end of next week with much activity to be going on in the #geothermal-hack-2021 channel. Here are some of the proposed projects. Even if you aren’t registered in the hackathon you can still follow the action.

Superstar with LiDAR — Are you dealing with .las files, but not of the wireline kind? Then this discussion will serve you up a platter of resources and advice for working with point-cloud data sets.

Feature combo pipelines — If, like Brendon, you’re doing some machine learning and you find yourself building a boatload of models all with different combinations of inputs and pre-processing steps, you’re life is going to be much easier if you have a way to keep track of these different permutations so you can apply it all again on other data.

Need a license for work — Pythonistas using Anaconda might be shocked to find out that it’s no longer free to use. Sort of. It depends on who you work for and the kind of work you are doing. This thread discusses the issues and reveals a shared frustration in comprehending the terms and conditions. There are also some thoughtful perspectives on supporting the free (or nearly free) software that many organizations become increasingly dependant on.

Tools for seeing — Geoscience very often relies on making graphics and visualization. This post pointing to the Python-only compilation called PyViz.org, shows you the collection of tools that are out there. It looks to be a comprehensive resource, particularly because the number of tools in the tool shed can seem so daunting.

News from the Underground

Here’s all the news from the Underground this week…

Have you signed up for TRANSFORM 2021 yet? Because it kicks off with the hackathon next Friday 16 April. The hackathon projects are starting to take shape and there is going to be a special Rendezvous session on next Wednesday 14 April at 16.00 UTC to discuss project ideas. Come along and let the project ideas wash over you and vie for your attention.

What to learn first? — Matt created an infographic entitled, Which language should I learn first? with some opinions about how to get started in programming for science, business, and fun. There’s more context in his blog post and this thread contains some good perspectives from others. There’s quite a bit of chat on Twitter about it too.

Colour science for colouring science — Alessandro’s posted in the #viz channel an excerpt from one of Edward Tufte’s books, appealing to those particular colour orderings that “have a natural visual hierarchy”. Check out the thread for some thoughtful considerations concerning the state of the art for colouring data.

Image modified from fabriocrameri.ch.

Singing with the birds — Jesse shared an article in #random with the opening line, “I had a dream one night where a blackbird was talking in human language”. The article then ventures into an exploration of converting human speech into birdsong. If you’re into signal processing, acoustics, and ornithology, you’re going to think this is really cool.

As always, if you want to highlight anything in these weekly posts, message @Evan on Swung.

News from the Underground

Things were pinging away in the main channels this week, with a few posts garnering loads of enthusiasm and important chatter.

The weirder the better — In the #viz channel, Nathan announced the latest Xeek challenge, Keep Geoscience Weird. This competition is all about new and novel ways of visualizing subsurface data. It’s a very open-ended competition — you can use any data that you like, as long as it’s related to the subsurface. I highly recommend reading the thread concerning the Terms & Conditions and motivations for engagement.

Sand vs shale — The longest thread of the week (150+ messages!) was in the #sedimentology channel. A simple question about computing running averages led to uncovering a bug in striplog, some plots (right), a hackathon project, and some weirdness in how Microsoft Excel exports CSV files.

Hello OSDU, how do you do? — The Open Subsurface Data Universe (OSDU) Forum is a consortium of ~200 members and is rolling out the first production release of its platform this week. For a bit of history on how the OSDU came to be, who’s involved, and where it’s headed, this thread might be a good summary.

But seriously. Who’s with me? — Has anyone ever given any serious consideration to prospecting and mining asteroids or other planetary bodies for resources? Turns out they have.

Teeny weeny ancient plant bits — Kieran threw some Carboniferous kerogen samples into the SEM and shared these gorgeous images. The discussion drifted naturally to “should I put 300 of these images online somewhere for others to look at and play with?”

How to get lost — Kleo asked for recommendations for introductory Python exercises, and got a load of responses. A few folks pointed to last year’s TRANSFORM tutorials. In another channel, Heba got a somewhat philosophical perspective from Hallgrim on the pursuit of programming: “[it’s] all about getting lost, banging your head against the wall, and the extreme pleasure of breaking through the wall. You are already lost, you’ve already found this community, so you have a great talent for what is ahead of you…”.

What was your favourite thread of the week?

News from the Underground

Here are the highlights from the past week.

Less than one month until Transform 2021 – The Software Underground’s T21 virtual conference is less than a month away, so it’s time to register and schedule your life during 16 – 23 April, 2021. Check out the calendar of events and make sure that you are tuned into the #t21-general channel.

SWUNG Hackathon Inside Transform – T21 kicks off with the Hackathon 16 – 18 April, but momentum from those projects will likely carry on, gathering eyeballs and contributors throughout the rest of the conference as well. In the #t21-hackathon channel, Filippo shared some instructions for proposing and discussing any would-be hackathon projects on this GitHub Discussion page.

git for you – One month in advance of his tutorial on git and GitHub at T21, Thursday 22 April, Steve has set up a Q & A in slido. Talk about a tutorial that is truly in service of others! It also means that you can might still get your questions answered if you, say, get pulled too deeply into a hackathon project.

Perils of improper sanitation – Are you aware of the perils of not sanitizing your inputs? This thread in #python has some nice links to explain what this is and when you should care.

Mapping partnerships – There are those that make maps, and there are those who want to make maps of those that make maps. This post is looking about how to structure a database to create a network of co-authorship of geoscience publications.

Probabilistically going to read it – I’ve got loads of love for those who put in the extra effort to make their work open access. Take for instance, this new publication that Júlio announced yesterday: Probabilistic Knowledge-based Characterization of Conceptual Geologic Models.