Repro zoo 2018

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Reproducibility Zoo at SEG AM, Anaheim, 2018

Beyond digital

The first wave of digital transformation was about digitization. The SEG Digital Library is fully digitized — from bibliographic records to the content. The Repro Zoo is an experimental step beyond 'just digital', with the goal of making the entire catalog of geoscience literature reproducible. This means accessible, openly licensed digital data, open implementations of algorithms, and complete scientific transparency in how results were obtained.

What is it?

Picture an open, welcoming space on the exhibition floor. People can wander up and immediately start contributing. Contributions can be as simple as a couple of votes or kudos clicks on the app, or as committed as a couple of hours of coding. Participants will use the data cited in SEG publications to test and reproduce geophysical scholarship. This project has the potential to be competitive as well, which could make the reproduction of the research an interesting spectator activity for other attendees. People could contribute in lots of ways — nominating papers or figures, helping digitize or enter data, coding algorithms and visualizations, testing the submissions, getting involved on the social media side, review and documentation, etc. anyone can participate. Goal: 1000 participants. Generally, there is much interest in the geoscience community for this type of experiential learning demonstrated by interest in hackathons and working workshops.

Why is it important?

Reproducible research is one of the tenets of scholarship. The act of reproducing another geoscientists findings has educational value for the researcher, the reproducing geoscientist, and the community as a whole. There’s much interest from the scientific community to strengthen reproducibility and reuse of research. This effort could nicely mirror and amplify the new data policy under development by the SEG Knowledge Management department and publications volunteers.

Papers to reproduce

An initial list of suggested papers follows. Ideally many people should propose and agree on top papers.

Most 'relevant' (roughly most cited) papers in various publications:

https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=source%3AThe+Leading+Edge+site%3Alibrary.seg.org&btnG=
https://scholar.google.com/scholar?q=source:Interpretation+site:library.seg.org&hl=en&as_sdt=0,5
https://scholar.google.com/scholar?q=source:Geophysics+site:library.seg.org&hl=en&as_sdt=0,5
https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=site%3Alibrary.seg.org&btnG=

Most downloaded articles in GEOPHYSICS:

Hydraulic fracture diagnostics from Krauklis-wave resonance and tube-wave reflections An overview of full-waveform inversion in exploration geophysics What can machine learning do for seismic data processing? An interpolation application Directional structure-tensor-based coherence to detect seismic faults and channels Complex seismic trace analysis Weak elastic anisotropy Sobel filter for edge detection of hexagonally sampled 3D seismic data AN EXPERIMENTAL INVESTIGATION OF FACTORS AFFECTING ELASTIC WAVE VELOCITIES IN POROUS MEDIA

Volunteer Sign Up:

https://docs.google.com/spreadsheets/d/1Ql7ORbz_5a0J5tse7YO_zEaFSNRopFO0GyjoVPE9NFQ/edit#gid=0]

install virtual machine with Madagascar, SU, and Python

Download the virtual machine from: https://drive.google.com/file/d/1sRojofwRbNVYtrzqU2e-CaU651xJmPAl
Download Virtualbox at: https://www.virtualbox.org/wiki/Downloads
Install and start VirtualBox
click the blue icon in the upper left corner of the virtual box window
Name your virtual machine - I called it zoo_linux
for type select Linux
for Version select Ubuntu(64-bit) and click continue
Use the recommended memory and click continue
Select "use and existing virtual hard disk" - click the folder icon to browse for the downloaded virtual machine (.vti file)


https://drive.google.com/file/d/1sRojofwRbNVYtrzqU2e-CaU651xJmPAl