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dev-hub Projects: Research Plans Above the Code

7 minute read

Published:

dev-hub started as a way to keep my code in shape: a task board of small upkeep jobs, and features for bigger pieces of work. But most of my repos exist because of research, and the reason for any piece of code exists is usually because it’s linked to a research project, not on a board.

dev-hub Features: Bigger Work on One Branch

9 minute read

Published:

In my first dev-hub post, every piece of work was a task: one self-contained change on its own branch, with its own pull request that I merge as soon as it’s done. That covers most upkeep. That’s generally my workflow, but not everyone’s, and some work shouldn’t reach main one piece at a time: a new module isn’t always useful until it’s complete and some works needs validating before it replaces the old path.

dev-hub Handback Mode: Running Tasks from a Claude Project

10 minute read

Published:

In my last post I described dev-hub, a private GitHub repo that acts as mission control for Claude across my repos. Most of the time I run dev-hub tasks from Claude Code, either on my machine or on the web, where Claude can push branches and open pull requests itself.

dev-hub: Mission Control for Claude Across My Repos

19 minute read

Published:

I have a handful of research and side-project repos that all need the same kind of upkeep: tests that were never written, dated packaging, automated checks (continuous integration, or CI) that don’t exist, outdated READMEs. None of it is hard, but it never makes it to the top of the list; a lot of development stops once things work, as in plenty of research codebases.

Vectorizing and Parallelizing JB2008

1 minute read

Published:

JB2008 is an emperical atmospheric neutral density model (long name Jacchia-Bowman 2008). It is the most recent itteration of the Jacchia-Bowman family at atmospheric models and incorporates both Solar and Geomagnetic activity into the modelling of atmospheric neutral denisty, temperature, and exospheric temperature.

skops - Machine Learning Model Persistence

2 minute read

Published:

Persisting ML/AI models (or model serialization) allows users to save models that they’ve trained so that they can be reloaded and reused. Model persistence is important as it can save time and allows models to be shared with other users without the need to retrain the model (which can be computationally expensive and time consuming) or share the training data set (which can be large).

Loading Data from the Web

1 minute read

Published:

Many of Pandas read functions have the ability to read files from the internet. This can be helpful you’re writing tutorials or examples and want them to work even if users don’t have the data. Or if you want to quickly look at data without downloading it.

Anaconda and VS Code

less than 1 minute read

Published:

Having problems accessing Anaconda from VS Code (Python: Select Interpreter)?

Python Paths

1 minute read

Published:

Often when working in science/research we are rapidly developing and modifying code (and maybe not following the very best practices for coding). In these instances we may not be writing, developing, or installing Python modules which can be accessed by the Python interpreter. Rather we may have a directory with set of scripts, functions, or classes. In Python in order to access these without installing a module we need to add the file path of our directory to the Python path. This can be easily acomplished using the sys module.

Python Environments

3 minute read

Published:

Environments in Anaconda and Python allow you to create a named and isolated copy of Python. Within these environments you can work with specefic versions of Python and packages without affecting your base installation. These enviroments make it easy to:

Spyder GUI scaling

less than 1 minute read

Published:

Experiencing weird scaling issues with Spyder?

Reloading a module

less than 1 minute read

Published:

Ever been actively editing a module while also using it? IPython (and JUPYTER) have some automagic to help with this.

Faster conda solver

less than 1 minute read

Published:

Have you found your Anaconda enviroments stalling when trying to install new packages via conda?

portfolio

MLTDM: Machine-learning thermospheric density model

Published:

A random-forest model of storm-time atmospheric neutral density, published in Space Weather (2025) and released as an open, installable Python package with a worked example notebook.

JB2008 in Python, ~11x faster

Published:

Vectorized and parallelized the Python port of the JB2008 empirical density model, cutting ~70,000 predictions from ~8 minutes to ~40 seconds.

Magnetosphere Online Seminar Series

Published:

An international online seminar series that kept the space physics community connected when conferences were cancelled during COVID-19.

publications

Near-Earth initiation of a terrestrial substorm

Published in Journal of Geophysical Research: Space Physics, 2009

Recommended citation: Rae, I. J., Mann, I. R., Angelopoulos, V., Murphy, K. R., Milling, D. K., Kale, A., et al. (2009). Near-Earth initiation of a terrestrial substorm. Journal of Geophysical Research: Space Physics, 114(7), 1-9.
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Ultralow-frequency modulation of whistler-mode wave growth

Published in Journal of Geophysical Research: Space Physics, 2011

Recommended citation: Watt, C. E. J., Degeling, a. W., Rankin, R., Murphy, K. R., Rae, I. J., & Singer, H. J. (2011). Ultralow-frequency modulation of whistler-mode wave growth. Journal of Geophysical Research: Space Physics, 116(10), 1-13.
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The Role of Ultralow Frequency Waves in Radiation Belt Dynamics

Published in Dynamics of the Earth's Radiation Belts and Inner Magnetosphere, 2012

Recommended citation: Mann, I. R., Murphy, K. R., Ozeke, L. G., Rae, I. J., Milling, D. K., Kale, A. A., & Honary, F. F. (2013). The Role of Ultralow Frequency Waves in Radiation Belt Dynamics. In Geophysical Monograph Series (Vol. 199, pp. 69-92).
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ULF wave derived radiation belt radial diffusion coefficients

Published in Journal of Geophysical Research: Space Physics, 2012

Recommended citation: Ozeke, L. G., Mann, I. R., Murphy, K. R., Rae, I. J., Milling, D. K., Elkington, S. R., et al. (2012). ULF wave derived radiation belt radial diffusion coefficients. Journal of Geophysical Research: Space Physics, 117(4), 1-16.
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Ground-based magnetometer determination of in situ Pc4-5 ULF electric field wave spectra as a function of solar wind speed

Published in Journal of Geophysical Research: Space Physics, 2012

Recommended citation: Rae, I. J., Mann, I. R., Murphy, K. R., Ozeke, L. G., Milling, D. K., Chan, A. A., et al. (2012). Ground-based magnetometer determination of in situ Pc4-5 ULF electric field wave spectra as a function of solar wind speed. Journal of Geophysical Research: Space Physics, 117(4), 1-17.
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Inner magnetospheric onset preceding reconnection and tail dynamics during substorms: Can substorms initiate in two different regions?

Published in Journal of Geophysical Research: Space Physics, 2014

Recommended citation: Murphy, K. R., Mann, I. R., Rae, I. J., Walsh, A. P., & Frey, H. U. (2014). Inner magnetospheric onset preceding reconnection and tail dynamics during substorms: Can substorms initiate in two different regions? Journal of Geophysical Research: Space Physics, 119(12), 9684-9701.
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The CASSIOPE/e-POP Magnetic Field Instrument (MGF)

Published in Space Science Reviews, 2015

Recommended citation: Miles, D. M., Mann, I. R., Ciurzynski, M., Barona, D., Narod, B. B., Bennest, J. R., et al. (2016). A miniature, low-power scientific fluxgate magnetometer: A stepping-stone to cube-satellite constellation missions. Journal of Geophysical Research: Space Physics, 121(12), 11,839-11,860.
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Accurately characterizing the importance of wave-particle interactions in radiation belt dynamics: The pitfalls of statistical wave representations

Published in Journal of Geophysical Research: Space Physics, 2016

Recommended citation: Murphy, K. R., Mann, I. R., Rae, I. J., Sibeck, D. G., & Watt, C. E. J. (2016). Accurately characterizing the importance of wave-particle interactions in radiation belt dynamics: The pitfalls of statistical wave representations. Journal of Geophysical Research: Space Physics, 121(8), 7895-7899.
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Diagnosing the Role of Alfven Waves in Magnetosphere-Ionosphere Coupling: Swarm Observations of Large Amplitude Nonstationary Magnetic Perturbations During an Interval of Northward IMF

Published in Journal of Geophysical Research: Space Physics, 2018

Recommended citation: Pakhotin, I. P., Mann, I. R., Lysak, R. L., Knudsen, D. J., Gjerloev, J. W., Rae, I. J., et al. (2018). Diagnosing the Role of Alfvén Waves in Magnetosphere-Ionosphere Coupling: Swarm Observations of Large Amplitude Nonstationary Magnetic Perturbations During an Interval of Northward IMF. Journal of Geophysical Research: Space Physics, 123(1).
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Magnetosphere-Ionosphere Coupling and Ionospheric Dynamics during Storms and Substorms: Role of Alfven Waves

Published in  Geomagnetism, aeronomy and space weather , 2019

Recommended citation: Mann, I. R. , Pakhotin, I. P. , Rae, I. J. , Murphy, K. R. , Ozeke, L. G., Knudsen, D. J., Kale, A., and Milling, D. K. (2019). Magnetosphere-Ionosphere Coupling and Ionospheric Dynamics during Storms and Substorms: Role of Alfven Waves in Mandea, M., Korte, M., Yau, A., & Petrovsky, E. (Eds.), pages 229-250. Geomagnetism, aeronomy and space weather : A journey from the earth's core to the sun.
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Ultra-Low-Frequency Wave-Particle Interactions

Published in  Geomagnetism, aeronomy and space weather , 2019

Recommended citation: Mann, I. R., Ozeke, L. G., Degeling, A., Murphy, K. R., and Rankin, R. (2019). Ultra-Low-Frequency Wave-Particle Interactions in Mandea, M., Korte, M., Yau, A., & Petrovsky, E. (Eds.), pages 190-194. Geomagnetism, aeronomy and space weather : A journey from the earth's core to the sun.
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Rapid Outer Radiation Belt Flux Dropouts and Fast Acceleration During the March 2015 and 2013 Storms: The Role of Ultra-Low Frequency Wave Transport From a Dynamic Outer Boundary

Published in Journal of Geophysical Research: Space Physics, 2020

Recommended citation: Ozeke, L. G., Mann, I. R., Olifer, L., Dufresne, K. Y., Morley, S. K., Claudepierre, S. G., et al. (2020). Rapid Outer Radiation Belt Flux Dropouts and Fast Acceleration During the March 2015 and 2013 Storms: The Role of Ultra-Low Frequency Wave Transport From a Dynamic Outer Boundary. Journal of Geophysical Research: Space Physics, 125(2).
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Driving of Outer Belt Electron Loss by Solar Wind Dynamic Pressure Structures: Analysis of Balloon and Satellite Data

Published in Journal of Geophysical Research: Space Physics, 2020

Recommended citation: Breneman, A. W., Halford, A. J., Millan, R. M., Woodger, L. A., Zhang, X.-J., Sandhu, J. K., et al. (2020). Driving of outer belt electron loss by solar wind dynamic pressure structures: Analysis of balloon and satellite data. Journal of Geophysical Research: Space Physics, 125, e2020JA028097.
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Imaging the magnetosphere-ionosphere system with ground-based and in-situ magnetometers

Published in Magnetospheric Imaging, 2022

Recommended citation: Murphy, K. R., Bentley, S. N., Miles, D., Sandhu, J. K., & Smith, A. (2022). Imaging the magnetosphere-ionosphere system with ground-based and in-situ magnetometers. In Y. Collado-Vega, D. Gallagher, H. Frey, & S. Wing (Eds.), Magnetospheric Imaging: Understanding the Space Environment through Global Measurements (pp. 287-340). Elsevier. https://doi.org/10.1016/B978-0-12-820630-0.00002-7
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Statistical Comparison of Electron Loss and Enhancement in the Outer Radiation Belt During Storms

Published in Journal of Geophysical Research: Space Physics, 2022

Recommended citation: Walton, S. D., Forsyth, C., Rae, I. J., Meredith, N. P., Sandhu, J. K., Walach, M.-T., & Murphy, K. R. (2022). Statistical comparison of electron loss and enhancement in the outer radiation belt during storms. Journal of Geophysical Research: Space Physics, 127, e2021JA030069. https://doi.org/10.1029/2021JA030069
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Statistical Characterization of the Dynamic Near-Earth Plasma Sheet Relative to Ultra-Low Frequency (ULF) Wave Growth at Substorm Onset

Published in Journal of Geophysical Research: Space Physics, 2023

Recommended citation: Smith, A. W., Rae, I. J., Forsyth, C., Watt, C. E. J., & Murphy, K. R. (2023). Statistical characterization of the dynamic near-Earth plasma sheet relative to Ultra-Low Frequency (ULF) wave growth at substorm onset. Journal of Geophysical Research: Space Physics, 128, e2022JA030491. https://doi.org/10.1029/2022JA030491
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Understanding quiet and storm time EMIC waves – Van Allen Probes Results

Published in Journal of Geophysical Research: Space Physics, 2023

Recommended citation: Remya, B., Halford, A. J., Sibeck, D. G., Murphy, K. R., & Fok, M.-C. (2023). Understanding quiet and storm time EMIC waves—Van Allen Probes results. Journal of Geophysical Research: Space Physics, 128, e2023JA031712. https://doi.org/10.1029/2023JA031712
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The Response of Electron Pitch Angle Distributions to the Upper Limit on Stably Trapped Particles

Published in Journal of Geophysical Research: Space Physics, 2023

Recommended citation: Walton, S. D., Mann, I. R., Olifer, L., Ozeke, L. G., Forsyth, C., Rae, I. J., et al. (2023). The response of electron pitch angle distributions to the upper limit on stably trapped particles. Journal of Geophysical Research: Space Physics, 128, e2023JA031988. https://doi.org/10.1029/2023JA031988
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Extreme Birkeland Currents Are More Likely During Geomagnetic Storms on the Dayside of the Earth

Published in Journal of Geophysical Research: Space Physics, 2023

Recommended citation: Coxon, J. C., Chisham, G., Freeman, M. P., Forsyth, C., Walach, M.-T., Murphy, K. R., et al. (2023). Extreme Birkeland currents are more likely during geomagnetic storms on the dayside of the Earth. Journal of Geophysical Research: Space Physics, 128, e2023JA031946. https://doi.org/10.1029/2023JA031946
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Persistent pitch angle anisotropies of relativistic electrons in the outer radiation belts

Published in Journal of Geophysical Research: Space Physics, 2023

Recommended citation: Greeley, A. D., Kanekal, S. G., Schiller, Q., Blum, L., Halford, A., Murphy, K., et al. (2024). Persistent pitch angle anisotropies of relativistic electrons in the outer radiation belts. Journal of Geophysical Research: Space Physics, 129, e2023JA031549. https://doi.org/10.1029/2023JA031549
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A survey of EMIC waves in Van Allen Probe data

Published in Journal of Geophysical Research: Space Physics, 2024

Recommended citation: Inglis, A. R., Murphy, K. R., & Halford, A. (2024). A Survey of EMIC waves in Van Allen Probe data. Journal of Geophysical Research: Space Physics, 129, e2024JA032666. https://doi.org/10.1029/2024JA032666
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Derivations of the Total Radiation Belt Electron Content

Published in Journal of Geophysical Research: Space Physics, 2024

Recommended citation: Pitzel, J. C., Cully, C. M., Ripoll, J.-F., Loridan, V., Huang, C.-L., Spence, H. E., et al. (2024). Derivations of the total radiation belt electron content. Journal of Geophysical Research: Space Physics, 129, e2024JA032940. https://doi.org/10.1029/2024JA032940
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Diamond Experiment In the MagnetOSphere (DEIMOS): a Collisionless Shocks and Solar Wind Mission Concept for the Lunar Gateway

Published in Journal of Geophysical Research: Space Physics, 2024

Recommended citation: Shonibare, T., Murphy, K. R., & Pakhotin, I. P. (2024). Diamond experiment in the magnetosphere (DEIMOS): A collisionless shocks and solar wind mission concept for the Lunar Gateway. Journal of Geophysical Research: Space Physics, 129, e2024JA032728. https://doi.org/10.1029/2024JA032728
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