Biophysics & Geophysics

Language Requirement(s): None. Usage Requirements: Java-Based Operating System

Java-based image processing program with Java plugins and recordable macros useful for image processing and analysis problems in biophysics. ImageJ can be run in browser!

Contributor: Jin Oueslati, Indiana University - Bloomington

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Language Requirement(s): None. Usage Requirements: Internet connection.

One of my favorite resources for current forecasting models, surface analysis data, and more for North America. Access just about any numerical model (Weather Data -> Numerical Models) and right click (1 second) on any geographic location per model to load most recent simulated atmospheric soundings, including condition cross-references with historical data. A guide for interpreting the sounding panel is provided here.

Contributor: Amelia Binau, Indiana University - Bloomington

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Language Requirement(s): None. Usage Requirements: Internet connection.

Spaceweather.com is a palatable website teeming with widgets monitoring current space weather conditions and data. News, solar wind conditions, near-earth asteroids, solar flare and thermosphere data, sunspots, aurora, cosmics rays - it's all here, including links to other relevant websites. It's a good place for amateurs, interested indivudials, or even perhaps those more heavily involved in space science research to brief up-to-date conditions and news. It also is filled with links to databases and labortories where these data are being collected. While a little bit commercialized, this website does digestibly bring together a lot of great resources in space physics.

Contributor: Amelia Binau, Indiana University - Bloomington

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Usage Requirements: Standard computer using any major operating system (even simple laptops can run it) and internet connection.

Provides interactive layer maps and datasets of various moons and planets including but not limited to Earth, Luna, Mars, Vesta, Venus, Pluto, etc. Developed at Arizona State University, the platform hosts open office hours, a Discord community, and a plethora of tutorials. JMARS has been used to plan many NASA missions, including "Mars Odyssey, Mars Global Surveyor, Mars Reconnaissance Orbiter, the Lunar Reconnaissance Orbiter, and the OSIRIS-REx asteroid sample return mission."

Contributor: Allison Loper, Purdue University - West Lafayette

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Usage Requirements: Only runs on Windows; requires a subscription but most universities have access.

World’s leading mapping and GIS processing software; essential for almost any GIS project. Analyze complex structures, conduct geospacial analysis & data management.

Contributor: Allison Loper, Purdue University - West Lafayette

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Language Requirement(s): C++, C, Fortran, or Python for pytraj. Usage Requirements: AMBER suite, compilers for appropriate languages, Linux or Unix terminal & Bash, Python-Compatable IDE for pytraj.

Amber allows for the simulation of biological macromolecules' dynamics through the use of an array of pre-programmed "force fields" from which the user can select. The program developers have created a detailed series of introductory courses for the suite found here and yearly reference manuals are published. The program central to AMBER is CPPTRAJ, which developers have created a Python wrapper for called pytraj.

Contributor: Amelia Binau, Indiana University - Bloomington

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Language Requirement(s): Python. Usage Requirements: Python-Compatable IDE. Designed for use with Jupyter notebooks.

CliMetLab is a Python and Jupyter notebooks-based package designed to streamline access to meteorological and climatological data for research purposes. Data are sourced as objects and can be manipulated using other common data science packages, including Pandas and NumPy. Use it to import GRIB, NetCDF, BUFR, and more (all common dataframe formats in meteorlogy), as well as databases such as NOAA's hurricane database (see Examples).

Contributor: Amelia Binau, Indiana University - Bloomington

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Language Requirement(s): Julia. Usage Requirements: Julia Compiler, Optional GPU Acceleration

3D gravity inversion allows for analysis of underground density distributions in the Earth, utilizing slight perterbations in the surface gravitational fields; however, such techniques tend to be very computational heavy. GravityInversionGPU.jl is a package that allows such analysis with reduced runtimes and computational load, utilizing data-space inversion to verifiably lower mathematical complexity. This package is specifically designed to be GPU-accelerated, further reducing computation times. More information on this package, including it's validation, can be found on the arXiv manuscript here.

Contributor: Amelia Binau, Indiana University - Bloomington

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Language Requirement(s): Python. Usage Requirements: Python-Compatible IDE, Jupyter Notebooks

SAIPy uses deep learning to process seimological waveforms quickly. Use the package for earthquake detection, determining earthquake magnitude, and more faster than traditional packages such as CREIME and DynaPicker. SAIPy's GitHub is complete with example notebooks and sample .mseed seismic waveform datasets for testing the package.

Contributor: Amelia Binau, Indiana University - Bloomington

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Usage Requirements: Python-compatible interpreter/IDE, internet connection. Language Requirements: Python.

Biopython is an all-in-one Python package for all things bioinformatics and biology-related computation. Documentation is complete and engaging to read, many examples of major functionalities are detailed, including gene sequencing, working with sequences, and loading/accessing major biological data repositories.

Contributor: Amelia Binau, Indiana University - Bloomington

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Language Requirement(s): None. Usage Requirements: Website hosts a wide variety of data in numeric, ASCII, graphical formats, and more.

The University of Oulu hosts a repository of geophysical data and research powered since 1914 by the Sodankylä Geophysical Observatory. Query geomagentic, cosmic ray, seismic, low-frequency, and high-altitude atmospheric data through their data archive. The observatory's cosmic ray group also hosts a continuous cosmogenic neutron monitor.

Contributor: Amelia Binau, Indiana University - Bloomington

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