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TensorCast.jl
It slices, it dices, it splices
This package lets you work with multi-dimensional arrays in index notation, by defining a few macros which translate this to broadcasting, permuting, and reducing operations. -
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ComponentArrays.jl
Arrays with arbitrarily nested named components
The main export of this package is the ComponentArray type. "Components" of ComponentArrays are really just array blocks that can be accessed through a named index. This will create a new ComponentArray whose data is a view into the original, allowing for standalone models to be composed together by simple function composition. In essence, ComponentArrays allow you to do the things you would usually need a modeling language for, but without actually needing a modeling language. The main targets are for use in DifferentialEquations.jl and Optim.jl, but anything that requires flat vectors is fair game. -
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MPI.jl
MPI wrappers for Julia
...Inspiration is taken from mpi4py, although we generally follow the C and not the C++ MPI API. (The C++ MPI API is deprecated.) MPI is based on a single program, multiple data (SPMD) model, where multiple processes are launched running independent programs, which then communicate as necessary via messages. As the main entry point for users, MPI.jl provides a high-level interface which loosely follows the MPI C API and is described in details in the following sections. The syntax should look familiar if you know MPI already, but some arguments may not be needed (e.g. the type or the number of elements of arrays, which are inferred automatically), others may be placed slightly differently, and others may be optional keyword arguments (e.g. for the index of the root process, or the source and destination of point-to-point communication functions). -
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Tullio.jl
Tullio is a very flexible einsum macro
Tullio is a very flexible einsum macro. It understands many array operations written in index notation -- not just matrix multiplication and permutations, but also convolutions, stencils, scatter/gather, and broadcasting. Used by itself the macro writes ordinary nested loops much like Einsum.@einsum. One difference is that it can parse more expressions, and infer ranges for their indices. Another is that it will use multi-threading (via Threads.@spawn) and recursive tiling, on large enough arrays. -
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Obsidian Visual Skills Pack
Generate Canvas, Excalidraw, and Mermaid diagrams from text
LLM-TLDR is a Python-based tool designed to dramatically reduce the amount of code a large language model needs to read by extracting the essential structure and context from a codebase and presenting only the most relevant parts to the model. Traditional approaches often dump entire files into a model’s context, which quickly exceeds token limits; LLM-TLDR instead indexes project structure, traces dependencies, and summarizes code in a way that preserves semantic relevance while shrinking... -
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nb-clean
Clean Jupyter notebooks of outputs, metadata, and empty cells
nb-clean cleans Jupyter notebooks of cell execution counts, metadata, outputs, and (optionally) empty cells, preparing them for committing to version control. It provides both a Git filter and pre-commit hook to automatically clean notebooks before they're staged, and can also be used with other version control systems, as a command line tool, and as a Python library. It can determine if a notebook is clean or not, which can be used as a check in your continuous integration pipelines.... -
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EllipsisNotation.jl
Julia-based implementation of ellipsis array indexing notation
Julia-based implementation of ellipsis array indexing notation. This implements the notation .. for indexing arrays. It's similar to Python, in that it means "all the columns before (or after)". Note: .. slurps dimensions greedily, meaning that the first occurrence of .. in an index expression creates as many slices as possible. Other instances of .. afterward are treated simply as slices. Usually, you should only use one instance of .. in an indexing expression to avoid possible confusion. -
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IndexedTables.jl
Flexible tables with ordered indices
IndexedTables provides tabular data structures where some of the columns form a sorted index. It provides the backend to JuliaDB, but can be used on its own for efficient in-memory data processing and analytics. -
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Javis
Julia Animations and Visualizations
Javis: Julia Animations and Visualizations. Javis makes generating simple animations a breeze! Want to learn more? Check out our documentation for tutorials, our contributing guidelines, and the mission of Javis.jl. We have a live Zulip stream that you can join to discuss Javis with other Javis users. -
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JuliaDB.jl
Parallel analytical database in pure Julia
JuliaDB is a package for working with large persistent data set. JuliaDB provides distributed table and array datastructures with convenient functions to load data from CSV. JuliaDB is Julia all the way down. This means queries can be composed with Julia code that may use a vast ecosystem of packages. -
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VividSTORM
Correlated confocal and SMLM data visualization and analysis
VividSTORM is a free and open-source standalone software with graphical user interface, for the correlated visualization and analysis of superresolution single molecule localization microscopy (SMLM) molecule lists and conventional pixel intensity-based images. The localization points (LPs) within this ROI can be analyzed using the selected built-in functions. NOTE: If you encounter issues not addressed by the user guide, please contact by message on this site or via e-mail for... -
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GMOL
A tool for 3D genome structure visualization
GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project... -
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TerminalMenus.jl
Simple interactive menus for the terminal (Now ships with Julia!)
This package has been merged into the Julia standard library. As such, you probably just want to using REPL.TerminalMenus and skip the Installation instructions. The RadioMenu allows the user to select one option from the list. The request function displays the interactive menu and returns the index of the selected choice. If a user presses 'q' or ctrl-c, request will return a -1. -
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x-ballistics
a browser based ballistics calculator for arrows and bullets
Browser based ballistics calculator for arrows and bullets: http://www.x-ballistics.eu/app/web/ballistics/index -
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Kinetic Model Builder
GUI for building, simulating and optimizing kinetic models.
...A series of video tutorials are available at https://www.youtube.com/watch?v=7I2XPkdOvCg&list=PL-J_lULjiFsCPL2pkz8_tFe_aJ4Fc8a8k&index=1. -
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ImagingAnalysis
Direct tissue-level image quantification package for Mathematica
ImagingAnalysis is a Mathematica package that performs grid-based analysis of time-lapse imaging data saved in a sequence of TIFF files. This package requires Mathematica 7.0. Revised on 14 May 2017: Bugs are fixed and incompatibility issues are resolved. The current version runs on Mathematica 11. -
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The system searches synonyms (and related words) in Wikipedia. WikIDF generates index database of Wikipedia (for Russian, English, and German). The continuation of this project is "wikokit" at code.google.com
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