diff --git a/Astronomy.md b/Astronomy.md new file mode 100644 index 0000000000..a85a09a32e --- /dev/null +++ b/Astronomy.md @@ -0,0 +1,23 @@ +* [AstroLibs](#astrolibs) +* [Astronomical Imaging](#astronomicalimaging) + + +* [JuliaAstro group on Github](https://JuliaAstro.github.io) + +# AstroLibs +* Astrodynamics.jl :: [An astrodynamics library](https://github.com/helgee/Astrodynamics.jl) in Julia. +* Cosmology.jl :: [Cosmology library](https://github.com/JuliaAstro/Cosmology.jl) for Julia. +* DustExtinction.jl :: [Models for the interstellar extinction due to dust](https://github.com/JuliaAstro/DustExtinction.jl). +* ERFA.jl :: [Julia wrapper for liberfa](https://github.com/JuliaAstro/ERFA.jl) +* JPLEphemeris.jl :: [The JPL Development Ephemerides](https://github.com/helgee/JPLEphemeris.jl) are the results of simulations of the Solar System used for spacecraft navigation and astronomical purposes. +* julia-astro :: [astronomy-related Julia code: skycoords.jl, dustmap.jl](https://github.com/kbarbary/julia-astro) +* Photometry.jl :: [Astronomical photometry library for Julia](https://github.com/kbarbary/Photometry.jl) +* SkyCoords.jl :: [Astronomical coordinate systems](https://github.com/kbarbary/SkyCoords.jl) in Julia. +* WCS.jl :: [Julia wrapper for wcstools library](https://github.com/kbarbary/WCS.jl) +* WCS.jl :: [wcslib wrapper for Julia](https://github.com/nolta/WCS.jl) +* WCSLIB.jl :: [wcslib wrapper for Julia](https://github.com/nolta/WCSLIB.jl) + + +# Astronomical Imaging +* FITSIO.jl :: [Flexible Image Transport System (FITS) support](https://github.com/JuliaAstro/FITSIO.jl) for Julia. + diff --git a/Biology.md b/Biology.md new file mode 100644 index 0000000000..1083443e21 --- /dev/null +++ b/Biology.md @@ -0,0 +1,31 @@ +* [Biotechnology](#biotechnology) +* [Neuroscience](#neuroscience) + + +* BioJulia on github :: [https://github.com/BioJulia/](https://github.com/BioJulia). The GoogleGroups mailing list/forums:: https://groups.google.com/forum/?fromgroups#!forum/biojulia-dev +* JuliaBio on github :: [https://github.com/JuliaBio](https://github.com/JuliaBio). The GoogleGroups mailing list/forums:: https://groups.google.com/forum/#!forum/julia-bio + +### Biotechnology +**Bioinformatics, genomics, agriculture, food science, medicine, genetic engineering, etc...** +* Bio.jl :: [Bioinformatics and Computational Biology Infrastructure](https://github.com/BioJulia/Bio.jl) for Julia. +* BioSeq.jl :: Julia's package for working on [Bioinformatics with DNA, RNA and Protein Sequences](https://github.com/diegozea/BioSeq.jl). +* Circuitscape.jl :: The [Julia implementation](https://github.com/tanmaykm/Circuitscape.jl) of the [Circuitscape lib in Python](http://www.circuitscape.org/) that uses electronic circuit theory to solve problems in landscape ecology. +* FastaIO.jl :: [Utilities to read/write FASTA format files](https://github.com/carlobaldassi/FastaIO.jl) in Julia. +* GaussDCA.jl :: [Multivariate Gaussian Direct Coupling Analysis for residue contact prediction in protein families](https://github.com/carlobaldassi/GaussDCA.jl). +* GeneticAlgorithms.jl :: is a [lightweight framework that simplifies the process of creating genetic algorithms](https://github.com/forio/GeneticAlgorithms.jl) and running them in parallel. +* OBC.jl :: [Optimal Bayesian classification for RNA-Seq data](https://github.com/binarybana/OBC.jl) +* pikaiaGAs.jl :: [Genetic algorithms](https://github.com/tmeits/pikaiaGAs.jl) +* Phylogenetics.jl :: The Julia package for [analysis of evolution and phylogeny](https://github.com/Ward9250/Phylogenetics.jl) +* Pagel.jl :: can [detect correlated evolution on phylogenies](https://github.com/porterjamesj/Pagel.jl) +* SeqUtils.jl :: [Seqencing analysis Utilities for Julia](https://github.com/nlhepler/SeqUtils.jl) +* SpikeSorter.jl :: [Spike sorting tool for experimental neuroscientists](https://github.com/grero/SpikeSorter.jl) +* smoothlife-jl :: [is an implementation of the SmoothLife algorithm](https://github.com/jamak/smoothlife-jl) in Julia. +* StatGenData.jl :: [Statistical analysis of genomic data](https://github.com/dmbates/StatGenData.jl) + +### Neuroscience +* ElectroJulia.jl :: [Julia functions to process electroencephalographic recordings](https://github.com/sam81/ElectroJulia.jl) + + + + + diff --git a/Chemistry.md b/Chemistry.md new file mode 100644 index 0000000000..e14e6c8f0a --- /dev/null +++ b/Chemistry.md @@ -0,0 +1,8 @@ + + +* ChemicalKinetics.jl :: [Simulation, Bayesian inference and Bayesian model selection for chemical kinetics](https://github.com/scidom/ChemicalKinetics.jl) in Julia. +* Qlab.jl :: is a [data manipulation and analysis tool based on the Savitzky–Golay filter](https://github.com/blakejohnson/Qlab.jl) - a digital filter that can be applied to a set of digital data points for the purpose of smoothing the data to increase the signal-to-noise ratio without greatly distorting the signal. Savitzky and Golay's paper is one of the most widely cited papers in the "Analytical Chemistry" journal. +* Synchrony.jl :: [Coherence/phase-locking statistics](https://github.com/simonster/Synchrony.jl) in Julia. + + + diff --git a/Physics.md b/Physics.md new file mode 100644 index 0000000000..4f4240855b --- /dev/null +++ b/Physics.md @@ -0,0 +1,17 @@ +* [Statistical Mechanics](#statisticalmechanics) + + +* auditory.jl :: [Auditory filterbanks in Julia](https://github.com/jfsantos/auditory.jl) +* CMSSW.jl :: [A work-in-progress wrapper for ROOT.jl](https://github.com/jpata/CMSSW.jl) +* Codata.jl :: https://github.com/kofron/Codata.jl +* HEP.jl :: [A collection of methods useful for HEP](https://github.com/jpata/HEP.jl) +* Physical.jl :: https://github.com/ggggggggg/Physical.jl +* Quantities.jl :: [Dimensions and Quantities](https://github.com/ElOceanografo/Quantities.jl) +* ROOT.jl :: [A toy experiment interfacing ROOT and Julia through FWLite](https://github.com/jpata/ROOT.jl). [ROOT](http://root.cern.ch) is a data analysis library widely used at experiments at CERN for HEP data analyses. +* ROOTDataFrames.jl :: [A wrapper for ROOT Trees through the Abstract DataFrame interface](https://github.com/jpata/ROOTDataFrames.jl) +* SALT.jl :: [SALT (steady-state ab-initio laser theory) solver package for Julia](https://github.com/xdavidliu/SALT.jl) +* Sparrow.jl :: [Visual Psychophysics package](https://github.com/rennis250/Sparrow.jl) for Julia. + +### Statistical Mechanics +* IsingModels.jl :: [The Ising model as a Julian distribution](https://github.com/johnmyleswhite/IsingModels.jl) + diff --git a/README.md b/README.md index bd554413b8..84a4fec3b7 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,9 @@ Mirrors: * [Algorithms.md](https://github.com/svaksha/Julia.jl/blob/master/Algorithms.md) :: AI, DataMining, Data Structures, ML, NLP, ... * [API.md](https://github.com/svaksha/Julia.jl/blob/master/API.md) :: API's for C++, Fortran, Go, Java, JavaScript, MATLAB, Perl, Python, R, ... * [Benchmarks-Optimization.md](https://github.com/svaksha/Julia.jl/blob/master/Benchmarks-Optimization.md) :: Benchmarks and Optimization toolkits. +* [Biology.md](https://github.com/svaksha/Julia.jl/blob/master/Biology.md) :: Bioinformatics, genomics, agriculture, food science, medicine, genetic engineering, Neuroscience, et. al... * [Build-Automation.md](https://github.com/svaksha/Julia.jl/blob/master/Build-Automation.md) :: Tools for continuous integration (CI), continuous delivery (CD), Packaging, release engineering (RE), release management (RM), software configuration management (SCM), etc... +* [Chemistry.md](https://github.com/svaksha/Julia.jl/blob/master/Chemistry.md) :: Analytical chemistry, cheminformatics, crystallography, nanochemistry, nuclear chemistry ... * [Computer-Graphics.md](https://github.com/svaksha/Julia.jl/blob/master/Computer-Graphics.md) :: Plotting, Graphics and other Visualization tools. * [Conferences-Papers.md](https://github.com/svaksha/Julia.jl/blob/master/Conferences-Papers.md) :: Julia-related Conferences (meetups, slides, talks, videos, etc..) and Research Papers (journal and conference publications). * [Cookbook.md](https://github.com/svaksha/Julia.jl/blob/master/Cookbook.md) :: blogs, cookbooks, cheatsheets, IJulia NoteBooks, etc... @@ -19,9 +21,9 @@ Mirrors: * [i18n-L10n.md](https://github.com/svaksha/Julia.jl/blob/master/i18n-L10n.md) :: Transliteration, Internationalisation (i18n) and Localisation (L10n) * [Mathematics.md](https://github.com/svaksha/Julia.jl/blob/master/Mathematics.md):: Algebra, Geometry,... anything Math related. * [NEWS.md](https://github.com/svaksha/Julia.jl/blob/master/NEWS.md) +* [Physics.md](https://github.com/svaksha/Julia.jl/blob/master/Physics.md) :: Julia software related to Physics. * [Programming-Concepts.md](https://github.com/svaksha/Julia.jl/blob/master/Programming-Concepts.md) :: Programming language concepts that are used in the type system, data types, etc.. * [QA.md](https://github.com/svaksha/Julia.jl/blob/master/QA.md) :: Test Driven Development, Sandbox, Functional/ Unit testing,... Quality-related tools. -* [Science.md](https://github.com/svaksha/Julia.jl/blob/master/Science.md) :: Astronomy, Biology, Chemistry, GIS, Meteorology, Physics,.. * [UI-UX.md](https://github.com/svaksha/Julia.jl/blob/master/UI-UX.md) :: User Interface software in Julia. * [Utilities.md](https://github.com/svaksha/Julia.jl/blob/master/Utilities.md) :: Handy toolkits for your Desktop and other general utilities. * [X-Platform-SW.md](https://github.com/svaksha/Julia.jl/blob/master/X-Platform-SW.md) :: Cross-Platform Software and API for Hardware arch. (ARM, MIPS, GPU, CUDA), language API, HPC, and other libraries. diff --git a/Science.md b/Science.md deleted file mode 100644 index e3cf2645ff..0000000000 --- a/Science.md +++ /dev/null @@ -1,82 +0,0 @@ -* [ASTRONOMY](#astronomy) -* [BIOLOGY](#biology) -* [CHEMISTRY](#chemistry) -* [GIS](#gis) -* [METEOROLOGY](#meteorology) -* [PHYSICS](#physics) - * ### Statistical Mechanics(#statisticalmechanics) - - -# ASTRONOMY -* [JuliaAstro group on Github](https://JuliaAstro.github.io) -* Astrodynamics.jl :: [An astrodynamics library](https://github.com/helgee/Astrodynamics.jl) in Julia. -* Cosmology.jl :: [Cosmology library](https://github.com/JuliaAstro/Cosmology.jl) for Julia. -* DustExtinction.jl :: [Models for the interstellar extinction due to dust](https://github.com/JuliaAstro/DustExtinction.jl). -* ERFA.jl :: [Julia wrapper for liberfa](https://github.com/JuliaAstro/ERFA.jl) -* FITSIO.jl :: [Flexible Image Transport System (FITS) support](https://github.com/JuliaAstro/FITSIO.jl) for Julia. -* JPLEphemeris.jl :: [The JPL Development Ephemerides](https://github.com/helgee/JPLEphemeris.jl) are the results of simulations of the Solar System used for spacecraft navigation and astronomical purposes. -* julia-astro :: [astronomy-related Julia code: skycoords.jl, dustmap.jl](https://github.com/kbarbary/julia-astro) -* Photometry.jl :: [Astronomical photometry library for Julia](https://github.com/kbarbary/Photometry.jl) -* SkyCoords.jl :: [Astronomical coordinate systems](https://github.com/kbarbary/SkyCoords.jl) in Julia. -* WCS.jl :: [Julia wrapper for wcstools library](https://github.com/kbarbary/WCS.jl) -* WCS.jl :: [wcslib wrapper for Julia](https://github.com/nolta/WCS.jl) -* WCSLIB.jl :: [wcslib wrapper for Julia](https://github.com/nolta/WCSLIB.jl) - -# BIOLOGY -* BioJulia on github :: [https://github.com/BioJulia/](https://github.com/BioJulia). The GoogleGroups mailing list/forums:: https://groups.google.com/forum/?fromgroups#!forum/biojulia-dev -* JuliaBio on github :: [https://github.com/JuliaBio](https://github.com/JuliaBio). The GoogleGroups mailing list/forums:: https://groups.google.com/forum/#!forum/julia-bio - -### Bioinformatics, Biotech, Genetics, .... -* Bio.jl :: [Bioinformatics and Computational Biology Infrastructure](https://github.com/BioJulia/Bio.jl) for Julia. -* BioSeq.jl :: Julia's package for working on [Bioinformatics with DNA, RNA and Protein Sequences](https://github.com/diegozea/BioSeq.jl). -* Circuitscape.jl :: The [Julia implementation](https://github.com/tanmaykm/Circuitscape.jl) of the [Circuitscape lib in Python](http://www.circuitscape.org/) that uses electronic circuit theory to solve problems in landscape ecology. -* FastaIO.jl :: [Utilities to read/write FASTA format files](https://github.com/carlobaldassi/FastaIO.jl) in Julia. -* GaussDCA.jl :: [Multivariate Gaussian Direct Coupling Analysis for residue contact prediction in protein families](https://github.com/carlobaldassi/GaussDCA.jl). -* GeneticAlgorithms.jl :: is a [lightweight framework that simplifies the process of creating genetic algorithms](https://github.com/forio/GeneticAlgorithms.jl) and running them in parallel. -* OBC.jl :: [Optimal Bayesian classification for RNA-Seq data](https://github.com/binarybana/OBC.jl) -* pikaiaGAs.jl :: [Genetic algorithms](https://github.com/tmeits/pikaiaGAs.jl) -* Phylogenetics.jl :: The Julia package for [analysis of evolution and phylogeny](https://github.com/Ward9250/Phylogenetics.jl) -* Pagel.jl :: can [detect correlated evolution on phylogenies](https://github.com/porterjamesj/Pagel.jl) -* SeqUtils.jl :: [Seqencing analysis Utilities for Julia](https://github.com/nlhepler/SeqUtils.jl) -* SpikeSorter.jl :: [Spike sorting tool for experimental neuroscientists](https://github.com/grero/SpikeSorter.jl) -* smoothlife-jl :: [is an implementation of the SmoothLife algorithm](https://github.com/jamak/smoothlife-jl) in Julia. -* StatGenData.jl :: [Statistical analysis of genomic data](https://github.com/dmbates/StatGenData.jl) - -# CHEMISTRY -* ChemicalKinetics.jl :: [Simulation, Bayesian inference and Bayesian model selection for chemical kinetics](https://github.com/scidom/ChemicalKinetics.jl) in Julia. -* Qlab.jl :: is a [data manipulation and analysis tool based on the Savitzky–Golay filter](https://github.com/blakejohnson/Qlab.jl) - a digital filter that can be applied to a set of digital data points for the purpose of smoothing the data to increase the signal-to-noise ratio without greatly distorting the signal. Savitzky and Golay's paper is one of the most widely cited papers in the "Analytical Chemistry" journal. -* Synchrony.jl :: [Coherence/phase-locking statistics](https://github.com/simonster/Synchrony.jl) in Julia. - - -# GIS -* GDAL.jl :: [Geospatial Data Analysis Library Wrapper for Julia](https://github.com/wkearn/GDAL.jl) -* GDALfuns.jl :: [GDAL wrapper for the Julia Programming language](https://github.com/meggart/GDALfuns.jl) -* GIS.jl :: [A package for the visualization and manipulation of geographic data](https://github.com/wkearn/GIS.jl) -* GeoIP.jl :: is a Julia package that can estimate the [geographic location of IP addresses](https://github.com/johnmyleswhite/GeoIP.jl). -* GMT.jl :: is a [package containing Julia bindings for the Generic Mapping Tools Library](https://github.com/joa-quim/GMT.jl), a.k.a "libgmt" - a set of libraries tht allows manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing Encapsulated PostScript File (EPS) illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3-D perspective views. - * *Forks* - * https://github.com/ihnorton/GMT.jl -* hillerislambers :: [Julia implementation of the HilleRisLambers et al. 2001 model of arid vegetation dynamics](https://github.com/wkearn/hillerislambers) -* SpatialStats.jl :: [Spatial Statistics](https://github.com/dchudz/SpatialStats.jl) - - -# METEOROLOGY -* CAIRS.jl :: [Continous Assimilation of Integrating Rain Sensors](https://github.com/scheidan/CAIRS.jl) -* Scriabin.jl :: [Radiative transfer in Julia](https://github.com/jsbj/Scriabin.jl) - - -# PHYSICS -* auditory.jl :: [Auditory filterbanks in Julia](https://github.com/jfsantos/auditory.jl) -* CMSSW.jl :: [A work-in-progress wrapper for ROOT.jl](https://github.com/jpata/CMSSW.jl) -* Codata.jl :: https://github.com/kofron/Codata.jl -* HEP.jl :: [A collection of methods useful for HEP](https://github.com/jpata/HEP.jl) -* Physical.jl :: https://github.com/ggggggggg/Physical.jl -* Quantities.jl :: [Dimensions and Quantities](https://github.com/ElOceanografo/Quantities.jl) -* ROOT.jl :: [A toy experiment interfacing ROOT and Julia through FWLite](https://github.com/jpata/ROOT.jl). [ROOT](http://root.cern.ch) is a data analysis library widely used at experiments at CERN for HEP data analyses. -* ROOTDataFrames.jl :: [A wrapper for ROOT TTrees through the Abstract DataFrame interface](https://github.com/jpata/ROOTDataFrames.jl) -* SALT.jl :: [SALT (steady-state ab-initio laser theory) solver package for Julia](https://github.com/xdavidliu/SALT.jl) -* Sparrow.jl :: [Visual Psychophysics package](https://github.com/rennis250/Sparrow.jl) for Julia. - -### Statistical Mechanics -* IsingModels.jl :: [The Ising model as a Julian distribution](https://github.com/johnmyleswhite/IsingModels.jl) -