CAT cleanup

fp4code · Feb 28, 2015 · 4b24c75 · 4b24c75
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diff --git a/Chemistry.md b/Chemistry.md
@@ -1,4 +1,4 @@
-**Analytical chemistry, Cheminformatics, Crystallography, Nanochemistry, Quantum/Nuclear chemistry ...**
+**Analytical chemistry, Cheminformatics, Physical/Organic chemistry, Crystallography, Nanochemistry, Quantum/Nuclear chemistry ...**
 
 + [Chemistry](#chemistry)
 + [Material Science](#material-science)
@@ -7,19 +7,13 @@
  + [Solid-State Chemistry](#solid-state-chemistry)
  + [Quantum Chemistry](#quantum-chemistry)
 
-
 ----
 
 # Chemistry 
-+ [ChemicalKinetics.jl](https://github.com/scidom/ChemicalKinetics.jl) :: Simulation, Bayesian inference and Bayesian model selection for chemical kinetics in Julia.
 + [Gillespie.jl](https://github.com/sdwfrost/Gillespie.jl) :: Stochastic Gillespie-type simulations using Julia.
 + [MethylUtils.jl](https://github.com/nw11/MethylUtils.jl) :: Utilities for bisulfite sequencing data.
 + [Qlab.jl](https://github.com/blakejohnson/Qlab.jl) :: is a data manipulation and analysis tool based on the Savitzky–Golay filter - 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](https://github.com/simonster/Synchrony.jl) :: Coherence/phase-locking statistics in Julia.
-+ [ThermodynamicsTable.jl](https://github.com/DANA-Laboratory/ThermodynamicsTable.jl) :: Thermodynamics table for critical values, heat capacity, etc..
-
-###### Resources
-+ [Computing colors of molecules with Julia](https://github.com/jiahao/ijulia-notebooks), the [Colors of chemistry notebook](http:https://jiahao.github.io/julia-blog/2014/06/09/the-colors-of-chemistry.html) and [Chemistry blog](http:https://jiahao.github.io/julia-blog/)
 
 ----
 
@@ -34,9 +28,15 @@
 ### [Colloidal Chemistry](#https://en.wikipedia.org/wiki/Category:Colloidal_chemistry)
 * [Brownian.jl](https://github.com/UniversityofWarwick/Brownian.jl) :: Simulation of Brownian-Based Stochastic Processes .
 
+
 ### [Solid-State Chemistry](https://en.wikipedia.org/wiki/Solid-state_chemistry)
-+ [Jumos.jl](https://github.com/Luthaf/Jumos.jl) :: JUlia MOlecular Simulation package.
++ [ChemicalKinetics.jl](https://github.com/scidom/ChemicalKinetics.jl) :: Simulation, Bayesian inference and Bayesian model selection for chemical kinetics in Julia.
 + [HydrocarbonNets.jl](https://github.com/Ismael-VC/HydrocarbonNets.jl) :: Artificial Hydrocarbon Networks (AHNs) in Julia.
++ [Jumos.jl](https://github.com/Luthaf/Jumos.jl) :: JUlia MOlecular Simulation package.
+
+###### Resources
++ [Computing colors of molecules with Julia](https://github.com/jiahao/ijulia-notebooks), the [Colors of chemistry notebook](http:https://jiahao.github.io/julia-blog/2014/06/09/the-colors-of-chemistry.html) and [Chemistry blog](http:https://jiahao.github.io/julia-blog/)
+
 
 ### Quantum Chemistry
 + [DynamicTimeWarp.jl](https://github.com/joefowler/DynamicTimeWarp.jl) :: Implement Dynamic Time Warping for sequence alignment in Julia.

diff --git a/Physics.md b/Physics.md
@@ -5,10 +5,10 @@
 * [Medical Physics](#medical-physics)
 * [Quantum Mechanics](#quantum-mechanics)
 * [Statistical Mechanics](#statistical-mechanics)
+* [Thermodynamics](#thermodynamics)
 
 ----
 
-* [AIDA.jl](https://github.com/jstrube/AIDA.jl) :: This package implements simple readers for legacy AIDA files.
 * [auditory.jl](https://github.com/jfsantos/auditory.jl) :: Auditory filterbanks in Julia.
 * [CMSSW.jl](https://github.com/jpata/CMSSW.jl) :: A work-in-progress wrapper for ROOT.jl.
 * [Codata.jl](https://github.com/kofron/Codata.jl)
@@ -18,7 +18,6 @@
 * [LambertW.jl](https://github.com/robertdj/LambertW.jl) :: Lambert's W function in Julia.
 * [Mass.jl](https://github.com/ggggggggg/Mass.jl) :: An experimental frameworks for TES pulse analysis. 
 * [Physical.jl](https://github.com/ggggggggg/Physical.jl)
-* [Psychro.jl](https://github.com/pjabardo/Psychro.jl) :: Thermodynamic properties of moist air (real gas mixture).
 * [Quantities.jl](https://github.com/ElOceanografo/Quantities.jl) :: Dimensions and Quantities.
 * [QuDOS.jl](https://github.com/acroy/QuDOS.jl) :: Quantum Dynamics of Open Systems in Julia.
 * [ROOT.jl](https://github.com/jpata/ROOT.jl) :: A toy experiment interfacing ROOT and Julia through FWLite. [ROOT](http:https://root.cern.ch) is a data analysis library widely used at experiments at CERN for HEP data analyses.
@@ -62,4 +61,9 @@
 * [IsingModels.jl](https://github.com/johnmyleswhite/IsingModels.jl) :: The Ising model as a Julian distribution.
 * [Boltzmann.jl](https://github.com/dfdx/Boltzmann.jl) :: Restricted Boltzmann machines and deep belief networks.
 
+----
+
+# [Thermodynamics](http:https://en.wikipedia.org/wiki/Category:Thermodynamics)
+* [Psychro.jl](https://github.com/pjabardo/Psychro.jl) :: Thermodynamic properties of moist air (real gas mixture).
++ [ThermodynamicsTable.jl](https://github.com/DANA-Laboratory/ThermodynamicsTable.jl) :: Thermodynamics table for critical values, heat capacity, etc..
 
diff --git a/Programming-Paradigms.md b/Programming-Paradigms.md
@@ -15,42 +15,43 @@
 
 # Data Formats
 **Libraries for Data serialization and File formats.**
-- [BEncode.jl](https://github.com/joshuamiller/BEncode.jl) :: A Julia library for BEncode metadata files used for encoding BitTorrent storage and transmission of loosely structured data.
-- [BGZF.jl](https://github.com/kmsquire/BGZF.jl) :: A Julia package to read/write BGZF compressed files.
-- [Brukerfile.jl](https://github.com/tknopp/Brukerfile.jwl) Read Bruker data files.
-- [COFF.jl](https://github.com/Keno/COFF.jl) :: A julia implementation of the PE/COFF file format.
-- [CSV.jl](https://github.com/tanmaykm/CSV.jl) :: reads CSV files.
-- [CSVReaders.jl](https://github.com/johnmyleswhite/CSVReaders.jl) :: A (beta) package designed to provide a standardized API for reading CSV files into arbitrary Julia data structures.
-- [DataFramesIO.jl](https://github.com/johnmyleswhite/DataFramesIO.jl) :: Advanced import/export tools for DataFrames: Stata, SPSS, Excel, JSON.
-- [DataRead.jl](https://github.com/WizardMac/DataRead.jl) :: can read files from Stata, SAS, and SPSS.
-- [DICOM.jl](https://github.com/ihnorton/DICOM.jl) :: DICOM interface for the Julia language.
-- [DWARF.jl](https://github.com/loladiro/DWARF.jl) :: Julia Package for parsing the DWARF file format.
-- [ELF.jl](https://github.com/loladiro/ELF.jl) :: Julia Package for working with ELF files.
-- [FastaIO.jl](https://github.com/carlobaldassi/FastaIO.jl) :: Utilities to read/write FASTA format files in Julia.
-- [Grisu.jl](https://github.com/quinnj/Grisu.jl) :: Port of Double-Conversion library to native Julia.
-- [HDF5.jl](https://github.com/timholy/HDF5.jl)
-- [HexEdit.jl](https://github.com/templarlabs/HexEdit.jl) :: Edit and display binary file data in hexadecimal format.
-- [IniFile.jl](https://github.com/JuliaLang/IniFile.jl) :: Reading and writing Windows-style INI files.
-- [JSON.jl](https://github.com/JuliaLang/JSON.jl) :: JSON parsing and printing.
-- [Json2.jl](https://github.com/ddolgi/Json2.jl) :: JSON encoder/decoder on Julia. 
-- [LibExpat.jl](https://github.com/amitmurthy/LibExpat.jl) :: A Julia wrapper for libexpat.
-- [LightXML.jl](https://github.com/lindahua/LightXML.jl) :: A light-weight Julia package for XML based on libxml2.
-- [MachO.jl](https://github.com/loladiro/MachO.jl) :: An implementation of the MachO file format.
-- [MatrixMarket.jl](https://github.com/ViralBShah/MatrixMarket.jl) :: Julia package to read MatrixMarket file format.
-- [MNIST.jl](https://github.com/johnmyleswhite/MNIST.jl) :: Tools for working with the MNIST data set. This package provides access to the classic MNIST data set of handwritten digits that has been used as a testbed for new machine learning methods. The MNIST data set is included with the package, downloaded into their original IDX format and are stored in the data/ directory.
-- [NetCDF.jl](https://github.com/meggart/NetCDF.jl) :: NetCDF support for a high-level and a medium-level interface for writing and reading netcdf files, for the Julia programming language.
-- [NIfTI.jl](https://github.com/simonster/NIfTI.jl) :: Julia module for reading NIfTI MRI files.
-- [NPZ.jl](https://github.com/fhs/NPZ.jl) :: Julia package that provides support for reading and writing Numpy .npy and .npz files.
-- [ObjFileBase.jl](https://github.com/Keno/ObjFileBase.jl) :: Common functionality for Object Files.
-- [OpenSlide.jl](https://github.com/ihnorton/OpenSlide.jl) :: OpenSlide bindings for Julia.
-- [PList.jl](https://github.com/ordovician/PList.jl) :: A module for reading and writing OS X plist in ASCII format. The binary and XML format is not supported presently.
-- [PLX.jl](https://github.com/simonster/PLX.jl) :: Julia module for reading Plexon PLX files.
-- [HarwellBoeing.jl](https://github.com/dpo/HarwellBoeing.jl) :: A reader for matrices and supplementary data written in the Harwell-Boeing format.
-- [Shapefile.jl](https://github.com/loladiro/Shapefile.jl) :: Parsing .shp files in Julia.
-- [StrPack.jl](https://github.com/pao/StrPack.jl) :: for encoding and decoding binary data streams and there is some [documentation](https://strpackjl.readthedocs.org/) at readthedocs.org.
-- [uJSON.jl](https://github.com/samuelcolvin/uJSON.jl) :: JSON library for Julia using ultraJSON.
-- [XPT.jl](https://github.com/lendle/XPT.jl) :: The XPT package reads SAS® software transport files and converts SAS software datasets to DataFrames.
-- [XSV.jl](https://github.com/benhamner/XSV.jl) :: CSV, TSV, etc. streaming and batch parser.
++ [AIDA.jl](https://github.com/jstrube/AIDA.jl) :: This package implements simple readers for legacy AIDA files.
++ [BEncode.jl](https://github.com/joshuamiller/BEncode.jl) :: A Julia library for BEncode metadata files used for encoding BitTorrent storage and transmission of loosely structured data.
++ [BGZF.jl](https://github.com/kmsquire/BGZF.jl) :: A Julia package to read/write BGZF compressed files.
++ [Brukerfile.jl](https://github.com/tknopp/Brukerfile.jwl) Read Bruker data files.
++ [COFF.jl](https://github.com/Keno/COFF.jl) :: A julia implementation of the PE/COFF file format.
++ [CSV.jl](https://github.com/tanmaykm/CSV.jl) :: reads CSV files.
++ [CSVReaders.jl](https://github.com/johnmyleswhite/CSVReaders.jl) :: A (beta) package designed to provide a standardized API for reading CSV files into arbitrary Julia data structures.
++ [DataFramesIO.jl](https://github.com/johnmyleswhite/DataFramesIO.jl) :: Advanced import/export tools for DataFrames: Stata, SPSS, Excel, JSON.
++ [DataRead.jl](https://github.com/WizardMac/DataRead.jl) :: can read files from Stata, SAS, and SPSS.
++ [DICOM.jl](https://github.com/ihnorton/DICOM.jl) :: DICOM interface for the Julia language.
++ [DWARF.jl](https://github.com/loladiro/DWARF.jl) :: Julia Package for parsing the DWARF file format.
++ [ELF.jl](https://github.com/loladiro/ELF.jl) :: Julia Package for working with ELF files.
++ [FastaIO.jl](https://github.com/carlobaldassi/FastaIO.jl) :: Utilities to read/write FASTA format files in Julia.
++ [Grisu.jl](https://github.com/quinnj/Grisu.jl) :: Port of Double-Conversion library to native Julia.
++ [HDF5.jl](https://github.com/timholy/HDF5.jl)
++ [HexEdit.jl](https://github.com/templarlabs/HexEdit.jl) :: Edit and display binary file data in hexadecimal format.
++ [IniFile.jl](https://github.com/JuliaLang/IniFile.jl) :: Reading and writing Windows-style INI files.
++ [JSON.jl](https://github.com/JuliaLang/JSON.jl) :: JSON parsing and printing.
++ [Json2.jl](https://github.com/ddolgi/Json2.jl) :: JSON encoder/decoder on Julia. 
++ [LibExpat.jl](https://github.com/amitmurthy/LibExpat.jl) :: A Julia wrapper for libexpat.
++ [LightXML.jl](https://github.com/lindahua/LightXML.jl) :: A light-weight Julia package for XML based on libxml2.
++ [MachO.jl](https://github.com/loladiro/MachO.jl) :: An implementation of the MachO file format.
++ [MatrixMarket.jl](https://github.com/ViralBShah/MatrixMarket.jl) :: Julia package to read MatrixMarket file format.
++ [MNIST.jl](https://github.com/johnmyleswhite/MNIST.jl) :: Tools for working with the MNIST data set. This package provides access to the classic MNIST data set of handwritten digits that has been used as a testbed for new machine learning methods. The MNIST data set is included with the package, downloaded into their original IDX format and are stored in the data/ directory.
++ [NetCDF.jl](https://github.com/meggart/NetCDF.jl) :: NetCDF support for a high-level and a medium-level interface for writing and reading netcdf files, for the Julia programming language.
++ [NIfTI.jl](https://github.com/simonster/NIfTI.jl) :: Julia module for reading NIfTI MRI files.
++ [NPZ.jl](https://github.com/fhs/NPZ.jl) :: Julia package that provides support for reading and writing Numpy .npy and .npz files.
++ [ObjFileBase.jl](https://github.com/Keno/ObjFileBase.jl) :: Common functionality for Object Files.
++ [OpenSlide.jl](https://github.com/ihnorton/OpenSlide.jl) :: OpenSlide bindings for Julia.
++ [PList.jl](https://github.com/ordovician/PList.jl) :: A module for reading and writing OS X plist in ASCII format. The binary and XML format is not supported presently.
++ [PLX.jl](https://github.com/simonster/PLX.jl) :: Julia module for reading Plexon PLX files.
++ [HarwellBoeing.jl](https://github.com/dpo/HarwellBoeing.jl) :: A reader for matrices and supplementary data written in the Harwell-Boeing format.
++ [Shapefile.jl](https://github.com/loladiro/Shapefile.jl) :: Parsing .shp files in Julia.
++ [StrPack.jl](https://github.com/pao/StrPack.jl) :: for encoding and decoding binary data streams and there is some [documentation](https://strpackjl.readthedocs.org/) at readthedocs.org.
++ [uJSON.jl](https://github.com/samuelcolvin/uJSON.jl) :: JSON library for Julia using ultraJSON.
++ [XPT.jl](https://github.com/lendle/XPT.jl) :: The XPT package reads SAS® software transport files and converts SAS software datasets to DataFrames.
++ [XSV.jl](https://github.com/benhamner/XSV.jl) :: CSV, TSV, etc. streaming and batch parser.
 
 ----
 
@@ -117,8 +118,8 @@ Packages and resources that support various programming styles, Software Archite
 + [OCCA.jl](https://github.com/ReidAtcheson/OCCA.jl) :: Julia interface into [OCCA2](https://github.com/tcew/OCCA2) by @tcew, an extensible multi-threading programming API written in C++.
 
 ### [Program Analysis](https://en.wikipedia.org/wiki/Category:Program_analysis)
-* [CallGraphs.jl](https://github.com/timholy/CallGraphs.jl) :: A package for analyzing source-code callgraphs, particularly of Julia's `src/` directory. The main motivation for this package was to aid in finding all functions that might trigger garbage collection by directly or indirectly calling `jl_gc_collect`; however, the package has broader uses.
-* [dataflow.jl](https://github.com/JeffBezanson/dataflow.jl) :: Introduction to dataflow analysis using julia.
++ [CallGraphs.jl](https://github.com/timholy/CallGraphs.jl) :: A package for analyzing source-code callgraphs, particularly of Julia's `src/` directory. The main motivation for this package was to aid in finding all functions that might trigger garbage collection by directly or indirectly calling `jl_gc_collect`; however, the package has broader uses.
++ [dataflow.jl](https://github.com/JeffBezanson/dataflow.jl) :: Introduction to dataflow analysis using julia.
 
 ### Reactive Programming
 + [React.jl](https://github.com/shashi/React.jl) :: Reactive programming primitives for Julia.