Software and Libraries

Virtual Box

  1. Oracle virtual box 
    1. Download site for all OSs.
    2. Quick installation manual (by Albert S. Kim): VirtualBox-HowTo (Ubuntu on Mac OSX)

Version control

  1. Subversion from Tigris and a Mac version from Collabnet
    1. How to use subversion with PuTTY on Windows

Word Processing

  1. Lyx: LaTex-based WYSIWIM (What You See Is What You Mean) editor

    1. Introduction to Latex and Lyx: Part 1, 2, 3, 4, and 5

  2. LaTex
    1. MacTex (download)
    2. MikTex (download): LaTex/Tex for Windows
    3. Editor for LaTex: TEXnic Center (Win), WinEdt (Win), TeXShop (Mac)
    4. Getting Stared with LaTex
    5. Computer Science, Cornell University
    6. Mathematics Department, Elon University
    7. Bibliography library: Natbib
    8. Roger’s online equation editor
    9. Templates for
      1. REVTex: Macro-packages designed to be used with LaTex2e for APS publication
      2. Elsevior journal publication, elsarticle class (download elsarticle.zip)
      3. beamer presentation (matrix), poster
    10. Commercial converting software by http://www.grindeq.com:
      1. LaTex-to-Word and
      2. Word-to-LaTex
  3. PDF Labs
    1.  pdftk (PDF Tool Kits): download and install, examples

Reference Management Software

  1. Comparative Review
    1. Wikipedia
    2. PennState
  2. Software
    1. BibTex (free with LaTex): The best way to organize references but initially (a little) difficult to learn how to use with LaTex. (BibTex with MS Word)
    2. Mendeley (free): Cross platform bibliography software having web access with group members. (I am currently using this software after Papers.) It export a BibTex file synchronously.
    3. Zotero (free): Another very good reference manager.
    4. Papers (commercial): The best bibliography software for Mac users (in my opinion).
    5. EndNote (commercial):  The best bibliography software for Windows users (in my opinion).

Scientific Visualization

Review of creating charts from Wikipedia

Drawing – publication quality

  1. Xfig: developer (www.xfig.org), Lawrence Berkeley National Lab

Plotting

  1. gnuplot (a portable command-line driven graphing utility)
    1. Developer site (http://www.gnuplot.info/)
    2. Windows version
    3. PDF manual for gnuplot 4.4
    4. Tutorial sites
      1. http://t16web.lanl.gov/Kawano/gnuplot/index-e.html
  2. Plot, a scientific 2D plotting program for Mac OS X.
  3. QtiPlot – Data Analysis and Scientific Visualization:  QtiPlot is ideal for student computer labs and offers a complete alternative solution to extremely expensive proprietary software like Origin, SigmaPlot, SPSS, Regressi or Igor Pro.
  4. Veusz is a GUI scientific plotting and graphing package. It is designed to produce publication-ready Postscript or PDF output. SVG, EMF and bitmap export formats are also supported. The program runs under Unix/Linux, Windows or Mac OS X, and binaries are provided. Data can be read from the text, CSV or FITS files, and data can be manipulated or examined from within the application.
  5. MagicPlot is a handy application for scientific and engineering data analysis, graphing, nonlinear curve fitting, and multi-peak fitting.

Graphics

  1. Molscript, a program for displaying molecular 3D structures.
  2. Open DX (Data Explorer) from IBM
  3. Paraview (Open-source, multi-platform data analysis, and visualization application), download
  4. Pizza.py Toolkit, a loosely integrated collection of visualization tools.
  5. PyMOL, a user-sponsored molecular visualization system
  6. Raster3D, a set of tools for generating high-quality raster molecular images
  7. VisIt (free interactive parallel visualization and graphical analysis tool for viewing scientific data) from Weapon and Complex Integration (WCI) directorate in Lawrence Livermore National Laboratory (LLNL)
  8. VMD (Visual Molecular Dynamics) from Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Bioinformatics, the University of Illinois at Urbana-Champaign
  9. VTK (Visualization Toolkit) from Kitware, Inc. (Image Gallery)

Blender

  1. Tutorials
    1. Blender Tutorial – Realistic Fluid Simulation
    2. Massive Particle Fluid Simulation, Blender Tutorial (Cycles)
    3. Blender 2.56 SPH Fluid Tutorial

 

Numerical Libraries (mostly developed using FORTRAN and partially C/C++)

  1. LAPACK (Linear Algebra Package)
    1. Example Programs by NAG (previously LINPACK)
    2. LAPACAK Quick Reference Guide to the Driver Routines
  2. BLAS (Basic Linear Algebra Subprograms)
  3. ATLAS (Automatically Tuned Linear Algebra Software)
  4. GOTO BLAS developed by Kazushige Goto
  5. PBLAS (Parallel Basic Linear Algebra Subprograms)
  6. BLACS (Basic Linear Algebra Communication Subprograms)
  7. ScaLAPACK (Scalable LAPACK)
  8. List of FORTRAN libraries http://fortranwiki.org/fortran/show/Libraries

Statistical Analysis

  1. Multi-variate Data Analysis

Molecular Dynamics (MD)

  1. AMBER (Assisted Model Building with Energy Refinement)
  2. CHARM (Chemistry at HARvard Macromolecular Mechanics) and CHARM++
  3. GROMACS (GROningen MAchine for Chemical Simulation)
  4. MDynaMix (Molecular Dynamics of Mixtures)
  5. NAMD (Not (just) Another Molecular Dynamics program)
    1. Installation guide using source

Smoothed Particle Dynamics (SPH)

  1. SPLASH (a free and open source visualisation tool for Smoothed Particle Hydrodynamics (SPH) simulations

Climate Modeling

  1. Weather Research & Forecasting (WRF) Model

Finite Element Method (FEM)

  1. FEM_CODES – Finite Element Method Demonstration Programs
  2. NASTRAN (MSC software)
  3. ANSYS
  4. MEANS: (Tsinghua University)

Engineering Software

  1. Hydrological Simulation Program – FORTRAN (HSPF) by USGS and EPA (download)
  2. MODFLOW-2005 version 1.19.01 by USGS (mf2k1_19_01.exe, mf2k1_19_01.tar.gz)
  3. Membrane software
  4. SWAT (Soil Water Assessment Tool)
  5. SeaWAT (A Computer Program for Simulation of Three-Dimensional Variable-Density Ground-Water Flow and Transport)
  6. SWAN (Simulating WAves Nearshore)
  7. CEDAS (Coastal Engineering Design and Analysis System)
  8. InVEST: Integrated Valuation of Environmental Services and Tradeoffs

Physics Software Package

  1. ROOT (object-oriented program and library developed by CERN, originally designed for particle physics data analysis)
  2. Geant 4 (a toolkit for the simulation of the passage of particles through matter.)
  3. HYSPLIT – Hybrid Single Particle Lagrangian Integrated Trajectory Model

Symbolic Calculation

  1. Maple:  Webinars
  2. SciLab

Microsoft Office

  1. Word
    1. LaTex to Word
    2. Word to LaTex
  2. Excel
    1. XNUMBERS 5.6 – Multi-Precision Floating Point Computing and Numerical Methods