STEM Apps

Biology, Chemistry:
  Bedtools: Genomic Arithmetic (Linux, Mac, Win)
  Bioclipse: Life Sciences (Linux, Mac, Win)
  Bioconductor  (Manuals): Genomic (Linux, Mac, Win)
  Biojava: Tools for Processing Data (Linux, Mac, Win)
  Bioperl: Biology (Linux, Mac, Win)
  Biopython: Tools for Computation (Linux, Mac, Win)
  Blast: Compare Biology Sequences (Linux, Mac, Win)
  Crustal Omega: Sequence Align (Linux, Mac, Win)
  geWorkbench: Integrated Genomic Data Analysis
  Gromacs: Chemistry (Linux, Mac, Win)
  Emboss: Biology (Linux, Mac, Win)
  IGV: Visualization Genome Browser (Linux, Mac, Win)
  Intermnine: Data Integration
  Jmol: Chem Structures (Linux, Mac, Win)
  Kitware: Chemistry (Linux, Mac, Win)
  OpenChemisty (Linux, Mac, Win)
  Taverna Workbench: Bio (Linux, Mac, Win)
  TheRealFishTracker: Fish Tracker
  Ugene: Bioinformatics Software (Linux, Mac, Win)
  Webspectra: Chemistry (Linux, Mac, Win)
  15 Bioinformatic Apps (Linux, Mac, WIn)
  11 Chemistry Tools (Linux, Mac, Win)

Math:
  Freemath: See Matlab (Linux, Mac, Win)
  Fusioncharts: Charts, Graphs (Linux, Mac, Win)
  Eigen:  Algebra, Matrices (Linux, Mac, Win)
  Genius See Matlab (Linux, Mac)
  Gnumeric: Spreadsheet (Linux, Mac, Win)
  Graphviz: Graph Visualization (Linux, Mac)
  Jpgraph: Graphing (Linux, Win)
  Math (Linux, Unix, Win)
  Matman: Manipulator (Linux)
  Maxima: Computer Algebra (Linux, Mac, Win)
  NumPy: Scientific Computing(Linux, Mac, Win)
  Octave: See Matlab (Linux, Mac, Win)
  Qalculate:Calculator (Linux)
  Sagemath: See Matlab (Linux, Mac, Win)
  Scilab: See Matlab (Linux, Mac, Win)
  Speedcrunch: Calculator (Linux, Mac, Win)
  Spreadsheets (Linux, Win) 
  Spread32 Spreadsheet (Win)
  Symbolic Logic (Win)
  Sympy: symbolic Math (Linux, Mac, Win)
  Tulip: Graphing (Linux, Win)
  4 Alternatives to Matlab (Linux, Mac, Win)
  6 Fractual Tools for Mathematics (Linux, Mac, Win)
  8 Best Geometry Apps (Linux, Mac, Win)
  42 of the Best Scientific Apps (Linux, Mac, Win)

Physics:
  CompHep: Compuations (Linux, Mac, Win)
  Elmer: Multiphysical (Linux, Mac, Win)
  Geant4: Particles (Linux, Mac, Win)
  Gerrus: Numerical (Linux, Mac, Win)
  McStas: Neutron Ray (Linux, Mac, Win)
  Octopus: Real-Time TDDFT (Linux)
  Openphysics (Linux, Mac, Win)
  Root: High-Energy Analysis  (Linux)
  Step: Interactive (Linux, Mac, Win)
  8 Astronomy Tools (Linux, Mac, Win)
  10 Best Physics Tools (Linux, Mac, Win)
Robotics:
  Peekabot: 3-D Visualization (Linux)
  5 Best Robotic Apps (Linux, Mac, Win)