Resources

The Catalog of Computational Resources

Programming Languages

  • Python
  • R
  • MATLAB
  • Shell Scripting
  • Basic Julia
  • Basic C++/C
  • Basic F#

Data Science Stack

Python

  • scikit-learn: http://scikit-learn.org/stable/

  • Pandas: http://pandas.pydata.org/

  • StatsModels: http://statsmodels.sourceforge.net/

  • Bokeh: http://bokeh.pydata.org/en/latest/

  • CVXOPT: http://cvxopt.org/

  • CVXPY: http://www.cvxpy.org/en/latest/

R

  • TidyVerse:http://tidyverse.org/

  • Caret: http://caret.r-forge.r-project.org/

  • Nloptr: https://cran.r-project.org/web/packages/nloptr/index.html

  • Shiny: https://shiny.rstudio.com/

Visualization Tools

  • Python Visualization Stack

  • R Visualization Stack Matlab Plotting

  • Bokeh: http://bokeh.pydata.org/en/latest/

  • Shiny: https://shiny.rstudio.com/

  • Inkscape: http://www.inkscape.org/en/

  • Xfig: http://www.xfig.org/

  • Circos: http://circos.ca/

  • Blender: http://www.blender.org/

  • VANTED: http://vanted.ipk-gatersleben.de/index.php?file=doc0.html

  • VMD: http://www.ks.uiuc.edu/Research/vmd/

Computational Biology Software’s

  • SBPOP package (Formerly Sbtoolbox2.): http://www.sbtoolbox2.org/main.php

  • Potters Wheel: http://www.potterswheel.de/

  • SBMLtoolbox: http://sbml.org/Software/SBMLToolbox

  • Cobrapy: https://github.com/opencobra/cobrapy

  • Open COBRA: http://opencobra.sourceforge.net/openCOBRA/Welcome.html

  • FluxMap: http://vanted.ipk-gatersleben.de/addons/fluxmap/

  • FbaSimVis: http://fbasimvis.ipk-gatersleben.de/

  • Clustalw2: http://www.ebi.ac.uk/Tools/msa/clustalw2/

  • BLAST: http://blast.ncbi.nlm.nih.gov/Blast.cgi

  • Mcell (Monte Carlo Cell): http://mcell.org/

Optimization Tools

  • CVX: http://cvxr.com/cvx/

  • CVXPortfolio: https://github.com/cvxgrp/cvxportfolio

  • TFOCS: http://cvxr.com/tfocs/

  • MATLAB and SBPOP optimization suite

  • Adaptive Simulated Annealing (MATLAB mex interface): http://www.ingber.com/

  • PSwarm: http://www.norg.uminho.pt/aivaz/pswarm/

  • Implicit Filtering and other solvers available from Prof. C. T. Kelly web page: http://www4.ncsu.edu/~ctk/

  • DACE: http://www.imm.dtu.dk/~hbni/dace/

  • Space Mapping: http://www.imm.dtu.dk/~kajm/Space_Mapping_Toolbox.html

  • SSMGO: http://www.iim.csic.es/~gingproc/ssmGO.html

Differential Equations Solvers

  • SUNDIALS: http://computation.llnl.gov/casc/sundials/main.html

  • XPPAUT: http://www.math.pitt.edu/~bard/xpp/xpp.html

  • MATCONT: http://www.matcont.ugent.be/

  • Radau5 and other solvers available as a mex interface to MATLAB: https://www-m3.ma.tum.de/Software/ODEHome

Version Control Tools:

  • Git: http://git-scm.com/

  • SVN: https://subversion.apache.org/

Writing Resources

Scientific Visualization and Communication

I have found following materials useful:

Thinking and Computational Skills

General Problem Solving Skills

  • Polya, G. How to Solve It: A New Aspect of Mathematical Method. Princeton University Press, 2014.

  • Burger, Edward B., and Michael Starbird. The 5 Elements of Effective Thinking. Princeton University Press, 2012.

  • Wilder, R. L. “The Role of Intuition.” Science 156, no. 3775 (May 5, 1967): 605–10.

  • Devlin, Keith J. Introduction to Mathematical Thinking. Keith Devlin, 2012.

  • Dweck, Carol. Mindset: The New Psychology of Success. Random House Publishing Group, 2006.

  • Lockhart, Paul. A Mathematician’s Lament. Bellevue Literary Press, 2009.

  • Ghose, Aurobindo. A System of Nation

Computing Skill

  • Software-Carpentry: http://software-carpentry.org/
  • Code Academy: http://www.codecademy.com/
  • Massive Open Online Courses:
    • High Performance Scientific Computing: https://www.coursera.org/course/scicomp
    • Introduction to Linux: https://www.edx.org/course/linuxfoundationx/linuxfoundationx-lfs101x-introduction-1621#.VCoV0vldV-4