RESOURCES

1. Fortran Codes

John Burkardt:  http://people.sc.fsu.edu/~jburkardt/Numerical Recipes: http://www.aip.de/groups/soe/local/numres/

Numerical methods: http://tonic.physics.sunysb.edu/docs/num_meth.html

Jon Squire:
http://www.csee.umbc.edu/~squire/
http://www.csee.umbc.edu/~squire/cs411_down.shtml#CS455

Others:
http://www.erogol.com/large-set-machine-learning-resources-beginners-mavens/
http://www.fortran.gantep.edu.tr/compiling-g95-basic-guide.html
http://math.berkeley.edu/~strain/Codes/index.html
ftp://ftp.eos.ncsu.edu/pub/math/zhilin/Packages/

2. Molecular Dynamics

PDB: http://www.rcsb.org/pdb/home/home.do
EMDB: http://www.emdatabank.org/
VMD: http://www.ks.uiuc.edu/Research/vmd/
NMAD: http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html  https://research.cchmc.org/wiki/index.php/NAMD_Tutorial#Restarting_.28continuing.29_simulation
AMBER: http://ambermd.org/tutorials/
Chimera: https://www.cgl.ucsf.edu/chimera/   http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html
SMD: http://www.ks.uiuc.edu/Research/smd_imd/titin/  http://www.ks.uiuc.edu/Research/mechanicals/
MMTSB: http://blue11.bch.msu.edu/mmtsb/Main_Page

3. Normal Mode Analysis

ANM: http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi
GNM: http://en.wikipedia.org/wiki/Gaussian_network_model
GNM and ANM Code: http://www.csb.pitt.edu/resources/gnm/   http://ignmtest.ccbb.pitt.edu/anmdocs/source.html
ProDy: http://prody.csb.pitt.edu/
NMWiz: http://prody.csb.pitt.edu/nmwiz/
Ivet Bahar: http://www.ccbb.pitt.edu/Faculty/bahar/index.php

4. Persistent Homology

Perseus: http://www.sas.upenn.edu/~vnanda/perseus/index.html
Javaplex: http://code.google.com/p/javaplex/ http://javaplex.github.io/javaplex/
Dionysus: http://www.mrzv.org/software/dionysus/
Comptop: http://comptop.stanford.edu/
fullerene: http://www.nanotube.msu.edu/fullerene/fullerene-isomers.html
Others: http://web.cse.ohio-state.edu/~tamaldey/course/CTDA/CTDA.html http://pub.ist.ac.at/~edels/ http://www.mrzv.org/ http://www.math.upenn.edu/~ghrist/index.html http://www.math.duke.edu/~hadams/research/ http://www.cs.dartmouth.edu/~afra/papers.html

5. Linux related

bash script: http://linuxconfig.org/bash-scripting-tutorial
putty and xming: http://www.siue.edu/~dbock/cmis565/PuTTYColorSettings.htm http://www.geo.mtu.edu/geoschem/docs/putty_install.html
python: https://docs.python.org/2/index.html
Image converter: http://image.online-convert.com/
MATLAB Codes: http://m2matlabdb.ma.tum.de/index.jsp

 

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