Biophysics Lab Notes

by James Gowdy (jamesgowdy@hotmail.co.uk) 2014

The notebooks in this repository are meant as notes on topics relevant to my PhD either:

Directly such as the crystallography, FT, eigenvalues of rotation and data reduction topics
Or indirectly as topics mentioned/assumed in litature which I have read in an attempt to answer research questions

They can be rendered online using nbviewer by clicking the links provided below or alternatively they can be downloaded from the repository homepage and run/edited locally with ipython using the notebook option.

Series and transforms stuff
- Taylor series expansion and series convergence conditions
- Fourier series and Fourier synthesis
Linear Algebra/ Numerical analysis
Mathematical optimisation
Dimensionality reduction and machine learning
- SVD - unfinished
- PCA - unfinished
Basic I/O functionality
Crystallography
Physics
Other random mathsy notes
Biochemistry
- Buffer component calculations
- Calculation of molar extinction coefficents for proteins
Other
- PLAN

Name		Name	Last commit message	Last commit date
MPL_recipes.ipynb		MPL_recipes.ipynb
PCA.ipynb		PCA.ipynb
QR.ipynb		QR.ipynb
README.md		README.md
SVD.ipynb		SVD.ipynb
Thesis60.docx		Thesis60.docx
Thesis64_alignment.docx		Thesis64_alignment.docx
bravais.jpg		bravais.jpg
buffer_calc.ipynb		buffer_calc.ipynb
calculus.ipynb		calculus.ipynb
cctbx.ipynb		cctbx.ipynb
complex.ipynb		complex.ipynb
conjugatedescent.ipynb		conjugatedescent.ipynb
core.py		core.py
cubic.ipynb		cubic.ipynb
dcd_io.ipynb		dcd_io.ipynb
density_sampling.ipynb		density_sampling.ipynb
diffusion.ipynb		diffusion.ipynb
eigen.ipynb		eigen.ipynb
fourierseries.ipynb		fourierseries.ipynb
foxtrot.ipynb		foxtrot.ipynb
gaussianelimination.ipynb		gaussianelimination.ipynb
gaussjordan_gaussian_LU.ipynb		gaussjordan_gaussian_LU.ipynb
gradientdescent.ipynb		gradientdescent.ipynb
gramschmidt.ipynb		gramschmidt.ipynb
hamburg6.pptx		hamburg6.pptx
hkl2xyphi.ipynb		hkl2xyphi.ipynb
integrals.ipynb		integrals.ipynb
interestingtopics.ipynb		interestingtopics.ipynb
inverse.ipynb		inverse.ipynb
io.py		io.py
lagrangemult.ipynb		lagrangemult.ipynb
leastsquares.ipynb		leastsquares.ipynb
levenberg_marquardt.ipynb		levenberg_marquardt.ipynb
magics.ipynb		magics.ipynb
math_recipes.ipynb		math_recipes.ipynb
matrix_multiplication.ipynb		matrix_multiplication.ipynb
mmcif_io.ipynb		mmcif_io.ipynb
mpllib.py		mpllib.py
normalmodes.ipynb		normalmodes.ipynb
optimise.md		optimise.md
optrot.ipynb		optrot.ipynb
pdb_io.ipynb		pdb_io.ipynb
plan.ipynb		plan.ipynb
polymer1.ipynb		polymer1.ipynb
polymer2.ipynb		polymer2.ipynb
polymer3.ipynb		polymer3.ipynb
protoparam.ipynb		protoparam.ipynb
recip_latt.ipynb		recip_latt.ipynb
recip_sym.ipynb		recip_sym.ipynb
rootfining_minimisation.ipynb		rootfining_minimisation.ipynb
series.ipynb		series.ipynb
sf_1d.ipynb		sf_1d.ipynb
sf_1d_both.ipynb		sf_1d_both.ipynb
sf_1d_subseries.ipynb		sf_1d_subseries.ipynb
sf_cctbx.ipynb		sf_cctbx.ipynb
sf_directsum.ipynb		sf_directsum.ipynb
sf_fft_old.ipynb		sf_fft_old.ipynb
simplex.ipynb		simplex.ipynb
spellchecked.ipynb		spellchecked.ipynb
texlib.py		texlib.py
veccalculus.ipynb		veccalculus.ipynb
waveequation.ipynb		waveequation.ipynb
xstalpy.py		xstalpy.py

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