## SageMathCloud tutorial for lecturers and teachers

June 13th, 2016

I was in a funk!

Not long after joining the University of Sheffield, I had helped convince a raft of lecturers to switch to using the Jupyter notebook for their lecturing. It was an easy piece of salesmanship and a whole lot of fun to do. Lots of people were excited by the possibilities.

The problem was that the University managed desktop was incapable of supporting an instance of the notebook with all of the bells and whistles included. As a cohort, we needed support for Python 2 and 3 kernels as well as R and even Julia. The R install needed dozens of packages and support for bioconductor. We needed LateX support to allow export to pdf and so on. We also needed to keep up to date because Jupyter development moves pretty fast! When all of this was fed into the managed desktop packaging machinery, it died. They could give us a limited, basic install but not one with batteries included.

I wanted those batteries!

In the early days, I resorted to strange stuff to get through the classes but it wasn’t sustainable. I needed a miracle to help me deliver some of the promises I had made.

Miracle delivered – SageMathCloud

During the kick-off meeting of the OpenDreamKit project, someone introduced SageMathCloud to the group. This thing had everything I needed and then some! During that presentation, I could see that SageMathCloud would solve all of our deployment woes as well as providing some very cool stuff that simply wasn’t available elsewhere. One killer-application, for example, was Google-docs-like collaborative editing of Jupyter notebooks.

I fired off a couple of emails to the lecturers I was supporting (“Everything’s going to be fine! Trust me!”) and started to learn how to use the system to support a course. I fired off dozens of emails to SageMathCloud’s excellent support team and started working with Dr Marta Milo on getting her Bioinformatics course material ready to go.

TL; DR: The course was a great success and a huge part of that success was the SageMathCloud platform

Giving back – A tutorial for lecturers on using SageMathCloud

I’m currently working on a tutorial for lecturers and teachers on how to use SageMathCloud to support a course. The material is licensed CC-BY and is available at https://github.com/mikecroucher/SMC_tutorial

If you find it useful, please let me know. Comments and Pull Requests are welcome.

## The ‘Happy Holidays’ number

December 23rd, 2015

Some numbers have something to say. Take the following, rather huge number, for example:

185325291040682644803531312384041336595151018761127807725763308064246070395230764956468856341399670487
514610052487586323067575687914642829757636555138456145938430191876551756992329818006401775522301219016
237245425891544032218544390861818271526845858747648909382915665997160517028671058273052955697138350617
856171748990490346558484883522495310587304606877332488244886849690319641412147118669050542398759303832
627672479768452329971883073420877438596419179762421854464516060347269129680634374662501202129049727949
71185874579656679344857677824

This number wants to tell you ‘Happy Holidays’, it just needs a little code to help it out.  In Maple, this code is:

n := 18532529104068264480353131238404133659515101876112780772576330806424607039523076495646885634139967048751461005248758632306757568791464282975763655513845614593843019187655175699232981800640177552230121901623724542589154403221854439086181827152684585874764890938291566599716051702867105827305295569713835061785617174899049034655848488352249531058730460687733248824488684969031964141214711866905054239875930383262767247976845232997188307342087743859641917976242185446451606034726912968063437466250120212904972794971185874579656679344857677824:
modnew := proc (x, y) options operator, arrow; x-y*floor(x/y) end proc:
tupper := piecewise(1/2 < floor(modnew(floor((1/17)*y)*2^(-17*floor(x)-modnew(floor(y), 17)), 2)), 0, 1):
points := [seq([seq(tupper(x, y), y = n+16 .. n, -1)], x = 105 .. 0, -1)]:
plots:-listdensityplot(points, scaling = constrained, view = [0 .. 106, 0 .. 17], style = patchnogrid, size = [800, 800]);


The result is the following plot

Thanks to Samir for this one!

The mathematics is based on a generalisation of Tupper’s self-referential formula.

There’s more than one way to send a message with an equation, however. Here’s an image of one I discovered a few years ago — The equation that says Hi

## Christmas cards with code and maths

December 13th, 2015

Way back in 2008, I wrote a few blog posts about using mathematical software to generate christmas cards:

I’ve started moving the code from these to a github repository. If you’ve never contributed to an open source project before and want some practice using git or github, feel free to write some code for a christmas message along similar lines and submit a Pull Request.

## Solving the nearest correlation matrix problem using Python

November 17th, 2014

Given a symmetric matrix such as

What’s the nearest correlation matrix? A 2002 paper by Manchester University’s Nick Higham which answered this question has turned out to be rather popular! At the time of writing, Google tells me that it’s been cited 394 times.

Last year, Nick wrote a blog post about the algorithm he used and included some MATLAB code. He also included links to applications of this algorithm and implementations of various NCM algorithms in languages such as MATLAB, R and SAS as well as details of the superb commercial implementation by The Numerical algorithms group.

I noticed that there was no Python implementation of Nick’s code so I ported it myself.

Here’s an example IPython session using the module

In [1]: from nearest_correlation import nearcorr

In [2]: import numpy as np

In [3]: A = np.array([[2, -1, 0, 0],
...:               [-1, 2, -1, 0],
...:               [0, -1, 2, -1],
...:               [0, 0, -1, 2]])

In [4]: X = nearcorr(A)

In [5]: X
Out[5]:
array([[ 1.        , -0.8084125 ,  0.1915875 ,  0.10677505],
[-0.8084125 ,  1.        , -0.65623269,  0.1915875 ],
[ 0.1915875 , -0.65623269,  1.        , -0.8084125 ],
[ 0.10677505,  0.1915875 , -0.8084125 ,  1.        ]])

This module is in the early stages and there is a lot of work to be done. For example, I’d like to include a lot more examples in the test suite, add support for the commercial routines from NAG and implement other algorithms such as the one by Qi and Sun among other things.

Hopefully, however, it is just good enough to be useful to someone. Help yourself and let me know if there are any problems. Thanks to Vedran Sego for many useful comments and suggestions.

## Waves from Circles with Mathematica

March 12th, 2014

A recent Google+ post from Mathemania4u caught my attention on the train to work this morning. I just had to code up something that looked like this and so fired up Mathematica and hacked away. The resulting notebook can be downloaded here. It’s not particularly well thought through so could almost certainly be improved on in many ways.

The end result was a Manipulate which you’ll be able to play with below, provided you have a compatible Operating System and Web browser. The code for the Manipulate is

Manipulate[
Graphics[Map[dotCirc,
circArray[circrad, theta, pointsize, extent, step, phase,
showcirc]]]
, {{showcirc, True, "Show Circles"}, {True, False}}
, {{theta, 0, "Dot Angle"}, 0, 2 Pi, Pi/10, Appearance -> "Labeled"}
, {{pointsize, 0.018, "Dot Size"}, 0, 1, Appearance -> "Labeled"}
, {{phase, 2, "Phase Diff"}, 0, 2 Pi, Appearance -> "Labeled"}
, {{step, 0.25, "Circle Separation"}, 0, 1, Appearance -> "Labeled"}
, {{extent, 2, "Plot Extent"}, 1, 5, Appearance -> "Labeled"}
, Initialization :>
{
dotCirc[{x_, y_, r_, theta_, pointsize_, showcirc_}] := If[showcirc,
{Circle[{x, y}, r], PointSize[pointsize],
Point[{x + r Cos[theta], y + r Sin[theta]}]}
,
{PointSize[pointsize],
Point[{x + r Cos[theta], y + r Sin[theta]}]}]
,
circArray[r_, theta_, pointsize_, extent_, step_, phase_,
showcirc_] := Module[{},
Partition[
Flatten[Table[{x, y, r, theta + x*phase + y*phase, pointsize,
showcirc}, {x, -extent, extent, step}, {y, -extent, extent,
step}]], 6]
]}]

If you can use the Manipulate below, I suggest clicking on the + icon to the right of the ‘Dot Angle’ field to expose the player controls and then press the play button to kick off the animation.

I also produced a video – The code used to produce this is in the notebook.
)

## Floating point addition is not associative

February 28th, 2014

A lot of people don’t seem to know this….and they should. When working with floating point arithmetic, it is not necessarily true that a+(b+c) = (a+b)+c. Here is a demo using MATLAB

>> x=0.1+(0.2+0.3);
>> y=(0.1+0.2)+0.3;
>> % are they equal?
>> x==y

ans =
0

>> % lets look
>> sprintf('%.17f',x)
ans =
0.59999999999999998

>> sprintf('%.17f',y)
ans =
0.60000000000000009

These results have nothing to do with the fact that I am using MATLAB. Here’s the same thing in Python

>>> x=(0.1+0.2)+0.3
>>> y=0.1+(0.2+0.3)
>>> x==y
False
>>> print('%.17f' %x)
0.60000000000000009
>>> print('%.17f' %y)
0.59999999999999998

If this upsets you, or if you don’t understand why, I suggest you read the following

Does anyone else out there have suggestions for similar resources on this topic?

## Fractals from iterating sines

August 23rd, 2013

In a recent blog-post, John Cook, considered when series such as the following converged for a given complex number z

z1 = sin(z)
z2 = sin(sin(z))
z3 = sin(sin(sin(z)))

John’s article discussed a theorem that answered the question for a few special cases and this got me thinking: What would the complete set of solutions look like? Since I was halfway through my commute to work and had nothing better to do, I thought I’d find out.

The following Mathematica code considers points in the square portion of the complex plane where both real and imaginary parts range from -8 to 8. If the sequence converges for a particular point, I colour it black.

LaunchKernels[4]; (*Set up for 4 core parallel compute*)
ParallelEvaluate[SetSystemOptions["CatchMachineUnderflow" -> False]];
convTest[z_, tol_, max_] := Module[{list},
list = Quiet[
NestWhileList[Sin[#] &, z, (Abs[#1 - #2] > tol &), 2, max]];
If[
Length[list] < max && NumericQ[list[[-1]]]
, 1, 0]
]
step = 0.005;
extent = 8;
AbsoluteTiming[
data = ParallelMap[convTest[#, 10*10^-4, 1000] &,
Table[x + I y, {y, -extent, extent, step}, {x, -extent, extent,
step}]
, {2}];]
ArrayPlot[data]

I quickly emailed John to tell him of my discovery but on actually getting to work I discovered that the above fractal is actually very well known. There’s even a colour version on Wolfram’s MathWorld site.  Still, it was a fun discovery while it lasted

Other WalkingRandomly posts like this one:

## Historical math videos of Lanczos from 1972.

February 6th, 2013

The University of Manchester has uploaded some videos of Cornelius Lanczos the  (re-)discoverer of the fast Fourier transform and singular value decomposition among other things.  Recorded back in 1972, these videos discuss his life and mathematics.  Worth taking a look.

Update: Manchester’s Nick Higham has written a more detailed blog post about these videos – http://nickhigham.wordpress.com/2013/02/06/the-lanczos-tapes/

## Full LaTeX on iPad with on device compilation and .dvi viewer

August 29th, 2012

While on the train to work I came across a very interesting blog entry.  Full LaTeX support (on device compilation and .dvi viewer) is now available on iPad courtesy of TeX Writer By FastIntelligence.  Here is the blog post telling us the good news http://litchie.com/blog/?p=406

At the time of writing, the blog is down (Update: working again), possibly because of the click storm that my twitter announcement caused..especially after it was picked up by @TeXtip.  So, here is the iTunes link http://itunes.apple.com/us/app/tex-writer/id552717222?mt=8

I haven’t tried this yet but it looks VERY interesting.  If you get a chance to try it out, feel free to let me know how you get on in the comments section.

Update 1: This version of TeX writer(1.1) cannot output to .pdf.  Only .dvi output is supported at the moment.

## New interactive mathematics website based on Sage

July 14th, 2012

If you have an interest in mathematics, you’ve almost certainly stumbled across The Wolfram Demonstrations Project at some time or other.  Based upon Wolfram Research’s proprietary Mathematica software and containing over 8000 interactive demonstrations, The Wolfram Demonstrations Project is a fantastic resource for anyone interested in mathematics and related sciences; and now it has some competition.

Sage is a free, open source alternative to software such as Mathematica and, thanks to its interact function, it is fully capable of producing advanced, interactive mathematical demonstrations with just a few lines of code.  The Sage language is based on Python and is incredibly easy to learn.

The Sage Interactive Database has been launched to showcase this functionality and its looking great.  There’s currently only 31 demonstrations available but, since anyone can sign up and contribute, I expect this number to increase rapidly.  For example, I took the simple applet I created back in 2009 and had it up on the database in less than 10 minutes!  Unlike the Wolfram Demonstrations Project, you don’t need to purchase an expensive piece of software before you can start writing Sage Interactions….Sage is free to everyone.

Not everything is perfect, however.  For example, there is no native Windows version of Sage.  Windows users have to make use of a Virtualbox virtual machine which puts off many people from trying this great piece of software.  Furthermore, the interactive ‘applets’ produced from Sage’s interact function are not as smooth running as those produced by Mathematica’s Manipulate function.  Finally, Sage’s interact doesn’t have as many control options as Mathematica’s Manipulate (There’s no Locator control for example and my bounty still stands).

The Sage Interactive Database is a great new project and I encourage all of you to head over there, take a look around and maybe contribute something.