I use Octave and totally ignore Matlab compatibility. This enables me to use the (IMO vastly superior) Octave syntax additions. On the odd occasion I need to go back to Matlab, I find the syntax incredibly restrictive. Small things like ++i, default parameters, and temporary expressions, all of which make life so much easier. I understand why this situation exists, but I think it's a terrible shame.

Then there's Octave's ASCII format for storing structures and multidimensional (>2 dim) arrays. That single feature alone is why I don't use Matlab.

I was at the recent Elsevier Epidemics 4 conference (a good conference by the way, they've discussed many important things and highlighted a lot of important work), and they noted that despite growing attendance over the last few years, they've received fewer and fewer submissions to their Epidemics journal, despite it being Open Access. I suspect the boycott is indeed starting to bite.

I'd rather Matlab was 100% compatible with Octave. I find myself increasingly frustrated with Matlab's shortcomings next to Octave -- mainly how it's so much easier to get multidimensional data out of C and into Octave compared to Matlab, which is primarily why I don't use Matlab. That and the syntax, where Octave beats Matlab hands down (if people like my code, but want to use my code in Matlab, they can convert it themselves).

At home I run GNU/Linux (Linux Mint), and all the software there (apart from Minecraft) is Free/OSS. I do have a copy of Windows to boot into so my wife can play Plants vs Zombies (I had it running under wine, but it didn't always work perfectly), and occasionally Half Life or Portal. I also have a lot of console games that aren't F/OSS. Really it's just the games that aren't, but I'm really not bothered by that.

At work (I'm a post doc research assistant, modelling E.coli O157 spread in cattle), in one office I run under Linux, and the only non-F/OSS program I run is Maple, because there's no good alternative that I'm aware of. At my other office I use a Mac, and also Word and Powerpoint. I have protested at length about this, and my boss will occasionally allow me to use LaTeX (which she used in the past), but in general it's the collaboration part where things fall down. Also no journal that I'm aware of (and am interested in submitting to) accepts ODF documents, and Libreoffice (while I find far better for actually working in than MS Office) almost never seems to manage converting documents to DOC without things going wrong, especially the references.

My PhD thesis was entirely written in LaTeX, and the work done in C++, GNU Octave, Inkscape, and Maple (the odd one out). For presentations I used a mix of OpenOffice/Libreoffice and LaTeX. Ultimately, if I could be 100% F/OSS at work (and home except for games) then I would, but I'm not the one who makes those decisions.

It's been the year of Linux on the desktop for me since around 2003, when the guys I shared a flat with deliberately set the anime server so windows users couldn't access it (I was dual booting at the time, and decided I didn't really need to stay in Windows any more).

Nowadays I'm a postdoc research assistant working in mathematical epidemiology; I do a lot of programming and writing (mostly in LaTeX), most people at work use Linux, and having it at work and home makes my life very easy.

Yes, there's occasionally a game I can't play under Linux that wine can't handle, so I do still have a partition for Windows, but I'm now so unused to Windows that it feels alien and clunky, and I miss all the features I've become accustomed too. Given how it can be just as difficult to fix problems when they occur in Windows, if it weren't for Windows massive market share, I'd question if it were ready for the desktop yet.

Your opinion as a non-scientist on the matter is of course equally valid as that of an expert in the field.

That said, it's fine to comment on why you think the experts may have conflicting interests (this sort of information must be declared in any scientific papers they publish).

No, the usual stuff: playing Minecraft, watching DVDs and other videos (we don't have a TV), spending ages on the Internet, and catching up on work. My wife uses it for those things too (except she prefers Plants vs Zombies to Minecraft).

2003 was the year of Linux on the Desktop for me. Has been ever since too.

Eh, I really liked GNOME towards the end of its version 2 cycle. The Mac OS ness didn't bother me at all, I thought it looked great and was really easy and nice to use. I've recently started using a Mac for work, and I'm pretty disappointed at how unimpressive it is in comparison. The way OS X handles multiple desktops seems like a total regression.

That funny row/column order in matrix indices (aka column major order) is because it's the correct mathematical order.

Consider that you can only multiply two matrices if matrix A is of size [i,j], and matrix B is of size [j,k], i.e. the number of rows in A must be equal to the number of columns in B. The product C=AB is then of size [i,k]. This works for any number of matrices, so, [i,j]*[j,k]*[k,l]*[l,m] is valid, and gives [i,m].

This naturally leads to the indexing you see in Fortran and Matlab, because it's the way mathematicians like it. If you had row major order, then [j,i]*[k,j]=[k,i], which is pretty horrible in comparison.

Thanks for the link. My problem is that there isn't any one bit you can point to and say "that's the slow bit" (unless it's telling the code which parameters to use, varying the parameters, and then graphing the results when done -- I'm currently doing those parts with bash and Octave, and to be fair I would probably be better off doing both of those in Python).

The main work is the simulation, and it's where I've got a trivially small amount of data (say a 20x20 lattice of sites containing the number of susceptible and infective animals), so I need arrays to store the numbers of individuals, the birth, death, infection, recovery, dispersal rates for each site, and one that keeps track of which sites need updating.

The bits you might think would be the slow bits (summing arrays, checking there are no groups with negative numbers of individuals, converting rate matrices into cumulative distribution functions and using a binary search to select an event) just don't seem to have that much of an effect on the performance. The only time that a part significantly stands out is when calculating dispersal across the entire lattice, rather than a nearest neighbour dispersal. The rest is just lots of small things that need to be done randomly and frequently.

I have profiled the model quite a bit, and the C code is over 300 times faster than the prototype written in Octave (taking advantage of vectorisation whenever possible, and using fast algorithms), but all the non-performance critical bits are either deeply embedded in the code (which is horrifically loopy by nature of the problem), or necessary for the rest to work. So Python isn't really going to help.

Sadly, with the exception of a few times where I get to sum an array, pretty much my whole model needs to be run in a fast language like C or Fortran (I use C, my supervisor uses F77). It's the kind of model (a spatial stochastic disease simulation) that doesn't really lend itself to coding up in Python. No matrices, just lots of little bits of data interrogation, calculating one event at a time, and so many loops (unavoidable) that it would just crawl in Python. If you try to start in Python and replace the slow bits with C, then before you know it it's more C than Python. In the end, I think doing the whole thing in C is just less work.

I do all the graphs, and the non-spatial deterministic versions in Octave (R's graphs are prettier, but R is less pleasant to use), where it does take advantage of Fortran for the ODE solver, but that's the only bit. I do generally prefer the 1-based array indexing though, the only places I've found 0-based indexing useful has been dealing with C's inability to handle multidimensional variable length arrays in an easy fashion, so I wasn't really convinced by 0-based arrays in general. Perhaps I'd have been better off with Fortran, but that's just the way it turned out.

Not American, so I don't know what a GPA is. I've got a PhD in mathematical epidemiology though, an MSc with distinction in applied maths, and I took all the subjects physically possible to take at school, and got A's in all of them. Good enough?

Meanwhile, Nintendo-Gamer (previously N-Gamer, NGC Magazine, N64 Magazine, Super Play), which I've been subscribed too since 1994 has also died.

I used to read that magazine over and over, copying the artwork, trying the cheats, spending hours which two games I was going to ask for for Christmas/my birthday (right next to each other).

Sad times.