I'm running experiments on a model, with a workflow like this: I work in a model (a software in Python) I change some parameters and run an experiment Then, I will store the results of the experi...

EDIT One option I contemplated but don't know enough about is to e.g. for windows write a batch script to: Search for a Python installation, download one and install if not present Then in...

The new Scipy v0.11 offers a package for spectral analysis. Unfortunately the documentation is sparse and there aren't many available examples. As a baby example, I'm trying to do period discovery...

I have been trying to process a good chunk of data (a few GBs) but my personal computer resists to do it in a reasonable time span, so I was wondering what options do I have? I was using python's c...

I have a book called "Scientific Programming with Python (2009)", in which example code makes heavy use of SciTools. I use Python 3.2 64 (thinking about having a parallel install / development envi...

I'm convinced that software testing indeed is very important, especially in science. However, over the last 6 years, I never have come across any scientific software project which was under regular...

I just took my first baby step today into real scientific computing today when I was shown a data set where the smallest file is 48000 fields by 1600 rows (haplotypes for several people, for chromo...

I would like to use the Windows Calculator in Scientific Mode in order solve a very basic Logarithm equation but, unfortunately, I couldn't do that. Here is the problem: log_5 125=? Thank...

What are the simplest way to use all cores off a computer for a python program ? In particular, I would want to parallelize a numpy function (which already exists). Is there something like openmp u...

I am dealing with large amounts of scientific data that are stored in tab separated .tsv files. The typical operations to be performed are reading several large files, filtering out only certain co...

Are parts of NumPy and/or SciPy programmed in C/C++? And how does the overhead of calling C from Python compare to the overhead of calling C from Java and/or C#? I'm just wondering if Python is a...

I'm developing a Monte Carlo simulation software package that involves multiple physics and simulators. I need to do online analysis, track of the dependency of derived data on raw data, and perfor...

I often hear people complain how expensive MATLAB licenses are. Then I wonder why they don't just use Octave or R. But is the latter right? Can you use R to replace MATLAB?

I've currently got a project running on PiCloud that involves multiple iterations of an ODE Solver. Each iteration produces a NumPy array of about 30 rows and 1500 columns, with each iterations bei...

I'm using C++ to perform scientific simulation on some things. At this moment, due to the increasing number of parameters, I found necessary to have a "logbook": a file where all the information ab...

Basically I'm interested in knowing if there exists any openGL 3D visualization toolkit for C for scientific uses?

I need to compare some theoretical data with real data in python. The theoretical data comes from resolving an equation. To improve the comparative I would like to remove data points that fall far ...

I'm looking for a Sparse Matrix library I can use from Ruby. I'm currently using the GNU Scientific Library bindings provided by the "gsl" gem, but my application would be better optimized if I use...

I am writing a code which had long mathematical equations with many trigonometric and other identities. Is there a way of visualising the same expression in latex and making a C or python expressio...

I need to solve nonlinear minimization (least residual squares of N unknowns) problems in my Java program. The usual way to solve these is the Levenberg-Marquardt algorithm. I have a couple of ques...

I'm using scipy.optimize.curve_fit, but I suspect it is converging to a local minimum and not the global minimum. I tried using simulated annealing in the following way: def fit(params): return...

I develop a scientific application (simulation of chromosomes moving in a cell nucleus). The chromosomes are divided in small fragments that rotate around a random axis using 4x4 rotation matrices....

How can I segment cells from an image taken on a microscope, along the lines of what was done here in Matlab? http://blogs.mathworks.com/steve/2006/06/02/cell-segmentation/ Also, if I take ...

I am interested in getting my hands dirty with numeric computation using Microsoft's Direct Compute framework. The whole concept seems to be a rather poorly documented business. Are there any usef...

The code below solves the 1D heat equation that represents a rod whose ends are kept at zero temparature with initial condition 10*np.sin(np.pi*x). How are the Dirichlet boundary conditions (zero...