I have a scientific data management problem which seems general, but I can't find an existing solution or even a description of it, which I have long puzzled over. I am about to embark on a major rewrite (python) but I thought I'd cast about one last time for existing solutions, so I can scrap my own and get back to the biology, or at l...
My hands have been itching to learn GPGPU programming for some time. I finally have some time on my hands so I want to use it as wisely as possible. I'm really interested in your guys experience with GPGPU programming, any pointers, references to good literature, links to sites, interesting projects etc. My interests lie mainly in scie...
I'm in the process of choosing a scientific library to use as a basis for a project. I need to do a lot of statistical, linear algebra, and signal processing tasks, and I figured there are probably some great libraries that already do this stuff better than I could program it myself. For c++, I know about Boost, but don't have much expe...
Dear all, we develop a data processing tool to extract some scientific results out of a given set of raw data. In data science it is very important that you can re-obtain your results and repeat the calculations, that led to a result set Since the tool is evolving, we need a way to find out which revision/build of our tool generated a ...
Hi, PL/I is a very old language but seemingly haven't got much publicity and appreciation as Fortran for scientific computing. Why is that? A search on the web does show that there are many PL/I codes for scientific computing. There is among others a scientific computing library which was developed by IBM in PL/I. But I haven't foun...
Hi, since Ada doesn't possess any good libraries for scientific computing, I was wondering if anyone has been able to use Matlab mathematical functions such as eig (for calculations of eigenvalues and eigenvectors) within Ada. I see that some interfaces exist for simulink and Ada. But I'm not a user of Simulink. I would like just to...
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 columns/rows, joining with other sources of data, adding calculated values and writing the result as another .tsv. The plain text is used for i...
Hi, 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 tests (ok most of them where not even version controlled). Now I'm wondering how you deal with software tests for scientific codes (numeric...
Hilbert-Huang Transform, Empirical Mode Decomposition... I have found it implemented in R and Matlab. I'd like to find an open source implementation of it in C#/F#/.NET. ...
Hello, I am working in scientific computing and developing a petsc-based application for a multi-cpu-system. For debugging purposes, I want to install that very software on my own pc, which is a dual-core system running Ubuntu (Karmic Koala). But I do not know which resources to use. There are debian packages, as well as sources-archi...
Let's say I'm writing a "DayData" class, containing the ivars NSString *symbol; //such as "AAPL" NSString *currency; //such as "USD" NSDate *day; double open; double high; double low; double close; The last four ivars are the open,high,low,close prices of that stock for that day. Say I'm using this class as the fundamental building-...
I currently use Python for most of my programming, but I'm interested in learning Clojure. What libraries do I need to reproduce the functionality I have with scipy, numpy, and matplotlib? Is there anything like the Enthought distribution? ...
I've been working with a lot of FORTRAN 77 lately, and though I had reservations at first, I now see some great qualities of the language. It is: Simple to learn (no object-oriented or functional-programming complications) Easy to read Blazing fast at number-crunching Those qualities are naturally attractive to non-programmer engine...
As part of a python simulation I have I take a 2d array and take the gradient of this array. This is done in scipy/numpy by convolving the 2d array with a filter with the appropriate weights. So my question is if I want to do this in clojure reasonably fast does it make sense to do this in pure clojure, or is it better to use a Java ...
Hello, I am going to benchmark several implementations of a numerical simulation software on a high-performance computer, mainly with regard to time - but other resources like memory usage, inter-process communication etc. could be interesting as well. As for now, I have no knowledge of general guidelines how to benchmark software (in ...
I'm trying to develop a physics simulation and I want to implement a fourth-order symplectic integration method. The problem is that I must be getting the math wrong, since my simulation is not working at all when using the symplectic integrator (as compared to a fourth-order Runge-Kutta integrator that works reasonably well for the simu...
Hello, I would like to off-load some computations from the CPU to the GPU of my cell-phone. Since OpenGL ES 2.x the GPU supports vertex and fragment shaders. How can I use the GPU to do some calculations. Are there any Getting-Started tutorials? As for now, I guess that I have to load the data in via textures render them to FBO (frame...
Anyone know of any simple Template for scientific paper which is easy to modify and looks great? So that i don't have to use several hour to find out the syntax. ...
I have a repeating signal that varies a little bit with each cycle of a process that repeats roughly every second, though the duration and the contents of each cycle vary from each other a little bit within some parameters. There are a thousand x,y coordinates for every second of my signal data. A small, but important, segment of the d...
Hello, I am developing a Finite Element System. As usual, the simulation consists of set of mesh nodes, each with a set of properties (floating-points), like for example several material properties, coordinates or physical quantities that evolve within time. You can either employ two extreme approaches: Property-wise: Maintain a sing...