A simple command to convert calendar dates to julian dates. Quite useful in timing situations where you need elapsed time between dates. Also useful for astronomy applications.
An open-source software aimed at unsupervised molecular alignment
SIGPROC - a collection of signal processing programs developed for pulsar data reduction has been developed and maintained since 1999. The package is used to search for and visualize the presence of pulsed signals in noisy radio astronomy data.
ferite is a modern, lighweight, portable, threadsafe scripting engine with a language that is very easy to pick up and leverage for any task. It\'s been designed for rapid deployment in other programs as well as stand alone use.
Chryzodus is a chryzode renderer using Allegro graphics library. Chryzodes are mathematically rendered images which are graphical representations of mathematical operations and relations between numbers. This is a proof maths can be incredibly beautiful !
Tomahawk is a command line utility that supports high speeds bidirectional replay (300-750 Mbps) of saved tcpdump(8) files. Tomahawk is great for testing the throughput and blocking capabilities of network-based intrusion prevention systems (NIPS).
Calculation of radiation view factors by adaptive integration. A cross-platform port of the public-domain code by George Walton.
Bisulfite alignment On Nodes of a cluster
Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2. Multiple compute nodes are not absolutely required, but will make the alignment process faster. Further details available on the Wiki page. Help also available on SEQanswers (http://seqanswers.com/forums/showthread.php?t=31314) or by creating a ticket here. You can now track the development on github (https://github.com/dpryan79/bison). There is now a tutorial available in the downloads here: http://sourceforge.net/projects/dna-bison/files/bison_tutorial.tar.gz/download .
msb is a program for encoding and decoding data to and from magnetic stripe binary according to the format specified in the ISO/IEC 7811 standards (Identification cards -- Recording technique).
PyRPL turns your Red Pitaya into a powerful analog feedback device.
The Red Pitaya is a commercial, affordable FPGA board with fast analog inputs and outputs. This makes it useful for quantum optics experiments, in particular as a digital feedback controller for analog systems. Based on the open source software provided by the board manufacturer, PyRPL (Python RedPitaya Lockbox) implements many devices that are needed for optics experiments with the Red Pitaya. PyRPL implements various digital signal processing (DSP) modules (see features below). It allows to arbitrarily interconnect the available DSP modules and retrieve signal values on timescales below 1 ms. The graphical user interface (GUI) provides a realtime display of the various measurement instruments and allows the easy configuration of DSP signal chains and feedback controllers. At the highest abstraction level, arbitrary feedback sequences can be defined to fulfill tasks as complex as approaching and locking a resonance of a high-finesse Fabry-Perot cavity (tested up to finesse=100,000).
The project has moved to GitHub: https://github.com/pixmeo/osirix
This is a suite of mathematical software solvers GUI
This is a suite of mathematical software solvers interface on DLV and other command-line solvers. It helps researchers and students to better comprehend their declarative definitions published on papers. The user can have links to the related papers and to the software of the corresponding definitions.
Lush is a Lisp dialect with extensions for object-oriented and array-oriented programming. Lush is intended for prototyping numerically intensive applications and is designed for easy integration of existing C/C++/Fortran codes.
The repository was moved to GitHub https://github.com/htrb/ngraph-gtk Japanese web page http://hito.music.coocan.jp/ngraph/ngraph-gtk.html
codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction. Given a set of species characterized by their DNA sequences as input, codonPhyML will return the phylogenetic tree that best describes their evolutionary relationship. Our paper describing codonPhyML has been published in the journal "Molecular Biology and Evolution" (MBE). For more details, follow the link: http://mbe.oxfordjournals.org/content/30/6/1270. codonPhyML is on the cover of MBE! Check this out (August 2013): http://mbe.oxfordjournals.org/content/30/8.toc. For the multimodel version of CodonPhyML, please use the 'codonphyml_multi.tgz' tarball.
manual da gsl em pt-BR
Manual da Gnu Scientific Library em português do Brasil. O manual possui código fonte no formato texinfo.
open2300 - reads/writes data from the Lacrosse WS2300 family of weather stations. Includes tools that send data to: logfiles, webpages with graphs, XML file, MySQL, Weather Underground, Citizen Weather. Library of 50+ functions for your own programs (C)
Checkpoint/Restart functionality for Linux processes
DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S. It works on most Linux applications, including Python, Matlab, R, GUI desktops, MPI, etc. It is robust and widely used (on Sourceforge since 2007). Among the applications supported by DMTCP are MPI (various implementations), OpenMP, MATLAB, Python, Perl, R, and many programming languages and shell scripting languages. With the use of TightVNC, it can also checkpoint and restart X-Window applications. The OpenGL library for 3D-graphics is supported through a special plugin. It also has strong support for HPC (High Performance Computing) environments, including MPI, SLURM, InfiniBand, and other components.
Mathematics script language for ODE and FE on Linux
Hmd is mathematics software for numerical computation of ordinary differential equations and finite elements. It has a console script interpreter, as well as a graphical interface script interpreter, for entering equations and statements, and a line plot display.
pfcalc is a pipe friction calculator using the Darcy-Weisbach equation. gpfcalc is a Gtk front-end for pfcalc. Qpfcalc is a Qt front-end for pfcalc.
eXtace is a 3D audio visualization tool (or eye candy depending on how you look at it). eXtace requires ESD (Esound) for its sound input source. It performs a FFT (fast fourier transform) on audio and displays it via various graphical modes.
The new site is at http://psychometricon.net/libirt/
The new site is at http://psychometricon.net/libirt/ Library of functions to estimate the items and abilities from the responses of subjects to a questionnaire. The IRT models supported are the logistic model, the multivariate logistic model, the graded model and smoothing by penalization and kernel.
GoAccess is a real-time Apache web log analyzer and interactive viewer that runs in a terminal and provides fast and valuable HTTP statistics for system administrators that require a visual report on the fly.
OpenTCP is a highly robust and portable implementation of the TCP/IP and Internet application-layer protocols intended for those who want to implement TCP/IP functionality in truly resource constrained environments (8/16-bit MCUs).
Pattern-based multi/many-core parallel programming framework
FastFlow is a C/C++ programming framework supporting the development of pattern-based parallel programs on multi/many-core, GPUs and distributed platforms. FastFlow run-time is built upon non-blocking threads and lock-free queues. Thanks to its very efficient CAS-free communication/synchronization support (e.g. few clock cycles core-to-core latency), FastFlow effectively supports the exploitation of fine grain parallelism, e.g. parallel codes managing very high frequency streams on commodity multi-core. FastFlow works on x86, x86_64, PPC, ARM, and Linux, Mac and Win XP/7. From Jan 1, 2018 code development migrated on GitHub at https://github.com/fastflow/fastflow