This tool, described in the July 2006 issue of IEEE Computer, determines how many servers to install such that average request response time is 'x' number of seconds. The tool is a Java application that is used for server sizing efforts.
Handy tools to process/analyze next generation sequencing (NGS) data
The NGS TOOLBOX is a collection of simple open source Perl scripts that perform basic analyses and processing steps using next generation sequencing (NGS) datasets. Each tool is designed to ensure convenient and intuitive usage. Installation and usage does not require any bioinformatics skills. All scripts work out-of-the-box. Advanced users may use the command line based Perl scripts to build automated sequence analyses/processing pipelines. If you use the NGS TOOLBOX you for publication purposes you can cite the following methods paper: Rosenkranz D, Han CT, Roovers EF, Zischler H, Ketting RF. Piwi proteins and piRNAs in mammalian oocytes and early embryos: From sample to sequence. Genomics Data 2015 5:309-313.
OpenGrowth is a program which constructs de novo ligands for proteins.
OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments. The details can be found in the original publication "OpenGrowth: an automated and rational algorithm for finding new protein ligands" (J. Med. Chem., http://dx.doi.org/10.1021/acs.jmedchem.5b00886). To use OpenGrowth, you will need OpenGrowth_1.0.zip and Resources_1.0.2.zip that can be found by clicking on the Files menu in the horizontal bar at the top (https://sourceforge.net/projects/opengrowth/files). OpenGrowthGUI, FOG2.0, and the 3Mer-Screen stand-alone can be found in OpenGrowth_1.0.zip. To prepare new fragments you need BuildingFragments_1.0.1.zip and the scripts for MD simulations are in MD-Scripts_1.0.1.zip. SMoG2016.tar.gz allows to compute a score with the newly developed function (J. Chem. Inf. Mod., http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00610). For any questions, please send emails exclusively at email@example.com.
Production (3 level) Programmer for Microchip PIC on Win9X,DOS,NT,Win2K. Flash and Eprom, 14 and 12 bit devices. Printer Port programmers and the BEL In-circuit Dual PRODUCTION Pic Programmer board.
PSRCHIVE is an application suite and development library for use in the storage and analysis of pulsar astronomical data. It includes an extensive range of algorithms and tools commonly used in a wide variety of experiments.
SAMP contains a few helpful math functions. Very helpful with Geometry and Triginometry! There are two different options for the interface, command line or GUI. However, the GUI is still in development. SAMP runs on most Windows machines and some Linux
Development of new data assimilation techniques for ocean models
ShoX is a scalable simulator for wireless networks written in Java. It is easy to install, configure and use, so that reliable and expressive scientific results can be gathered in a short time. Documentation: http://sourceforge.net/apps/mediawiki/shox
ThanDxflib is a library, written in Fortran 77, which makes the creation of .dxf drawings easy. The dxf files may be read by any CAD program.
DNA sequencing quality values, base calling and trace processing
Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Originally developed by Paracel, a Celera Business, this code base was released as open source in 2006. TraceTuner was used by Celera to call 30+ million reads from both Drosophila and human genome sequencing projects. In 2000, Applied Biosystems bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the customers of these capillary electrophoresis sequencers. Later versions of TraceTuner, which support mixed base calling, have been used by the research community, the private biotech sector, and the U.S. government as components of different variant detection, genotyping and forensic software applications (e.g. Applied Biosystems SeqScape, Paracel Genome Assembler, MTexpert, etc.).
wRASP is a Windows program that simulates the flight of a rocket in one dimension (one degree-of-freedom). It can be used to get an idea of how high a rocket kit might fly with a particular motor and what the best ejection delay time might be.
This package collects and displays Oregon Scientific weather data.
WxTools (Weather Data Tool Suite) is a collection of software for collecting and displaying weather data from Oregon Scientific weather stations (though the code could be generalised for other weather data sources). The software works with the Oregon Scientific WMR180 weather station (and probably also similar models such as the WMR88 and WMR100) as well as the older WMR928. Sample weather data is provided.
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.
AMoRE is a collection of algorithms that deal with automata, monoids, regular expressions. Learn about the theory - this is not another regexp package.
Astro Info is a multi-lingual astronomical ephemeris for the PalmOS that provides data for our solar system and other objects. If you wish to get involved, please download a copy of the source code from CVS.
Generates highly configurable bohr models
Generates highly configurable bohr models in any resolution for all elements. You can export all bohr models as a specific format in a click of a button. Requires .NET Framework 4.5
Step-by-step instructions for making your HVAC (Heating, Ventilation & Air Conditioning) system state-of-art. Covers airflow balancing, temperature control & zoning, energy conservation measures, remote access, 1-wire, XBee devices, home automation
FcaBedrock is a tool for creating context files for Formal Concept Analysis. It can convert existing data sets in flat-file CSV or 3-column CSV, to Burmeister (.cxt) or FIMI (.dat) context files.
A tool for directed ortholog search in ESTs and proteins
HaMStR is a profile hidden Markov model based tool for a directed ortholog search in EST or protein sequence data. The program takes a pre-defined core group of orthologous sequences (core orthologs) and a set of sequences from a search taxon as input. HaMStR then combines in a two-step strategy a pHMM based search and a reverse search via BLAST to extend the core ortholog group with novel sequences from the search taxon.
The purpose of the project is to build a world class open source Enterprise integration engine. <br>Uses of JEngine include healthcare systems/hospitals HL7 interface engine, intergration of HL7 with EMR and Practice Management Systems.
This code performs the finite volume numerical simulation of a general integrate and fire neuron model driven by a stochastic direct current input.
A MATLAB spectral clustering package to handle large data sets (200,000 RCV1 data) on a 4GB memory general machine. We implement various ways of approximating the dense similarity matrix, including nearest neighbors and the Nystrom method.
Pascal Units for Medical Applications
The PUMA Repository is a collection of Pascal units for medical informatics. It contains reusable source code for a wide field of health-care application development. The code includes converting functions for measurement units and an HL7 engine. PUMA is compatible with Lazarus and Free Pascal. Some of the units also support other Pascal implementations including Delphi, winsoft Pocket Studio and other compilers.