Benetech Human Rights Program Utility Library: Collection of utilities used by the Benetech Human Rights programming for processing human rights data in preparation for statistical analysis. Library handles DSV files, name canonicalization, binarray, et
ModelicaFloChrt is a script/Perl process that extracts information from Modelica library html help files and generates flow charts of module connectivity in eps and pdf formats.
Derive copy number status from targeted sequencing data
CoDeCZ derives copy number state from targeted sequencing data on gene or exon level. Results are NOT true copy number however, but they are semi-quantitative: It uses the modified z-score to calculate deviation in normalized coverage per specified region. The higher the Z-score, the higher the copy number. The final z-score depends on the quality of the data and the makeup of the reference pool.
An End-to-End Analysis Pipeline for BS-seq
BSpipe is a comprehensive pipeline from sequence quality control and mapping to functional analysis of differentially methylated regions: (1) sequencing quality assessment, (2) sequence cleaning, (3) sequence read mapping, (4) methylation quantification, (4) sample comparisons based on methylation profile, (5) identification of DMRs (differentially methylated regions), (6) annotation of DMRs, (7) functional analysis of differentially methylated genes, (8) generation of input files for visualization, and (9) support for advanced sequencing technologies such as TAB-seq, OxBS-seq, MAP-it, and NOMe-seq.
TechnoForge aims to be a website operated for the purpose of fostering hardware development and technical documentation creation under Open-Source Initiative -approved licenses or other arrangements relating to hardwware and/or documentation development.
This project is for particle accelerator start-to-end simulation. The project contains software infrastructure for setting up model run as service/client mode.
TrimAl is a bioinformatic tool that cleans multiple protein or nucleotide sequence alignment. The clean alignment (as a result of the TrimAl cleaning process) is used for phylogenetic reconstruction. TrimAl improves the quality of the reconstructed trees
FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.
NIKS (Needle in a K-stack) - detection of mutations in NGS data
To get access to the code, please check it out with svn as described in the code section.
Boolean Expression Solver is a command-line utility that generates a truth table for a given Boolean expression.
Very basic RRDtool tutorial. It is an example in that way. It can save you a couple of days of discovering on your own. In any case you have to read the manual _before_ that ;)
A service-oriented, single-source, Java integration server with virtual Service Stores(TM) that expose services via web services, HTTP and more. Service Flows provide process automation. Mainframe, database, email, web, soap & ftp adapters are included.
Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.
CTAS package is a set of tools for the Computed Tomography (CT) and Tomosynthesis (TS) reconstruction for the parallel beam geometry (usually available at the synchrotron sources).
miscelaneous c++ code, scripts, commands, in matters as radar, signal processing, realtime gnuplot, 2D/3D graphics
Command Line Office (Console Office) a collection of tools (shell scripts) providing a range of every-day's tasks to be conveniently performed on the command line, like email, file, document, dictionary lookup (many with colored highlighting features)
pipestatus - source file for UNIX/POSIX shell that allows to obtain an exit status of every program in a pipe.
CDS plots and analyzes output from numerical climate models. It is capable of comparing climate model simulations and/or observational data. It consists mostly of a series of MathWorks Matlab language scripts and reads data in NetCDF format.
Chemiinformatics: ND qsar -- dimensions involved in biological activity are more than the tree dimensions our mind can easily perceive.
HPC cloud computing for OpenFOAM (R) users
Bioinformatic tools for analyzing an orfeome using translated ORFs and compares each ORF to the provided Orfeome/Proteome. Our script uses NCBI BLAST run locally and MySQL as the main engines in a new and interisting way. It is designed specifically for Poxvirus genomes, and provides the VACV-COP nomenclature and Cowpox Ortholog groups per each ORF. The BLAST stats are generated when compared to the Proteome you provide. It can be easily adapted for other genomes.
The developed graphical interface is based on the SKILL language which is a Lisp dialect used as a scripting language and PCell (Parameterized Cells) description language used in many EDA software suites by Cadence Design Systems.
Integrator for gEDA (GPL EDA) Suites & Bridge gEDA to Kicad
Gschem-finalizer is free & open source EDA-tool to finalize gEDA-gschem schematic project. It integrates several programs such gEDA (gschem, gnetlist, and NG-SPICE), GNU a2ps, psutils, and some basic GNU/Linux or UNIX programs. This software is written based PHP language & running on GNU/LINUX OS variants & UNIX OS variants. Features: 1. Generate netlists (SPICE 3F5, GEDA PCB, Kicad PCB/EESchema) 2. Pre-testing (additional DRC) 3. Result multi-pages in single file PDF output compilation with operating point description. 4. "Smartly" generate SPICE netlist for analog, digital, or mixed analysis simulation. 5. Generate Kicad netlist from gEDA schematic format. & More... See the manual for more info (http://gschemfinalizer.sourceforge.net/) The example of results are available at http://sourceforge.net/projects/matrix14freeamp/files/
ChesROMS is developing a ROMS model of the Chesapeake Bay to help in the prediction of Harmful Algal Blooms. We hope to catalyze a new method of community modeling with involvement beyond the core researchers of the ChesROMS project.
parastructure is a perl script collection to run the population genetics software STRUCTURE from Pritchard et al. 2000 (http://pritch.bsd.uchicago.edu/structure.html) in parallel on a cluster (beowulf type). Each run of K (the number of populations) is executed separately on each CPU of the cluster trough queue system based on PBS. A summary statistics table and distruct figures (Noah Rosenberg: http://www.stanford.edu/group/rosenberglab/distruct.html) are built at the end of the run. A patch for the structure (ran.c) is also provided in order to correct the generation of the seed number.