Search Results for "simple-xml"

A header file (cexcept.h) that provides Try/Throw/Catch macros similar to those available in C++ for error handling.

CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files.

Wordom is a (simple) command line utility conceived to spare the user some time in manipulating, converting and analyzing molecular structure and molecular simulations files. Due to its simplicity, it is easy to add your own analysis module.

The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.

September 2021: the code repository has migrate to https://github.com/UWPR/Comet Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are tab-delimited text, Percolator pin, SQT, and pepXML Documentation and project website: http://comet-ms.sourceforge.net

MAGeCK2 is here: https://github.com/davidliwei/mageck2 Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at...

The ChIP-Seq software provides methods for the analysis of ChIP-seq data and other types of mass genome annotation data. The most common analysis tasks include positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-depleted regions.

Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project. MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data....

FieldTrip is the Matlab toolbox for EEG and MEG data. It includes algorithms for simple and advanced analysis, such as importing, preprocessing, time-frequency analysis, source reconstruction, statistical testing and connectivity analysis.

RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.

Dynamis is a simple ODE solver implemented in C for studying dynamical systems (e.g. population biology).

Diva is a command-line tool for dispersal-vicariance analysis, a simple method for inferring the distributional history of organisms (Ronquist, F. 1997. Systematic Biology 46:193-201).

This library is a lightweight implementation of genetic algorithm, contains the most popular types of chromosomes and the basic algorithms for selection, elitism, crossing and mutation.

HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.

Simple static viewer of abnormal read pairs in second-generation alignment data.

CellMC is a multi-platform XSLT-based SBML compiler producing executable SSA models based on the optimised direct method.

Neurospaces is a development center for tools in computational neuroscience. See http://www.neurospaces.org/

Simple console program intended for factor or principal components analysis. It calculates the optimal number of factors using the Horn's parallel analysis, computes the Kaiser-Meyer-Olkin and a few other measures of sampling adequacy.

A tool to calculate atoms exposition to a probe in a three dimensional molecule structure.

runsbml - Pathway Simulation Tool emulates the dynamics of biological pathways by calculating concentrations of biochemical compounds at different times and conditions.

UltraLife simulates Conway's Game of Life, either automatically or one step at a time, with the ability to detect stable patterns and simple repeating states. It also simulates other cellular automata systems.

Sphinx Os is a 32-bit kernel with a simple GUI Made mainly for experimental purposes and fun too

Distributed Genetic Programming SRVM (Simple Risc Virtual Machine) Distributed function approximator of nonlinear functions with automatic induction of machine code.