Search Results for "c programming"

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.

...There is a bunch of free programs on the internet for the same purpose. What discriminate between PDBManip and those programs is that PDBManip uses AngelScript language which is very similar to C/C++ language, to write scripts to do our editing tasks. I know that the text-manipulation script languages such as Awk and Perl are available, and many users, uses these to do their works. However, in developing PDBManip, I have customized scripting language, by adding predefined PDB related variables and functions, in such a way that a user with a very basic knowledge of programming can easily write very eligible scripts, even for very complicated editing and manipulating tasks. ...

ShuffleFastaSeq is a Windows form application, written in C#, to shuffle FASTA-formatted sequences. The random permutation is obtained using a simple variation of the Fisher-Yates alghorithm implemented by Durstenfeld (https://en.wikipedia.org/wiki/Fisher%E2%80%93Yates_shuffle) ( Knuth DE. The art of computer programming: seminumerical algorithms. 3rd ed. Boston: Addison-Wesley; 1997). The input file contains one or more sequences in FASTA format.

This program implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences.

HeatmapGenerator is a graphical user interface software program written in C++, R, and OpenGL to create customized gene expression heatmaps from RNA-seq and microarray data in medical research. HeatmapGenerator can also be used to make heatmaps in a variety of other non-medical fields. HeatmapGenerator is peer-reviewed published software (http://www.scfbm.org/content/9/1/30). Please cite: [Khomtchouk et al.: "HeatmapGenerator: High performance RNAseq and microarray visualization...

SMALT aligns DNA sequencing reads with genomic reference sequences. It employs hashing combined with dynamic programming.

This software detects homologous recombination events (HREs) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of...

The SBML ODE Solver is a command-line tool and programming library (ISO/ANSI C) for construction and numerical integration of an ODE system, derived from an SBML based description of a biochemical reaction network. Development has moved to https://github.com/raim/SBML_odeSolver . Please download the latest version from there!

Sehr Gut Libs (sglibs) is a set of utility libraries for general and scientific programming. It includes stack and string manipulation, CGI I/O, config file parsing, and sequence-processing for molecular biology.

Genetic programming environment to inference context free grammars base on positive and negative examples of language.

JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.

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

A CUDA parallel parser for nondeterministic grammars based on a Bison-generated GLR Parser. Parsing has been used to syntactically analyze programming language. Usually, parsing programming languages is deterministic, i.e., there exists exactly one valid way to syntactically interpret the input. In this project, non-deterministic parsing is used as means to predicting RNA secondary structures. In non-deterministic parsing, more than one syntactic interpretation is valid. This is where...