Search Results for "basic programming software"
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Showing 27 open source projects for "basic programming software"
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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.
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
...All software developed for EvidentialGene is publicly available. See project wiki/blog for notes. -
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The source code has been migrated and is now hosted on Github: https://github.com/jenetics/jenetics Jenetics is an advanced Genetic Algorithm, Evolutionary Algorithm and Genetic Programming library, respectively, written in modern day Java. It is designed with a clear separation of the several algorithm concepts, e. g. Gene, Chromosome, Genotype, Phenotype, Population and fitness Function. Jenetics allows you to minimize or maximize the given fitness function without tweaking it. In...
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CSBB-v3.0
CSBB - Computational Suite for Bioinformaticians and Biologists
CSBB is a command line-based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java, python and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux,... -
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WrapImaJ
Multi-platform API for Image Processing systems in Life Sciences
WrapImaJ purposes to be a multi-platform wrapper for different Image Processing systems for: - using the Java programming language. The purpose of WrapImaJ is not to combine an exhaustive collection of all functionalities of different imaging system, but to offer a simple, concise Application Programming Interface (API) - allowing to develop imaging software, the source code of which is independent from the underlying imaging system on which it relies. ... -
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JBioFramework
Growing suite of proteomics simulations for educational purposes
JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. As we continue to develop the software over the coming months/years and attempt to quantify the success of our efforts with testing and reviews, user input is very important. Please don't hesitate to review the software below or email Paul Craig [pac8612@rit.edu] with larger descriptions/bugs/feature ideas. ... -
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owl reasoning over big biomedical data
A OWL reasoning framework for the analysis of big biomedical data
A general OWL reasoning framework for the analysis of big biomedical data and implement a MapReduce-based property chain reasoning prototype system. OWL reasoning method is ideally suitable for problems involved complex semantic associations because it is able to infer logical consequences based on a set of asserted rules or axioms. MapReduce framework isused to solve the problem of scalability. In our experiment, we focus on the discovery of associations between Traditional Chinese Medicine... -
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Phanto_maJ
build three dimensional structure
PhantomaJ is a software which aims to help users designing complexe three dimensional structures and building phantom banks. This software, implemented as an ImageJ plug-in, has been designed to be intuitive. PhantomaJ is thus "ready to use" for most users, but advanced users can choose to modify specific parameters such as intersection mode, intensity decrease function or virtual real three dimension. -
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JGAP is a Genetic Algorithms and Genetic Programming package written in Java. It is designed to require minimum effort to use, but is also designed to be highly modular. JGAP features grid functionality and a lot of examples. Many unit tests included. Legal notice/Impressum: Klaus Meffert An der Struth 25 D-65510 Idstein sourceforge <at> klausmeffert.de
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Your monitoring isn't a stack. It's a pile. Fix that.Replace Datadog, New Relic, and Sentry without adding three more dashboards.
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math lib for .NET. n-dim arrays, complex numbers, linear algebra, FFT, sorting, cells- and logical arrays as well as 3D plotting classes help developing algorithms on every platform supporting .NET. Sources from SVN, binaries: http://ilnumerics.net
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BAIT
Software to help analyse Strand-Seq data
Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. -
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locusvu
Tool for genomics;automates data retrieval from db;enables workflows
...The tool can be easily extended to add support for other databases (eg. Ensembl) or to fetch information from other tables in the database. Thus, LocusVu provides a basic framework that can be used by users and developers alike in simplifying existing workflows and creating newer ones to support data analysis in genomics. -
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hrefinder
Detection of homologous recombination events from SNP data
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. -
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Pysimony
A Pythonic Implementation of Parsimony Inference of Phylogeny
...I have clearly avoided object-oriented programming. Nevertheless, I distribute this imagining it might someday be slightly educational or at least provide a laugh at the pathetic attempt it makes to reinvent the wheel -
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OptimizeSNP
Selects SNPs and samples with known genotypes for microarray design
...I obtained AMPL from trial version of MOSEK at http://www.mosek.com/. CPLEX 12.0 can be obtained from http://www-01.ibm.com/software/integration/optimization/cplex-optimizer/. A free acadamic license can be obtained by filling out IBM academic initiative application. -
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Basic Electronical Medical Management (BEMM) is an application to control medical data of a set of patients. It is built on top of open source technologies, to provide an integration skeleton of mvn, Datanucleus, Spring, Vaadin, Acceleo technologies.
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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.
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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!
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A repository linking to eight Bioinformatics Resource Centers (BRCs) sponsored by the NIAID. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of bioterrorism
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HZL Beta 2 is the updated version of a software application based on MS-Access, designed to manage and digitize botanical and zoological collections.
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EXPR is a software package for the recording and analysis of animal behaviour. Recording is done by pressing particular keyboard keys on the computer. The software then saves the sequence and timing of behaviours. Note that the DOS (1995: https://sourceforge.net/projects/expr/files/expr/fb-port-expr-00-1995/EXPR-binary-DOS-0.0.1995.tar.gz/download) version is currently the only fully functional and is recommended for use. On modern computers, DOS software can run in DOSBOX (https://www.dosbox.com/).
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Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.
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Protein Mass Spectrometry: cprobid is a software for identification peptides from MS/MS spectra. The output of this program is compartable with TransProteomic Pipeline software package (sashimi project).
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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.
