Search Results for "gene"

MCScanX is a toolkit for detecting gene synteny and collinearity, aiding in the evolutionary analysis of gene arrangements across multiple genomes. It extends the original MCScan algorithm by incorporating additional utilities for visualization and downstream analyses.

...Whether it's a public cloud, private cloud, or hybrid cloud, JuiceFS is available on any cloud of your choice and delivers flexibility, availability, scalability and strong consistency for your data-intensive applications. Purposely built to serve big data scenarios such as self-driving model training, recommendation engine, and Next-generation Gene Sequencing, JuiceFS specializes in high performance and easier management of tens of billion of files management. We bring JuiceFS to developers with the hope that it will be easy to use, reliable, high-performance, and solve all your file storage problems in a cloud environment.

This package includes a few programs for rapid functional annotation for metagenomic sequences, including, 1) Gene prediction by FragGeneScan; 2) Similarity search by RAPSearch2; 3) Functional annotation in GO (Gene Ontology) and EC (Enzyme Commission) based on similarity search results; 4) From EC to metabolic pathway reconstruction by MinPath. Inputs: Just sequencing reads (or assemblies) Outputs: Protein-coding genes (or gene fragments); similarity search; functional annotations (in GO and EC); metabolic pathways.

Open|SpeedShop is an open source multi platform Linux performance tool which is targeted to support performance analysis of applications running on both single node and large scale IA64, IA32, EM64T, AMD64, PPC, Blue Gene, ARM and Cray platforms.

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 contrast to other GA implementations, the library uses the concept of an evolution stream (EvolutionStream) for executing the evolution steps. Since the EvolutionStream implements the Java Stream interface, it works smoothly with the rest of the Java Stream API. ...

GAKNN is a data mining software for gene annotation data. GAKNN is built with k- Nearest Neighbour algorithm optimized by the genetic algorithm. Gene annotation datasets saved under .csv or .arff formats with Gene Ontology or FunCat categorization can use GAKNN to predict gene functions.

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 software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline." ...

...This may be useful to reverse-engineer human constructs like electronic equipment, manufactured machines, or bureaucratic hierarchies; but also to decompose natural constructs like gene-relation or protein-relation nets.

The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

This software provides a hybrid GO-based semantic similarity algorithm for evaluating the functional similarity between GO terms or gene products. The software uses the pre-downloaded GO database files and the GO annotation files. It allows the users to set organisms, and evidence codes ignored. The software is composed of five modules, getGODAG, getGOAnno, hrssmatrix, hrsstps and hrsspps.

TOPS provides the benchtop scientist with a free toolset to analyze, filter and visualize data from functional genomic gene-gene and gene-drug interaction screens with a flexible interface to accommodate various different technologies and analysis algorithms in addition to those already provided here.

Hoea is a python module for hierarchical ontology enrichment analysis, which facilitated GO (Gene Ontology)/KO (KEGG Orthology) enrichment analysis at any desktop.

This is a multi-select tree widget for tkinter for python. This is an extension of Gene Cash's Tkinter tree widget (available from http://home.cfl.rr.com/genecash/) which works with python 2.5 as well as Python 3k.

The Gene Expression Programming Framework in Java. It separates the process of evolution from the process of interpretation of the chromosome, allowing the use of various schemes in the chromosome.

Conrad is both a high performance Conditional Random Field engine which can be applied to a variety of machine learning problems and a specific set of models for gene prediction using semi-Markov CRFs.

SORGE; a visualisation tool for the activity and structural hierarchy of chromosomal, genomic, and gene annotation