Search Results for "java" - Page 14
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Showing 893 open source projects for "java"
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Javamony
A Student's Approach to the Phylogenetic Problem
Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem. Javamony is invoked as follows: java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ... Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve... -
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locsmoc
piecewise polynomial curves for genomic signals
Locsmoc produces piecewise polynomial models for one-dimensional signals of the type encountered in genomics. The project wiki contains an overview of the tool and usage examples. -
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ezBioNet is a biological modeling and simulation tool of molecular interaction that occurred in a cell. We aim that this software can be used for collecting biological data and making biological models to simulate it by biological researchers. ezBioNet can build a detailed biological model including signal transduction, enzyme kinetics, expression network, etc. It also support number of numerical analysis method to simulate the biological reaction networks.
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Modern MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Support available in Google group (https://groups.google.com/d/forum/13cmfa-openflux).
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The Self-Organizing Map Maker for Education and Research. Features include 3D-visualization of the training process, various 2D and 3D map topologies, easy extensibility to additional topologies.
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ScreeningAssistant 2 is a modular software dedicated to perform various simple and advanced chemoinformatics analysis around chemical libraries.
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Face Detect (JavaCV)
Face Detection and Facial Feature Extraction using JavaCV
A simple Face detection program using JavaCV and OpenCV . Implementing facial feature extraction and face recognition. -
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FastMap is Java based software that performs quantitative trait locus mapping for gene expression data (eQTL Mapping).
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A tool to visualize, analyze and store genomic positioning data.
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JGBA
This project is a genome browser and annotation tool in java.
This project is a genome browser and annotation tool in java. -
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An integrated bioinformatics toolkit for analysis of ChIPseq data from the Illumina DNA sequencing platform. Includes filtering, quality control, simulation, peakfinding, visualization, and comparison of samples.
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iPiG
Integrating PSMs into Genome browser visualisations
iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/). iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in text format and provides results in genome track formats (BED and GFF3 files), which can be easily imported into genome browsers. For more details about iPiG and it's functionallity, please... -
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(AB)² Simulation
Simulation for Physics / Bilogics Systems
Supports flow Simulation for Physics and Meso-Compartimental Simulations for Biological Systems. Uses a Container-Flow based System. -
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EvoPromoter is a JAVA application that detects promoter regions in aligned nucleotide sequences using phylogenetic hidden markov models.
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An IDE for CellML 1.1 user models developed in UNSW as an open source project. Author: Mitchell Lanesbury 2012
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Linking Yabi with RDA
This software system enables publication of YABI workflows to the RDA.
Modern life science research requires bringing together Biology and Information technology. To help make this process easier, the CCG has developed YABI, an Internet based workflow application that is aimed at biologists who wish to conduct bioinformatics analysis. YABI integrates bioinformatics tools and data via an intuitive workflow creation and management environment. YABI can be used to access the NCI-SF in Bioinformatics and the tools available through the Embl Australia EBI mirror... -
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Easily find and extract specific chemical reactions from the BioModels database.
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CallSim
low-volume read processing base corrector
CallSim is a software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. CallSim provides a final classification or rescue of a base/indel in reads, where putative variants have been identified via typical SNP/indel workflows. plots rendered by: JFreeChart library http://sourceforge.net/projects/jfreechart/ -
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samsn
A tool to handle multi-stage mass spectrometry data
The source code for SAMSN can be found in github at https://github.com/miquelrojascherto/samsn -
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The Blast2SNP is able to pick out synonymous, non-synonymous mutations and indels from draft assembly sequences by performing BLAST search against the reference ORF sequences.
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Linking BPA with RDA
This software system enables publication of ISA-Tab files to RDA.
BioPlatforms Australia (BPA) has funded a number of datasets generation initiatives around important research themes and scientific challenges faced by Australian researchers to provide a unique public resource for the benefit of Australian life sciences research. These large scale genomic, proteomic and metabolomic datasets are being generated and centrally managed by Bioplatforms Australia in collaboration with leading scientists, research institutes and government agencies. With the... -
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Pontos
Pontos calculates distance matrices from DNA sequence alignments.
Pontos is an easy-to-use, graphical Java program for the calculation of uncorrected distance (or similarity) matrices from DNA sequence alignments in PHYLIP format. It also creates "difference" alignments from regular ones (and vice-versa). It can handle gaps and ambiguities in different ways. Gaps can be: - all used; - all ignored; - ignored only at the ends of the sequences, in a pairwise manner; - ignored only at the ends, but now globally (in effect trimming the whole alignment... -
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mPSQed
Alignment editor and multiplex pyrosequencing assay designer
Molecular-based diagnostic assays are the gold standard for infectious diseases today, since they allow a rapid and sensitive identification and typing of various pathogens. While PCR can be designed to be specific for a certain pathogen, a subsequent sequence analysis is frequently required for confirmation or typing. The design of appropriate PCR-based assays is a complex task, especially when conserved discriminating polymorphisms are rare or if the number of types which need to be... -
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Evoker is a graphical tool for plotting genotype intensity data in order to assess quality of genotype calls. It implements a compact, binary format which allows rapid access to data, even with hundreds of thousands of observations. PLEASE NOTE: This source repository is no longer active. See the github link above for the latest version.
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