Search Results for "java projects on linux" - Page 13
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Showing 792 open source projects for "java projects on linux"
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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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A tool to visualize, analyze and store genomic positioning data.
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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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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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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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EvoPromoter is a JAVA application that detects promoter regions in aligned nucleotide sequences using phylogenetic hidden markov models.
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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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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... -
Rezku Point of SaleRezku is an all-inclusive ordering platform and management solution for all types of restaurant and bar concepts. You can now get a fully custom branded downloadable smartphone ordering app for your restaurant exclusively from Rezku.
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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.
...R would be 0.5 different from A or G); - ignore ambiguities in each pairwise comparison; - remove all columns, globally, that show any ambiguity. Pontos was written in Linux, but should run in any system where Java works. Pontos is licensed under the GPL version 3. -
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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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JFinisher
JFinisher is software for alignment, editing and manipulation DNA seqs
JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and... -
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TRMSim-WSN (Trust and Reputation Models Simulator for Wireless Sensor Networks) is a Java-based simulator aimed to test Trust and Reputation models for WSNs. It provides several Trust and Reputation models and new ones can be easily added.
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SemaRule Navigator is an Integrated Suite of Open-Source and Free-License Software, placing Semantic and Text Analysis Technologies in the toolbox of Researchers, Students, and Enterprises.
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Index biological data (genbank sheets, Uniprot...) in a Solr indexer, with index shard support and provides a query interface. Project goal is to create a virtual image with indexer and web interface to query and visualize biological data.
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Lindenmayer ist ein Programm zur Visualisierung von L- bzw Lindenmayer-Systemen mittels hübscher Baumgrafiken. Die ausführbaren Dateien und Hinweise zum Quellcode finden Sie auf unserer Homepage unter http://lindenmayer.berlios.de/.
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Phenex is an application for annotating taxa and phenotypes in character matrix files with ontology terms. Phenex saves ontology annotations alongside traditional character matrix data using the NeXML format standard for evolutionary data. Current Phenex development is taking place at GitHub: https://github.com/phenoscape/Phenex
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ATOM is an OMERO client which allows automated import of image data into OMERO. ATOM is provided as is without any guarantees or warranty. The author is not responsible for any damage or losses of any kind caused by the use or misuse of the programs.
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Screensaver is a Lab Information Management System (LIMS) for high-throughput screening of small molecule and RNAi biological assays. It is a Java/JSF/Hibernate/Spring web application that is actively being developed and used at Harvard Medical School. Note: The Screensaver project has moved to GitHub at https://github.com/hmsiccbl/screensaver.
