Search Results for "java project netbeans" - Page 2
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Showing 154 open source projects for "java project netbeans"
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BioC
We describe a simple XML format to share text documents and annotation
A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are... -
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The objective of this project is to provide an innovative tool for visualization of multiples genomes. Written in Java, it presents a simple and intuitive user interface to view and manipulate the relationships between groups of genes.
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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BABA stands for Basic-Algorithms-of-Bioinformatics Applet. This project aims to create a set of bioinformatic algorithms presented didactically. The algorithms available at the moment are: Needleman&Wunsch, Smith&Waterman, Four Russians and Nussinov.
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This ohnlp project has released "pipelines" that were contributed by members of the OHNLP Consortium. The pipelines are based on the Apache UIMA framework. medKAT/P, MedCoref, MedTagger, MedXN, and cTAKES are licensed under Apache License V2.0. MedTime is licensed under GNU General Public License version 3.0 (GPLv3). cTAKES development has moved to apache.org. See http://ctakes.apache.org/
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SILA
Automated bacterial and archaeal genome annotation system
SILA is a system for automated annotation of bacterial and archaeal genomes. It provides accurate gene prediction using a combination of tools (Prodigal and HGF) and a web site for task management and visualization of annotation. This project is in alpha stage. Please use the online service available at: http://www.bioinfo.ufpr.br/SILA/login.jsp Documentation (portuguese only): http://hdl.handle.net/1884/34801 -
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Bamformatics
Toolkit and GUI for sequencing data analysis
The Bamformatics project aims to provide a coherent and consistent approach to analysis of high-throughput sequencing data. Its toolkit includes, among others, programs to identify variants and to compute various types genomic tracks. It also provides a graphical user interface to facilitate general bioinformatic workflows. The project wiki contains further details. -
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This project implements a Cytoscape plugin for viewing and manipulating pathway maps for metabolic models created by the Model SEED (http://www.theseed.org/models). See the "Files" area for README. See Project Homepage for Tutorial.
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GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
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openModeller is a complete C++ framework for species potential distribution modelling. The project also includes a graphical user interface, a web service interface and an API for Python.
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Systems Biology Simulation Core Library
Accurate and efficient Java library that simulates biological models
This project has been moved to https://github.com/draeger-lab/SBSCL. -
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A Tool for Retrieval, Visualization and Analysis of biological Pathways. Import a Gene or Protein Set from any Excel file. Automatically find signaling Pathways from KEGG. Integrate your Data in Seconds with a live interactive Force-directed Layout.
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The MCISB Project contains software solutions developed in the Manchester Centre for Integrative Systems Biology, University of Manchester.
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PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/MutationMapper) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/MutationMapper/releases/latest). Predict functional consequences of mutations identified from sanger sequencing.
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The Protein Similarity Network
Human protein similarity network used to predict drug safety.
This is the protein similarity network - PSIN. Here, the nodes are human proteins and they are linked only if they share considerable sequence similarity. We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do... -
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...The command line tools of Hadoop-BAM should be understandable to all users, but they are limited in scope. See the SeqPig project for a higher-level interface to the file formats supported by Hadoop-BAM: http://seqpig.sourceforge.net See Seal for Hadoop-based read alignment tools, Seal: http://biodoop-seal.sourceforge.net
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Taxy is a tool for browsing and quering data organized as a taxonomy. Through the use of plugins it allows to connect to different data sources, such as the NCBI species taxonomy or the catalogue of biomedical services of the EU project ACGT.
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GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded. This project has moved to GitHub: https://github.com/GenomeView/genomeview
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Exreco
EXperimental REplicator COllider
The project is moved to GitHub : https://github.com/bekisz/exreco/ Exreco is a agent based platform for the simulation and study of the Darwinian evolutionary process. It aims to support the exploration of genetically rooted phenomena like - aging (programmed cell death) - sexual and asexual reproduction - altruism of individuals - spread of diseases The typical way of using Exreco starts by defining the behavior of your replicators ( agents that can reproduce and evolve over... -
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GeneticThesaurus
Annotation of genetic variants in repetitive regions
GeneticThesaurus enables analysis of genetic variation in repetitive regions. See project wiki for details. -
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The target system of this project is to develop mathematically efficient program code generator from cellml like biological models described by mathematical markup languages.
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VSViewer3D
3D Virtual Screening Viewer
This project is an interactive viewer for 3D virtual screening data. -
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GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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Coulson Plot Generator
Graphics generator for pie diagram matrix from spreadsheets
For comparative plus/minus spreadsheet data, Coulson Plot Generator application creates a multiple pie diagram, for a rapid visual comparison of subunit occupancy across a range of entities. Numbers of pies, segments, labels and colours are customisable. Creates an editable PDF from a comma separated text file. Now with zoom capability and more memory, for larger datasets. Save images in several formats including SVG. -
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Deem
Analyze time-course data with significance tests, clustering, modeling
Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional...