Search Results for "nfsen-plugins"

NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering,...

OpenChrom is a tool for gas chromatography and mass spectrometry. The focus is to handle data files from different GC/MS and GC/FID systems and vendors. Its functionality and algorithms can be extended using a flexible plugin approach, based on Eclipse RCP.

Maui is the Maltcms User Interface, a rich client application for Chromatography-Mass Spectrometry and related research areas.

MoSGrid focuses on the configuration and provision of Grid services for molecular simulations and annotation of the results with metadata and their provision for data mining and knowledge generation. It is based on Liferay technology togethe with gUSE.

An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).

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.

SBSI (Systems Biology Software Infrastructure) is a suite of tools for systems biology, such as parallelized numerical algorithms, and a Java, Eclipse RCP based client for visualizing results, running simulations, and integrating SBML based plugins.

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.

Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.

Development of exact and approximate methods (Importance Sampling and MCMC based) for computing likelihoods under the standard population genetic models of mutation,migration & recombination. Project issues are mainatined at https://freecode4susant.atlassian.net/browse/COALESCENT

Based on HL7 v.2.3.1 Orders & Results Reference Information Model (RIM)s, The project is NOT a CPOE per-se. Instead, the project provides "applications" that allow EHR's to perform Outpatient Orders and Results via HIE, and collect these into their EHRs to feed the EHR "CPOE module / section" (ex. with prescribed drugs, ordered labs and results, ....) The first module in the project was the "ePrescribing application"; certified by RxHub and SureScripts back in 2007. New...

An api for domain level interaction with SNOMED CT and an implementation based on a storage engine using a native SNOMED distribution stored in neo4j as a backend.

An IDE for CellML 1.1 user models developed in UNSW as an open source project. Author: Mitchell Lanesbury 2012

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.

The plugin allows automatic highlighting of pathways in an easy and understandable manner.

Knime (http://www.knime.org) nodes for sequence bioinformatics. Sequime is an eclipse plug-in for the KNIME data mining platform, providing additional nodes for reading, processing and visualizing sequence information.

A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.

The Edinburgh Pathway Editor (EPE) is a tool and framework that allows the drawing and manipulation of Biological Networks, such as signalling or matabolic pathways. The editor supports several notations including SBGN and Cytoscape notations.

Anna is lightweight Java framework to build pipeline systems of any kind. It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.

URBAN – a Unified Rule-Based and Allosteric Network compiler and simulator for quantitative modelling in systems and synthetic biology

CEGA is a highly extendable layout plugin for Cytoscape based on an Evolutionary Algorithm. In contrast to other layout algorithms, CEGA lets users decide which features are important for the visualization of their graphs.

D-finder is a bioinformatic search algorithm for the identification of D-sites in JNK interacting proteins. The algorithm is a combination of pattern matching and a hidden markov model (HMM) based on a training set of known JNK D-sites.

A Cytoscape Plug-in Project to Predict transcription states of genes in a Biological Network based on a Bayes Network model

4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.