Search Results for "informatics" - Page 3

CyReposition is an open source Cytoscape Plugin for the reuse of existing Cytoscape network layouts in new Cytoscape projects. This project migrated to github https://github.com/matthiaskoenig/cy2reposition

SLEDRIDE: Simplified Learning about Expression Data Running in a Desktop Environment. To provide a general workbench for pipe-lining microarray gene expression data from supervised learning results into unsupervised learning methods.

Chipster is a biologist-friendly analysis software for high-throughput data. It contains over 200 analysis tools for next generation sequencing (NGS), microarray and proteomics data. Users can combine tools in automatic analysis workflows, which can be shared. Chipster's interactive visualizations allow users to select datapoints and create new gene lists. For NGS data Chipster contains a built-in genome browser, which highlights SNPs and automatically indexes BAM files and calculates...

ZAE is a Zoomable multiple sequence Alignment Editor

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.

The Shrimp suite provides interactive visualizations of graph-based data. Creole (Eclipse plug-in) visualizes Java source code. Jambalaya (Protege plug-in) visualizes ontologies (including OWL), & Stand-Alone Shrimp visualizes RSF/GXL/PRJ/PPRJ files.

ProteinShader is a molecular visualization tool that can produce illustrative renderings of proteins that approximate what an artist might create using pen and ink. This free platform-independent program is written in Java and OpenGL Shading Language.

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.

A visualization and design tool for RNA secondary structure

A Java-based tool to visualize, integrate and analyze LC-MS/MS proteomics data.

MZ-Analyzer is a tool for visualization and analysing of multiple mass spectrometry data in 2D and 3D mode, including the function of quantitating the LC-peak of the specified identified peptides.

LAMINA (Leaf shApe deterMINAtion) is a tool to provide classical measures of leaf shape (blade dimensions) and size (area) as well as measures that indicate asymmetry in leaf shape and measures of herbivory damage (missing leaf area).

Geneview is a visualisation tool to display genetic sequence data stored in nucleic sequence databases like <A HREF="http://www.ncbi.nlm.nih.gov/Genbank/">GenBank</A>.

JPhylo is a Java based visualization program used to display sequences of phylogenetic trees.

Create and simulate Hybrid Petri Nets.

This program will provide a new way to visualize molecular marker data.

MASQOT-GUI is an open-source, platform-independent application for two-channel microarray spot quality control. Included is a set of tools for gridding, segmentation, quantification, multivariate spot quality assessment and data visualization.

PROMPT is a system for retrieval, analysis, mapping and comparison of proteins. It allows easy mapping of different types of sequence IDs, data retrieval and integration, a multitude of analysis and comparison algorithms and a full-blown easy to use GUI.

Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical represetations from Gene Ontology (GO) annotated interactions maintained by the BioGRID.

Structure is a framework for two-dimensional molecular visualization written in Java and based on Octet.

This software system serves as both a DICOM image viewer as well as a diagramming tool for collaborating notes on the given image sets. This my Computer Science graduate thesis project at Loyola Marymount University.

Urbigene contains SciFOAF and MyFOAFExplorer, two tools used to build a scientific FOAF network from NCBI pubmed and to browse it.

CompuCell3D is a software framework for multimodel simulations of biocomplexity problems. It has been developed as an ongoing project for the Interdisciplinary Center for the Study of Biocomplexity at the university of Notre Dame.

The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io

MirkE is a platform-independent Java application using Hibernate, HSQLDB and Colt designed to facilitate common but tedious calculations on spectrophotometric and colormetric data for molecular and cellular biology assays.