Open Source Data Visualization Software

Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export).

The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.

RasTop is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules based on the popular Rasmol software. The program is aimed at the rapid visualization and analysis of molecules.

Java Treeview - An Open Source, Extensible Viewer for Microarray Data in the PCL or CDT format

QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. It is maintained by the Gurevich lab at HIPS (https://helmholtz-hips.de/en/hmsb). For the most up-to-date description, please visit http://quast.sf.net. Below are just some highlights. QUAST computes several well-known metrics, including contig accuracy, the number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and manual). A comprehensive analysis results in summary tables (in plain text, tab-separated, and LaTeX formats) and colorful plots. The tool also produces web-based reports condensing all information in one easy-to-navigate file. QUAST and its three follow-up papers (MetaQUAST, Icarus, QUAST-LG) papers were published in Bioinformatics; the last paper (WebQUAST) is out in Nucl Acid Research.

BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.

The project has moved to GitHub: https://github.com/pixmeo/osirix

MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection

MicroArray Genome Imaging and Clustering Tool (MAGIC tool) is a platform-independant java program for analyzing MicroArray data (.tiff scans & .txt godlists) via graphs and clustering operations (including QT-clustering). http://www.bio.davidson.edu/magic

TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.

This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.

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

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).

NOVA is a program designed to analysis complexome profiling data (Heide et al., 2012). A graphical user interface (GUI) provides various visualization tools, such as heat maps and 2D plots. Several hierarchical clustering algorithms (e.g., single linkage, average linkage, Wards linkage), different distance measures (e.g., Euclidean distance, Manhattan distance, Pearson distance), and various normalization techniques are implemented. Many additional functions like zooming, searching for proteins, image export, and automatic file format recognition support intuitive handling for biologists. Giese, et al. NOVA: a software to analyze complexome profiling data. Bioinformatics, 2015, 31(3): 440-441

The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging (http://www.svi.nl/) for parallel batch deconvolutions.

Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.

Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.

GATA is a graphic alignment tool for comparative sequence analysis. It makes use of BLAST to graphically align two DNA sequences, creating box- line- box representations of window scored local alignments. GATA also displays extensive GFF gene annotation.

Compare SBML Test Suite Results =============================== The [SBML Testsuite](http://sbml.org/Facilities/Online_SBML_Test_Suite) allows developers of ODE based simulators to test their implementation against a large number of test cases that test a wide aspect of the [SBML Specifications](http://sbml.org/Documents/Specifications). While implementing my simulator [RoadRunner](http://roadrunner.sf.net) I wanted to be able to compare it using a wider range of parameters: - filter for new tests - filter for tests with specific tags - mark elements that I know I did not implement

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.

PANDA is a comprehensive and flexib tool for quantitative proteomics data analysis, which is developed based on our solid foundations in quantitative proteomics for years. Several novelties have been implemented in it. First, we implement the advantage algorithms of LFQuant (Proteomics 2012, 12, (23-24), 3475-84) and SILVER (Bioinformatics 2014, 30, (4), 586-7) into PANDA. Second, we consider the state-of-art concept of quantification reliability in this quantitative workflow. On the levels of spectra, peptides and proteins, PANDA works out a few quantitative filters and new scores for quantification confidence. Third, PANDA is designed for processing proteomics big data in parallel.

CQRlib is an ANSI C implementation of a utility library for quaternion arithmetic and quaternion rotation math.

A base for programs. Includes algorythms for Q-learning and SOM's etc. too. Examples: Hamron: Simulates evolution, uses the 2D-renderer. DriveUnit: created for school, for a robotic arm, uses the 3D-renderer. Hlearn: http://www.sagenb.org/home/pub/8

VMS Draw provides general utilities (e.g. normalization, conversion, and other manipulations of several spectra at the same time) and a flexible graphical user interface (GUI) for an easy use by non-specialists which allows a seamless flow of information between experimentally and theoretically oriented researchers. Finally, it permits effective interactions with other electronic structure codes [e.g., nuclear magnetic resonance (NMR), microwave] even if Gaussian 16 offers the widest set of methods for computational spectroscopy.

XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s