Open Source Linux Data Visualization Software - Page 38

Toxmatch is a flexible and user-friendly open-source software application that encodes several chemical similarity indices to facilitate the grouping of chemicals into categories and read-across. The core functionalities include the ability to compare datasets based on various structural and descriptor-based similarity indices as well as the means to calculate pair wise similarity between compounds or aggregated similarity of a compound to a set.

Efficiently create compact, highly customizable tree layouts - Based on Walker's algorithm with enhancements suggested by Buchheim, Jünger, and Leipert the software builds tree layouts in linear time. I.e. even trees with many nodes are built fast. Downloads are available at https://sourceforge.net/projects/treelayout/files/. For detailed documentation look at the TreeLayout web site http://treelayout.sourceforge.net/. Development for TreeLayout has moved to https://github.com/abego/treelayout/.

Tunelator processes tunnel profile data for surveying work. It provides a powerfull grid editor, 3D preview, export to Prowin, Ispol, MDT and DXF (2D and 3D views with convenient layering).

A 3D viewer for molecular charge distributions. Implemented in OpenGL with GLUT. Includes a small OpenGL windowing library/widget set.

VERDI is a flexible, efficient, and modular Java-based visualization software tool that is used to visualize multivariate four dimensional gridded environmental datasets such as those output by air quality models.

A generic geospatial analysis and viewing capability using Perl scripts that provides the foundation and structure for readily creating KML data files from disparate data sources. KML files can be read and viewed by Google Earth and other tools.

An implementation of Bruhn et al.'s fast variational optical flow algorithm using the OpenCV image processing library. The code calculates dense flow fields with a user-specified level of precision.

Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.

Vistools is a set of tools to easily visualize some scientific data, without need to learn difficult API, so you can see your 3d results very quickly. Also some sci tools for which we made it, including vector field tracing and simple optimization.

The Visu program is a lightweight GTK+ interactive visualization tool for 2D or 3D simulation data, rendering through the VTK library. Features include: reading data in a variety of formats, display the data as scalars, vectors, height fields, and lev

Visual Turing Machine is a tool for visually designing Turing machines. This means no coding in abstract scripting languages, but simple point&click design. It uses the a..z symbol set, plus the "empty" # symbol, and also simulates an infinite tape.

Vizz is a open source library in C/C++ which makes distributed visualization using VTK a piece of cake. Vizz is a library developed over VTK for simple, uncomplicated VTK development in distributed (client/sever) environments.

Webcockpit is a Web Application Generator for realtime charting and monitoring solutions. Generates JSP code to create chart images and HTML tables from SQL queries. Supports Drill-Down and pluggable look&feel. Uses JFreeChart, Displaytag and Cewolf.

Code libraries and media files contributed by Whoola, Inc. Includes Whoola Cyberspace, a virtual reality web browser with fly-through hyperlinks. The source code includes a COLLADA loader for Xith. Click on the "Home Page" link above to install.

A Java software for 3D visualization of graphs/networks. It implements many graph layout algorithms (such as force-directed methods), graph generators (such as scale-free networks) and graph modifiers. Most functions can be accessed through its GUI.

Wow Log Parser is a combat log parser for the game World of Warcraft. The purpose of the program is to parse the files generated with the /combatlog command. The source code can be found on: http://www.gurre.eu/wowlogparser/forum

A program aimed to allow users to record the results of a 3D survey of a site; to verify the measurements are internally consistant and provide a visual representation of the site.

The X3DToolKit is a developer's API that allows you to load X3D files into a logical graph. That graph can then be traversed and converted into your favorite Graphic Scenegraph or can be rendered using X3DTK's OpenGL scenegraph.

ZEE HAS MOVED TO GITHUB (see "Zee Web Site" link).

This toolkit allows complete control of a microscopy setup from Labview, Matlab, Scilab, Python, .Net, VB, IgorPro, Mathematica and more. Included is a standalone program for image acquisition and scripting control of a scientific microscope.

ClutrFree allows the visualization and interpretation of gene expression data clusters for multiple clustering experiments. Data is integrated with ontological annotations (GO), and enrichement of annotations (hypergeometric distribution) is computed.

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

This is a fork of Panorama Tools / libpano13-2.9.21 Mercurial. PTOptimizer is part of panorama tools, a great software for aligning and stitching several partially overlapping photos in order to get a bigger photo. When you have only a small or medium number of images and control points, the original PTOptimizer does the optimization in a fairly short time. However if you have a large number of images (several hundrets or more than thousand) and control points, PTOptimizer typically needs much time (up to several days) for the optimization of the parameters. fastPTOptimizer decreases the processing time for large panoramas (a speedup factor of 100 or more can be achieved). This is possible by exploiting the sparseness of the mathematical optimization problem. The original PTOptimizer uses the well proven Levenberg Marquardt optimizer lmdif from the minpack software. fastPTOptimizer uses a "sparse" optimizer lmdif_sparse that uses the SuiteSparse library.

giv, The G(reat|tk|NU) Image Viewer, is a 8-bit to 32-bit and floating point image and vector viewer for gtk+. It is designed especially for scientific vision and computational geometry and has support for drawing vector graphics on top of an image.

Signaling pathways are complex and intertwined processes. The perturbation of biological systems can reveal the complicated interplay and dependencies of pathway components. isiKnock is a software to automatically conduct and visualize in silico knockouts for signaling pathways (Hannig et al. 2019). isiKnock predicts the knockout behavior based on the calculation of signal flows at steady state. For an explanation of the concept of in silico knockouts, we refer to Scheidel et al. 2016 and Amstein et al. 2017. Hannig et al. (2019) isiKnock: in silico knockouts in signaling pathways, Bioinformatics, 35(5), 892–894 Amstein et al. (2017) Manatee invariants reveal functional pathways in signaling networks. BMC systems biology, 11(1), 72. Scheidel et al. (2016) In silico knockout studies of xenophagic capturing of Salmonella. PLoS computational biology, 12(12), e1005200.