Open Source Python Data Visualization Software - Page 3

The Open-Source PyMOL repository has been moved to github: https://github.com/schrodinger/pymol-open-source We still use the pymol-users mailing list here on sourceforge. Please subscribe for community support: https://pymol.org/maillist (Note: SourceForge email newsletter and special offers are optional and can be unchecked) The PyMOL community wiki has its own home: https://pymolwiki.org/

QtiPlot is a user-friendly, platform independent data analysis and visualization application similar to the non-free Windows program Origin.

UPDATE: Chromium is no longer updated or maintained. The project is frozen. Chromium is a flexible framework for scalable real-time rendering on clusters of workstations, derived from the Stanford WireGL project code base.

The Simple Medical Imaging Library Interface (SMILI), pronounced 'smilie', is an open-source, light-weight and easy-to-use medical imaging viewer and library for all major operating systems. The main sMILX application features for viewing n-D images, vector images, DICOMs, anonymizing, shape analysis and models/surfaces with easy drag and drop functions. It also features a number of standard processing algorithms for smoothing, thresholding, masking etc. images and models, both with graphical user interfaces and/or via the command-line. See our YouTube channel for tutorial videos via the homepage. The applications are all built out of a uniform user-interface framework that provides a very high level (Qt) interface to powerful image processing and scientific visualisation algorithms from the Insight Toolkit (ITK) and Visualisation Toolkit (VTK). The framework allows one to build stand-alone medical imaging applications quickly and easily.

RPy is a very simple, yet robust, Python interface to the R Programming Language. It can manage all kinds of R objects and can execute arbitrary R functions (including the graphic functions). RPy has been superseded by the RPy2 project: https://rpy2.github.io/

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.

BertViz is an interactive tool for visualizing attention in Transformer language models such as BERT, GPT2, or T5. It can be run inside a Jupyter or Colab notebook through a simple Python API that supports most Huggingface models. BertViz extends the Tensor2Tensor visualization tool by Llion Jones, providing multiple views that each offer a unique lens into the attention mechanism. The head view visualizes attention for one or more attention heads in the same layer. It is based on the excellent Tensor2Tensor visualization tool. The model view shows a bird's-eye view of attention across all layers and heads. The neuron view visualizes individual neurons in the query and key vectors and shows how they are used to compute attention.

IPyPlot is a small python package offering fast and efficient plotting of images inside Python Notebooks. It's using IPython with HTML for faster, richer and more interactive way of displaying big numbers of images.

Vispy is an open-source, high-performance interactive visualization library in Python, designed for creating scientific visualizations and interactive plots. It leverages the power of modern Graphics Processing Units (GPUs) through OpenGL to render large datasets efficiently. Vispy supports a wide range of visualization types, including 2D plots, 3D visualizations, volume rendering, and more, making it suitable for scientific research, data analysis, and educational purposes.

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.

PyNomo is a package for creating nomograph(s) [nomogram(s)] using Python language.

SBEVSL is a collaborative project between Dowling and RIT on the development of a Structural Biology Extensible Visualization Scripting Language, so that users can move freely among various molecular graphics tools, such as rasmol, pymol, raster3d, etc.

MicroView is a 2D/3D image viewer and analysis tool. It is written in Python and uses VTK for all of its graphical capabilities.

Free 3D Acropolis is a model 3D in hight resolution of the Acropolis of Athens shortly after its construction.

SciGraphica is a scientific data visualization and analysis application, supplying many of the basic plotting features for 2D and 3D charts. It features opening several worksheets and plots to work with at the same time and PS output.

A library and reference application for viewing and analysing raster and vector geospatial data.

Released August 22, 2013 Lubuntu Blends: Biochemistry 13.04 (Raring) v5.44 Linux Kernel Image 3.8.0-29 Lubuntu Blends are pre-installed Wubi disk image remixes of Ubuntu and Debian Science meta packages, A custom boot loader allows installations to be copied and automatically booted from most external or USB flash drives. Once up and running, use earlier Lubuntu Remix README instructions here until documentation is updated. https://sourceforge.net/projects/portable-linux/files/ Installation 1. Download the Wubi installer http://releases.ubuntu.com/saucy/wubi.exe 2. Install any flavor of Ubuntu. 3. Swap out the root.disk with the ones provided here. Overview LAMP stack running on localhost (127.0.0.1). Scientific, productivity & media packages include R (Rattle Data Miner), GridEngine, Condor, cooperative computing tools, WINE, LibreOffice, Evolution, Clinica, Neuro Debian Desktop, PsycoPy, OpenVibe, 3DSlicer, Paraview, Openshot. Cheers, Gregory Remington

MayaVi is a free, cross platform, easy to use scientific data visualizer. It provides a GUI to ease the visualization process, is written in Python and uses the Visualization Toolkit (VTK) for the graphics.

GXSM -- Gnome X Scanning Microscopy: A multi-channel image and vector-probe data acquisition and visualization system designed for SPM techniques (STM,AFM..), but also SPA-LEED/LEED/LEEM data analysis. A plug-in interface allows any user add-on data-processing and special hardware and instrument support. Latest: NC-AFM and related explorative methods as SQDM can be configured. High-Speed external PAC-PLL hardware option with digital DSP link. Based on several hardware options it supports a commercially available DSP hardware and provided also Open Source Code for all the low level signal processing tasks and instrument controls in a most flexible and adaptable manner. All latest software is available via github.com/pyzahl/Gxsm4 (source code) or as binary for Ubuntu on https://launchpad.net/~totto/+archive/ubuntu/gxsm

The Python Computer Graphics Kit is a collection of Python modules that contain the basic types and functions to be able to create 3D computer graphics images (focusing on Pixar's RenderMan interface).

VR Juggler is a virtual platform for virtual reality application development created at the Virtual Reality Applications Center at Iowa State University. Applications developed in VR Juggler can transparently move between a wide range of VR systems.

PBS Cluster Viz is a project to display information useful to admins and users about a computing cluster managed by a PBS-compatible resource manager. Information includes load and job distribution. Interactive as well as static output is available.

PyVib2 is a program for analyzing vibrational motion and vibrational spectra. It is an open source "all-in-one" solution for scientists working in the field of vibrational spectroscopy (Raman and IR) and vibrational optical activity (ROA and VCD).

NanoCap is a generic application for the construction of low energy fullerene and capped nanotube structures. It provides an ideal tool to accompany the study of finite carbon molecules using computer simulation. The implementation involves a standalone application which includes a GUI and allows for dynamic visual inspection through 3D rendering. In addition, the NanoCap core libraries can be used in custom Python scripts that enabled the user to produce structures in bulk or to include the structure generation routines into pre-existing code.

VizStack is a framework to run GPU-enabled applications. You may set up tiled displays, and run popular applications on them. VizStack can convert nodes into a shared remote visualization farm. Individual GPUs can be allocated to users too.