Open Source Python Data Visualization Software - Page 2

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning. Planning genetic constructs with many parts and assembly steps, such as recombinant metabolic pathways, are often difficult to properly document as is evident from the poor state of documentation in the scientific literature. The pydna python package provide a human-readable formal description of cloning and genetic assembly strategies in Python which allow for simulation and verification. Pydna can be used as executable documentation for cloning.

ccplot is an open source command-line program for plotting profile, layer and earth view data sets from CloudSat, CALIPSO and Aqua MODIS products.

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.

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

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.

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/

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.

A Python interface to the gnuplot plotting program.

Mantid Project (www.mantidproject.org)

Make sure to download from the link below and not the big giant button. I'm not sure how to fix that, so if you know!

GPlates is a plate-tectonics program. Manipulate reconstructions of geological and paleo-geographic features through geological time. Interactively visualize vector, raster and volume data. PyGPlates is the GPlates Python library. Get fine-grained access to GPlates functionality in your Python scripts.

The best OpenStreetMap editor for POIs and entrances. The best app for on-the-ground surveying for OpenStreetMap! Add shops and amenities, survey benches and trees, collect addresses, or use them as walking papers. This editor does not make you think. Just go to a mall, and start Every Door. You'll see mapped shops around you: tap on the checkmark for any that are still there, and add shops that are not on the map. That's the entire process: you can keep your entire town up-to-date thanks to this simple editor. There is also a micromapping mode for verifying and adding benches and street lamps. And an entrance mode for adding building attributes and entrances, which are merged automatically into building contours.

GemGIS is a Python-based, open-source geographic information processing library. It is capable of preprocessing spatial data such as vector data (shape files, geojson files, geopackages,…), raster data (tif, png,…), data obtained from online services (WCS, WMS, WFS) or XML/KML files (soon). Preprocessed data can be stored in a dedicated Data Class to be passed to the geomodeling package GemPy in order to accelerate the model-building process. Postprocessing of model results will allow export from GemPy to geoinformation systems such as QGIS and ArcGIS or to Google Earth for further use.

Turn Python notebooks to web applications with open-source Mercury framework. Hide code and add interactive widgets. Non-technical users can tweak widgets and execute notebook with new parameters. The core of Mercury is Open Source under AGPLv3. We provide Mercury Pro with additional features, dedicated support and friendly commercial license. Mercury is a perfect tool to convert Python notebook to interactive web application and share with non-programmers. You define interactive widgets for your notebook with the YAML header. Your users can change the widgets values, execute the notebook and save result (as PDF or html file). You can hide your code to not scare your (non-coding) collaborators. Easily deploy to any server. Mercury is dual-licensed. Looking for dedicated support, a commercial-friendly license, and more features? The Mercury Pro is for you.

TransPose is a human pose estimation model based on a CNN feature extractor, a Transformer Encoder, and a prediction head. Given an image, the attention layers built in Transformer can efficiently capture long-range spatial relationships between keypoints and explain what dependencies the predicted keypoints locations highly rely on.

folium builds on the data wrangling strengths of the Python ecosystem and the mapping strengths of the leaflet.js library. Manipulate your data in Python, then visualize it in on a Leaflet map via folium. folium makes it easy to visualize data that’s been manipulated in Python on an interactive leaflet map. It enables both the binding of data to a map for choropleth visualizations as well as passing rich vector/raster/HTML visualizations as markers on the map. The library has a number of built-in tilesets from OpenStreetMap, Mapbox, and Stamen, and supports custom tilesets with Mapbox or Cloudmade API keys. folium supports both Image, Video, GeoJSON and TopoJSON overlays. To create a base map, simply pass your starting coordinates to Folium. To display it in a Jupyter notebook, simply ask for the object representation. The default tiles are set to OpenStreetMap, but Stamen Terrain, Stamen Toner, Mapbox Bright, and Mapbox Control Room, and many others tiles are built in.

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).

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

GDL - GNU Data Language, a free IDL (Interactive Data Language, see http://ittvis.com/idl/) compatible incremental compiler.

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.

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

Garmon (Gnome/GTK+ Car Monitor) is a tool that lets you connect to an OBD-II compliant vehicle using an ELM327 based scanning device. It supports monitoring live and freeze frame data as well as reading and clearing DTCs. It is written in python.

GUESS, or the Graph Exploration System, is a system and language for visualizing and manipulating graph structures and creating new visualization applications.

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/