Ed's Big PlansSoftware Snippets
This is a collection of select free software and source code that I’ve posted on this site.
In general, I classify Software Snippets to be small objects that stand-alone, can be downloaded then be compiled or run immediately and can be included as a library to other software.
Items posted here are licensed under Creative Commons Attribution 3.0 Unported.
All code is provided as-is, without any warrantee expressed or implied.
Feel free to contact me, as I’m always happy to offer my support.
Visualization and Image Processing Projects
Fuzzy C-Means Greylevel Segmentation — Python — 2011.04.20
- Uses fuzzy-c means to decide the best grey-values to use as cluster centers. Produces segmented grey-level PNG bitmaps.
- Download here: ( FCMProject.tgz — Python source )
- More information: Fuzzy c-means for greylevel image segmentation
Heatmap Renderer — C# — 2011.01.21
- A function that takes 2D arrays of double values and produces corresponding heatmaps. Produces heatmaps in PNG bitmap format.
- Download here: ( tgz | zip — C# source: demo main, example data used below, makefile )
- More information: C# & Science: A 2D Heatmap Visualization Function (PNG)
Bioinformatics and Phylogeny Projects
Interactive Phylogeny Diagrams — Python & JavaScript — 2010.10.31
- A Newick string parser and SVG renderer using JS in XHTML. Compatible for Mozilla and WebKit family of renderers. Users may click on phylogeny tree nodes to display the multiple sequence alignment at that node along with other information. An included Python script within the tgz is used to make the data compatible with the viewer.
- Download here: ( auto_phylo_diagram.tgz — Python script, makefile, IL-1 data, JS renderer, demo xhtml )
- More information: Simple Interactive Phylogenetic Tree Sketches JS+SVG+XHTML
Edit String Adder — Ruby, JavaScript — 2010.07.24
- A library that performs edit string operations. The Ruby version contains the product function that adds two edit strings together. The JavaScript version additionally contains a function that applies an edit string to an amino acid or nucleotide sequence.
- Download here: ( editStringAdder.rb — Ruby implementation | editStrings.js — JS implementation )
- More information: Bioinformatics: Edit Strings (Ruby, JavaScript)
Phylogenetic Tree Parser — JavaScript — 2010.06.25
- A parser that builds up a binary tree using recursive descent. Takes a Newick format string as input and returns a light weight tree using JavaScript objects.
- Download here: ( parse_newick.js — JS implementation | index.html — demo )
- More information: Parsing a Newick Tree with recursive descent
