Computational Biology

Computational Biology is an interdisciplinary field of science which, on the one hand, uses computing to analyse biological systems and, on the other hand, investigates biological systems as computing systems.

Information Theory in Computational Biology

• Tom Schneider: 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence

Computational Biology Software

• transsys is a system for modelling gene regulatory networks
• gna
• cytoscape
• Bioclipse
• dCAS cDNA Annotation System
• gridqtl
• Sourmash tools for MinHash based sketches of genomic sequences

R Packages / Collections

• BioConductor
• adegenet is a package for exploratory analysis of genetic data, such as genome wide SNPs etc.

Standards

• MIRIAM is a standard for annotating models

Gene Expression Analysis

• Bioconductor
• Analysing yeast time course microarray data by Colin Gillespie

Genome Assembly etc

• wgs (aka Celera Assembler / CABOG)
• mira
• cortex
• velvet
• BamUtil
• NCBI Genome Workbench
• pysam
• BamView

Databases etc

• model organism encyclopedia of DNA elements (modENCODE)

Related Stuff

• Convex Optimization and Euclidean Distance Geometry