BioShell ver. 2.x documentation page

This page provides documentation for BioShell package version 2.x (in JAVA) Documentation for the yet unrealeased BioShell package version 3.0 beta is located here


BioShell in version 2.0 comes as a set of programs (executables run on a JAVA virtual machine) and a JAVA library. The links below show how to install the package and provide one-line commands to perform basic bioinformatics tasks with the programs. A bunch of example Jython script are also given to show how to use the library.

Installation guide

Provides instructions how to download and install the package

BioShell programs

The Java version of BioShell comes with the following programs:

  • apps.ACorr - calculates autocorrelations based on given scalar and vector - type observables
  • apps.Hist - prepares 1D and 2D histograms
  • apps.Seqc - converts between sequence formats, such as FASTA, PIR, SEQ
  • apps.Clust - hierarchical clustering of various data, e.g. protein models (originaly published as ‘HCPM’)
  • apps.Strc - structure converter utility, e.g. extracts chains from PDB
  • apps.PRAline - aligns sequences and sequence profiles
  • apps.RmsCalc - calculates crmsd, tm-score, GDT and other scores of structure (dis)similarity
  • apps.StrCalc - basic calculations on biomolecular structures. Evaluates angles, distances, contacts etc.
  • apps.Trac - converts trajectories computed by CABS protein modeling software
  • apps.BBQ - Backbone Building from Quadrilaterals
  • apps.PsiBlastSearch - performs multiple runs of PsiBlast program in several threads
  • apps.PsiBlastAnalyse - analyses multiple output files from PsiBlast
  • apps.WHAM - Weighted Histogram Analysis Method : calculates density of states from energy observations simulated in canonical ensembles at multiple temperatures
  • apps.StatPhys - statistical physics calculations based on density of states (computed by WHAM)

To call a program, say e.g. java apps.RmsCalc in your terminal. Also , you may want to browse the cookbook to see what you can brew with these tools.

BioShell Cookbook

Handy one-liners to solve daily problems. Shows how to convert file formats and perform basic calculations.

BioShell scripts

Example jython scripts show how to apply BioShell library to structural bioinformatics problems

BioShell API documentation

API documentation for the JAVA BioShell library

Other resources

The following sites may be useful in learning python: