Libraries

Overview

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• Bioinformatic Utilities - BIU
• Energy Landscape Library - ELL

Bioinformatic Utilities - BIU

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This C++ programming library provides classes and functions often used in the bioinformatics context of our group. It collects data structures and class hierarchies for biomolecule modeling and general useful functionalities as program parameter parsing, string conversions, etc.

Current Status

• String conversions etc.
• Program parameter parser
• Random number generation
• Lattice proteins and related operations (e.g. move sets)
• RNA support
• …

For a full list of features, see documentation.

Documentation

• The current online HTML documentation can be found here.
• Older versions:
  • 1.7.0

Downloads

You can download the BIU-library including configure scripts:

• biu-2.3.7.tar.gz - 2016-08-08
• biu-2.3.6.tar.gz - 2011-04-02
• biu-2.3.5.tar.gz - 2010-10-27
• biu-2.3.3.tar.gz - 2009-10-13
• biu-2.3.1.tar.gz - 2009-07-21
• biu-2.2.0.tar.gz - 2008-12-16
• biu-2.0.1.tar.gz - 2008-07-10 - Note: incompatible to 1.* !
• biu-1.7.0.tar.gz - 2008-06-19
• biu-1.6.0.tar.gz - 2008-05-08
• biu-1.5.0.tar.gz - 2008-02-13
• biu-1.3.0.tar.gz - 2007-10-22
• biu-1.2.2.tar.gz - 2007-07-11
• biu-1.1.tar.gz - 2007-03-15
• biu-1.0.tar.gz - 2006-06-19

Contributing Group Members

• Martin Mann
• Sebastian Will
• Daniel Maticzka
• Hannes Kochniß

Energy Landscape Library - ELL

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The ELL-library provides a platform for generic algorithms to study kinetics and structure of energy landscapes with discrete states. These algorithms need an abstract representation of these states to be applied to a multitude of state instances and their corresponding energy or fitness landscapes.

Main Publications

• Martin Mann, Sebastian Will, and Rolf Backofen. The energy landscape library - a platform for generic algorithms. Proceedings of 1st BIRD’07, OCG, 217, 83-86, 2007.

Current Status

Generic Algorithms

• A set of walks to traverse energy landscapes (random, adaptive, gradient, Monte Carlo)
• Exhaustive landscape flooding (single and multiple basins)
• Sampling-based macro-state transition rate estimation

Landscape Models

• Lattice protein representations with Pull-Move and Pivot-Move neighborhoods for different lattice models with arbitrary distance-based energy functions
• RNA representation with single base pair indel, interfacing the Vienna RNA package
• Ising spin glass models (ring of spins)
• Number Partitioning Problem (ring of spins)

General Features

• Strict separation of algorithm and landscape model layer
• Memory-efficient compressed State representations
• Generic neighborhood generators
• Global and flexible setup of random number generators

For a full list of features, see documentation.

Documentation

• The online HTML documentation of the current version can be found here.
• Older versions:
  • 2.3.0

Downloads

You can download the ELL-library including configure scripts and documentation:

• ell-3.2.4.tar.gz - 2016-08-08 - BIU(2.3.7)
• ell-3.2.3.tar.gz - 2013-05-02 - BIU(2.3.6)
• ell-3.2.2.tar.gz - 2010-10-27 - BIU(2.3.6)
• ell-3.2.0.tar.gz - 2009-10-13 - BIU(2.3.3)
• ell-3.1.1.tar.gz - 2009-07-21 - BIU(2.3.0)
• ell-3.0.0.tar.gz - 2008-12-16 - BIU(2.2.0)
• ell-2.3.0.tar.gz - 2008-06-19 - BIU(2.0.0)
• ell-2.2.0.tar.gz - 2008-05-27 - BIU(1.6.1 < 2.0.0)
• ell-2.1.0.tar.gz - 2008-05-08 - BIU(1.6.0 < 2.0.0)
• ell-2.0.0.tar.gz - 2008-02-13 - BIU(1.5.0)
• ell-1.0.1.tar.gz - 2007-07-11 - BIU(1.2.2)
• ell-0.3.2.tar.gz - 2007-03-15 - BIU(1.1)
• ell-0.3.1.tar.gz - 2007-03-06 - BIU(1.0)
• ell-0.3.tar.gz - 2007-02-27 - BIU(1.0)
• ell-0.2.tar.gz - 2006-12-05 - BIU(1.0)
• ell-0.1.tar.gz - 2006-06-21 - BIU(1.0)

For installation instructions, see documentation and the included INSTALL file.

Dependencies

The ELL depends on the following libraries:

• The Bioinformatic Utility library (BIU) - mandatory
• The Vienna RNA package - optional for RNA support

Contributing Group Members

• Martin Mann
• Sebastian Will
• Daniel Maticzka
• Hannes Kochniß
• Andreas Richter

RNA Energy Landscape Tools

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Based on the energy landscape library, a set of tools to investigate the structure and topology of RNA energy landscapes has been implemented. These programs allow for:

• Minima sampling
• Exact calculation of barrier trees or saddle networks
• Approximation of barrier trees
• Barrier estimation using a heuristic by Morgan and Higgs

Downloads

You can download the RNA energy landscape tools including configure scripts and documentation:

• hybkin-1.0.2.tar.gz - 2008-05-20 - BIU(1.6.0), ELL(2.1.0), VRNA(1.6.4)

For installation instructions, see the included INSTALL file.

Dependencies

The RNA energy landscape tools depend on the following libraries:

• The Bioinformatic Utility library (BIU)
• The Energy Landscape Library (ELL)
• The Vienna RNA package

Contributing Group Members

• Martin Mann
• Andreas Richter
• Sebastian Will
• Hannes Kochniß
• Daniel Maticzka
• Dmitry Gubenko