Libraries

Overview

• Bioinformatic Utilities - BIU
• Energy Landscape Library - ELL

Bioinformatic Utilities - BIU

This C++ programming library provides a classes and functions often used in the bioinformatics context of our group. It collects data structures and class hierarchies for biomolecule modelling and general usefull 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

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.
  In 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 neighborhood for different lattice models with arbitrary distance based energy functions
• an RNA representation with single base pair indel, interfacing the Vienna RNA package for energy calculation
• 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) - Note: incompatible to 2.* and 1.* !
  • 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 install instructions see documentation and 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