GNU Octave Research Articles

A Program for Nonlinear Fitting of Soil Water Retention Curve Written in Numerical Calculation Language GNU Octave

A Program for Nonlinear Fitting of Soil Water Retention Curve Written in Numerical Calculation Language GNU Octave

Metatool 5.0: fast and flexible elementary modes analysis

Elementary modes analysis is a powerful tool in the constraint-based modeling of metabolic networks. In recent years, new approaches to calculating elementary modes in biochemical reaction networks have been developed. As a consequence, the program Metatool, which is one of the first programs dedicated to this purpose, has been reimplemented in order to make use of these new approaches. The performance of Metatool has been significantly increased and the new version 5.0 can now be run inside the GNU octave or Matlab environments to allow more flexible usage and integration with other tools. The script files and compiled shared libraries can be downloaded from the Metatool website at http://pinguin.biologie.uni-jena.de/bioinformatik/networks/index.html. Metatool consists of script files (m-files) for GNU octave as well as Matlab and shared libraries. The scripts are licensed under the GNU Public License and the use of the shared libraries is free for academic users and testing purposes. Commercial use of Metatool requires a special contract.

Connectivity matrix method for analyses of biological networks and its application to atom-level analysis of a model network of carbohydrate metabolism

An approach for analysis of biological networks is proposed. In this approach, named the connectivity matrix (CM) method, all the connectivities of interest are expressed in a matrix. Then, a variety of analyses are performed on GNU Octave or Matlab. Each node in the network is expressed as a row vector or numeral that carries information defining or characterising the node itself. Information about connectivity itself is also expressed as a row vector or numeral. Thus, connection of node n1 to node n2 through edge e is expressed as [n1, n2, e], a row vector formed by the combination of three row vectors or numerals, where n1, n2 and e indicate two different nodes and one connectivity, respectively. All the connectivities in any given network are expressed as a matrix, CM, each row of which corresponds to one connectivity. Using this CM method, intermetabolite atom-level connectivity is investigated in a model metabolic network composed of the reactions for glycolysis, oxidative decarboxylation of pyruvate, citric acid cycle, pentose phosphate pathway and gluconeogenesis.

Method for the Optimization of Kinematic and Dynamic Properties of Parallel Kinematic Machines

The following paper introduces an approach, which allows the consideration of the kinematic as well as the dynamic properties of parallel kinematic machines. Based on the results of a preceding kinematic optimization, a FEM-model with arbitrary input parameters is designed. The full kinematic functionality of struts and joints used is ensured. By coupling the FEM-model to the GNU Octave numerical program system, a variety of movements including machining forces can be simulated. A Broyden-Fletcher-Goldfarb-Shanno optimization algorithm, using GNU Octave, was written and coupled to the FEM-system. Now, this algorithm is able to influence the model's arbitrary input parameters during the optimization process. Thus, the model is optimized automatically for a certain machining process and/or dynamic behavior. This procedure is demonstrated using the example of a delta robot structure originally designed by Raymond Clavel [7].

GNU TeXmacs

GNU TeXmacs [vdH01, vdH02, Gro01] is a free software, which can both be used as a scientific text editor and as a front-end for computer algebra systems. The editor allows you to write structured documents via a wysiwyg (what-you-see-is-what-you-get) and user friendly interface. New styles may be created by the user. The program implements high-quality typesetting algorithms and T E X fonts, which allow the user to produce professionally looking documents.The high typesetting quality still goes through for automatically generated formulae, which makes TeXmacs suitable as an interface for computer algebra systems, or other types of "plugins". Currently, there are interfaces with Axiom, Giac, GNUplot, Graphviz, Gtybalt, Macaulay2, Maxima, Mupad, GNU Octave, Pari, Qcl, GNU R, Reduce, Scilab and Yacas. TeXmacs also supports the Guile/Scheme extension language, so that you may customize the interface and write your own extensions to the editor.In our demonstration, we plan to show briefly how to edit mathematical texts with TeXmacs, how to use computer algebra systems, and how to add interfaces with new systems in a very efficient way.

Econometrics with Octave

GNU Octave is an open-source implementation of a (mostly Matlab compatible) high-level language for numerical computations. This review briefly introduces Octave, discusses applications of Octave in an econometric context, and illustrates how to extend Octave with user-supplied C++ code. Several examples are provided. Copyright © 2000 John Wiley & Sons, Ltd.