Introduction
HOWTO
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Software Architecture
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IMPORTANT
- Copying and Distribution
PHT is (Copyright) 2003-2004 and it is distributed by the University of Cologne as `Free Software' in a licensing agreement similar in some aspects to the GNU General Public License. Note also that PHT is not part of the GNU software nor are any of its authors connected with the Free Software Foundation. We only share some common beliefs about software distribution. This version is based directly on KEGG and BRENDA Knowledge base and research literatures. We have combined best of the concepts and algorithms to design the solution for this problem for your appreciation and scientific goal. We protect your and our rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy and distribute the unmodified software or modify it for your own purpose. Please read the section NOTICE for important notices which apply to this package. If you are not going to make changes to PHT, you are not only permitted to freely make copies and distribute them, you are encouraged to do so, provided you do the following: * 1. Either include the complete documentation, especially the section Notice, with what you distribute or provide a clear indication where people can get a copy of the documentation; * 2. Please give credit where credit is due citing the version and original authors properly; and * 3. Please do not give anyone the impression that the original authors are providing a warranty of any kind. If you would like to use major pieces of PHT in some other program, make modifications to PHT, or in some other way make what a lawyer would call a "derived work", you are not only permitted to do so, you are encouraged to do so. In addition to the things we discussed above, please do the following: * 4. Please explain in your documentation how what you did differs from this version of PHT; and * 5. Please make your modified source code available. This version of PHT is not in the public domain, but it is given freely to the community in the hopes of advancing science. If you make changes, please make them in a responsible manner, and please offer us the opportunity to include those changes in future versions of PHT. Also, for our protection, we want to make certain that everyone understands that there is NO WARRANTY OF ANY KIND for the PHT. With respect to any software or documents for which a copyright exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT.
Pathway Hunter Tool (PHT) 3.0 Notice
General Notice Creative endeavors depend on the lively exchange of ideas. There are laws and customs which establish rights and responsibilities for authors and the users of what authors create. This notice is not intended to prevent you from using the software and documents in this package, but to ensure that there are no misunderstandings about terms and conditions of such use. Please read the following notice carefully. If you do not understand any portion of this notice, please seek appropriate professional legal advice before making use of the software and documents included in this software package. In addition to whatever other steps you may be obliged to take to respect the intellectual property rights of the various parties involved, if you do make use of the software and documents in this package, please give credit where credit is due by citing this package, its authors and the URL or other source from which you obtained it, or equivalent primary references in the literature with the same authors. Some of the software and documents included within this software package are the intellectual property of various parties, and placement in this package does not in any way imply that any such rights have in any way been waived or diminished. With respect to any software or documents for which a copyright exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT. THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS. Information in this document is subject to change without notice and does not represent a commitment on the part of the supplier. This package is sold/distributed subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or otherwise circulated without the supplier's prior consent, in any form of packaging or cover other than that in which it was produced. Glossary of terms [1] KEGG: Knowledge base on molecular interaction networks, including metabolic pathways in organisms http://www.genome.ad.jp/kegg/kegg2.html. LIGAND: Database of Chemical Compounds and Reactions in Biological Pathways available at http://www.genome.ad.jp/ligand/. [2] BRENDA: The Comprehensive Enzyme Information System is a is available via the Internet at http://www.brenda.uni-koeln.de. Note: These knowledge bases are available free of charge for academic, non-profit users. PHT uses and provides these knowledge bases to its users under "AS IS" terms and conditions. Note: Any comments, suggestions or questions about this modified version of PHT should be directed to asad@ebi.ac.uk.
