BLM - a program for exact querying with arbitrary topologies =========================== This file describes the installation, and usage of BLM. Gram is the graph motif solver accompanying the paper It has been tested on: * Debian GNU/Linux (x86_64) 6.0 Java SE-1.6 with OpenJDK Runtime Environment (IcedTea6 1.8.7) The current version of BLM can be found at http://fpt.akt.tu-berlin.de/blm/ 0. Requirements / Installation ------------------------------ Java SE-1.6 is required for compilation of the source files. A current version of a Java Runtime Environment has to be installed for executing the Java Bytecode 1. Exemplary Usage -------- Call BLM from the /src folder with java main/BLM ../Human\ Complexes\ CORUM.txt ../human-int.txt ../yeast-int.txt ../Human-yest-sequence-sim.txt .. After execution the BLM-0.1 folder will contain a folder called "Homomorph" Each file (with the exception of stats.txt) in this folder contains the matching proteins for the complex that the file is named after. stats.txt contains some data concerning the running time needed for executing the program 1. Detailed Instructions --------------------------------------- A more detailed instruction can be found in the Javadoc which are contained in the folder /doc/ 2. Limitations ---------------------------------- Currently, BLM is only able to compute exact matches for the corresponding matching types (injective homomorphism and subgraph isomorphism). For each execution of the mapping algorithm, a running time limit of 30 minutes is hard-coded in the algorithm source files. Changing the running time limit requires recompiling. 3. Terms of Usage ----------------- (C) 2011 Christian Komusiewicz BLM is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. BLM is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with BLM. If not, see . -- May 2nd 2011, Christian Komusiewicz