| 1 | ================================================================== |
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| 2 | $Id: 3rd-party-components.txt 3510 2007-06-19 06:56:23Z nicklas $ |
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| 3 | |
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| 4 | Copyright (C) Authors contributing to this file. |
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| 5 | |
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| 6 | This file is part of BASE - BioArray Software Environment. |
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| 7 | Available at http://base.thep.lu.se/ |
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| 8 | |
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| 9 | BASE is free software; you can redistribute it and/or |
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| 10 | modify it under the terms of the GNU General Public License |
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| 11 | as published by the Free Software Foundation; either version 2 |
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| 12 | of the License, or (at your option) any later version. |
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| 13 | |
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| 14 | BASE is distributed in the hope that it will be useful, |
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| 15 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 16 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 17 | GNU General Public License for more details. |
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| 18 | |
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| 19 | You should have received a copy of the GNU General Public License |
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| 20 | along with this program; if not, write to the Free Software |
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| 21 | Foundation, Inc., 59 Temple Place - Suite 330, |
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| 22 | Boston, MA 02111-1307, USA. |
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| 23 | ================================================================== |
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| 24 | |
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| 25 | ================================= |
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| 26 | 3rd-party components used by BASE |
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| 27 | ================================= |
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| 28 | |
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| 29 | Here is list of 3rd-party components used by BASE. All the jar files |
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| 30 | needed are included in the <base>/lib directory or in |
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| 31 | <base>/www/plugins sub-directories for plug-ins based on others |
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| 32 | work. The URLs given here can be used if you need more information or |
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| 33 | need to update some component. |
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| 34 | |
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| 35 | |
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| 36 | Hibernate 3 |
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| 37 | ----------- |
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| 38 | An object/relational persistence and query service for Java. Shields |
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| 39 | us from most SQL and gives us database independece. |
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| 40 | |
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| 41 | More info : http://www.hibernate.org/ |
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| 42 | Version : 3.2.4.SP1 |
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| 43 | License : LGPL (hibernate.license.txt) |
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| 44 | Jar files : hibernate3.jar, antlr-2.7.6.jar, asm.jar, asm-attrs.jar, |
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| 45 | cglib-2.1.3.jar, commons-collections-2.1.1.jar, commons-logging-1.0.4.jar |
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| 46 | dom4j-1.6.1.jar, ehcache-1.2.3.jar, jta.jar, c3p0-0.9.1.jar |
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| 47 | |
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| 48 | Note: Most of the jar files above are other 3rd-party components used by Hibernate. |
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| 49 | Base doesn't use these components directly. |
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| 50 | |
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| 51 | Log4j |
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| 52 | ----- |
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| 53 | A loggins system that makes it easy to turn on or off debugging just by |
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| 54 | editing a configuration file. This component is also used by Hibernate |
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| 55 | and we are using the same version that ships with Hibernate. |
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| 56 | |
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| 57 | More info : http://logging.apache.org/log4j/docs/ |
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| 58 | Version : 1.2.14 |
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| 59 | License : Apache License 2.0 (apache.license-2.0.txt) |
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| 60 | Jar files : log4j-1.2.14.jar |
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| 61 | |
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| 62 | JDOM |
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| 63 | ---- |
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| 64 | A library for parsing and generating XML files. |
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| 65 | |
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| 66 | More info : http://www.jdom.org/ |
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| 67 | Version : 1.0 |
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| 68 | License : Apache-style open source license (jdom.license.txt) |
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| 69 | Jar files : jdom.jar, jaxen-1.1-beta-7.jar, saxpath.jar |
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| 70 | |
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| 71 | |
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| 72 | Java Advanced Imaging (JAI) |
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| 73 | --------------------------- |
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| 74 | An image toolkit from SUN. The package consists of a few jar files and |
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| 75 | libraries for native code for different operating systems. At the moment |
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| 76 | we are only using the jar files but we must also distribute the native |
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| 77 | code libraries in order to follow the license. |
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| 78 | |
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| 79 | More info : http://java.sun.com/products/java-media/jai/index.jsp |
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| 80 | Version : 1.1.2 |
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| 81 | License : Sun Microsystems Binary Code License (jai.license.txt) |
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| 82 | Jar files : jai_core.jar, jai_codec.jar, mlibwrapper_jai.jar |
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| 83 | Other : lbmlib_jai.so, checkmmx.exe, mlib_jai.dll, mlib_jai_mmx.dll |
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| 84 | |
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| 85 | |
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| 86 | Java Servlet API |
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| 87 | ---------------- |
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| 88 | Required for creating servlets and tag libraries. From SUN. This |
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| 89 | library is only required for compiling and are not included in the |
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| 90 | distribution. The web server/servlet container should already have |
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| 91 | these API installed (that's what makes it a servlet container). |
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| 92 | |
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| 93 | More info : http://java.sun.com/products/servlet/index.jsp |
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| 94 | Version : 2.4 |
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| 95 | License : N/A |
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| 96 | Jar files : jsp-api.jar, servlet-api.jar |
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| 97 | |
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| 98 | |
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| 99 | Xerces |
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| 100 | ------ |
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| 101 | A toolkit for handling XML documents. From the Apache Software |
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| 102 | Foundation. These libraries are also needed by JDOM. |
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| 103 | |
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| 104 | More info : http://xml.apache.org/xerces2-j/index.html |
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| 105 | Version : 2.9.0 |
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| 106 | License : Apache Software License (xerces.license.txt) |
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| 107 | Jar files : xerces-2.9.0.jar, xml-apis.jar |
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| 108 | |
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| 109 | |
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| 110 | MySQL Connector/J |
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| 111 | ----------------- |
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| 112 | A JDBC driver for the MySQL database from MySQL. This library is only |
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| 113 | needed if you are using MySQL as your database. |
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| 114 | |
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| 115 | More info : http://www.mysql.com/products/connector/j/ |
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| 116 | Version : 5.0.6 |
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| 117 | License : GPL (gpl.license.txt) |
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| 118 | Jar files : mysql-connector-java-5.0.6-bin.jar |
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| 119 | |
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| 120 | |
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| 121 | PostgreSQL JDBC driver |
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| 122 | ---------------------- |
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| 123 | A JDBC driver for the PostgreSQL database. This library is only |
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| 124 | needed if you are using PostgreSQL as your database. |
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| 125 | |
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| 126 | More info : http://jdbc.postgresql.org/ |
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| 127 | Version : 8.1.407 |
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| 128 | License : BSD License (postgres.license.txt) |
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| 129 | Jar files : postgresql-8.1-407.jdbc3.jar |
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| 130 | |
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| 131 | |
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| 132 | X-Doclet |
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| 133 | -------- |
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| 134 | Used at compile-time only to generate the XML files needed by |
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| 135 | Hibernate for the database mapping. These libraries are not included in |
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| 136 | the distribution. |
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| 137 | |
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| 138 | More info : http://xdoclet.sourceforge.net/xdoclet/index.html |
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| 139 | Version : 1.2 |
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| 140 | License : XDoclet License (xdoclet.license.txt) |
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| 141 | Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar, |
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| 142 | xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar, |
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| 143 | commons-collections-2.1.1.jar, commons-logging-1.0.4.jar |
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| 144 | |
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| 145 | |
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| 146 | Java Math Expression Parser |
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| 147 | --------------------------- |
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| 148 | Parses and evaluates mathematical expressions in string. Supports |
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| 149 | most operators and funcations as well as variables. |
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| 150 | |
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| 151 | More info : http://www.singularsys.com/jep/ |
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| 152 | Version : 2.4.0 |
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| 153 | License : GPL (gpl.license.txt) |
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| 154 | Jar files : jep-2.4.0.jar |
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| 155 | |
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| 156 | |
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| 157 | JFreeChart |
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| 158 | ---------- |
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| 159 | Plotting package for bar charts, line charts, pie charts and xy plots. |
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| 160 | |
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| 161 | More info : http://www.jfree.org/ |
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| 162 | Version : 1.0.3 |
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| 163 | License : LGPL (lgpl.txt) |
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| 164 | Jar files : jfreechart-1.0.3.jar jcommon-1.0.6.jar |
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| 165 | |
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| 166 | |
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| 167 | MultiExperiment Viewer |
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| 168 | ---------------------- |
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| 169 | MeV is a versatile microarray data analysis tool, incorporating |
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| 170 | sophisticated algorithms for clustering, visualization, |
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| 171 | classification, statistical analysis and biological theme discovery. |
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| 172 | |
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| 173 | More info : http://www.tm4.org/ |
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| 174 | Version : Modified version based on official v4.0 release |
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| 175 | License : The Artisic License (http://www.tm4.org/artistic_license.pdf) |
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| 176 | Jar files : <base>/www/plugins/org/tigr/microarray/mev/*.jar |
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| 177 | |
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| 178 | Note: Most of the jar files above are other 3rd-party components used |
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| 179 | by MeV. BASE doesn't use these components directly. For access to the |
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| 180 | modifed source go to http://trac.thep.lu.se/tracs/BASE-hacks |
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| 181 | |
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| 182 | |
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| 183 | Silk icon set |
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| 184 | ------------- |
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| 185 | A very nice icon set containing 1000 icons. The entire icon set |
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| 186 | is available in the "misc" directory. We have converted the icons |
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| 187 | to GIF format (since we didn't want to scan through all web pages |
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| 188 | and replace .gif with .png). We have also created some new icons which |
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| 189 | are merely combinations of other icons, ie. taking an arrow on one icon |
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| 190 | an putting it on another. |
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| 191 | |
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| 192 | More info : http://www.famfamfam.com/lab/icons/silk/ |
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| 193 | Version : 1.3 |
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| 194 | License : Creative Commons Attribution 2.5 License |
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| 195 | (http://creativecommons.org/licenses/by/2.5/) |
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| 196 | |
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| 197 | |
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| 198 | SvnAnt |
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| 199 | ------ |
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| 200 | An 'ant' task implementation for accessing subversion from the ant buildfile. |
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| 201 | |
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| 202 | More info : http://subclipse.tigris.org/svnant.html |
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| 203 | Version : 1.1.0.RC2 |
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| 204 | License : Apache Software License 1.1 (apache.license.txt) |
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| 205 | Jar files : svnant.jar, javasvn.jar, svnClientAdapter.jar, svnjavahl.jar |
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| 206 | ganymed.jar |
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| 207 | |
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| 208 | |
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| 209 | Docbook |
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| 210 | ------- |
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| 211 | A set of DTD:s and stylesheets for creating documentation. We use |
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| 212 | the DocBook styler suite (see below) but has upgraded it to Docbook 4.5. |
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| 213 | |
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| 214 | More info: http://www.docbook.org/ |
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| 215 | Version : 4.5 |
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| 216 | License : docbook.license.txt |
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| 217 | Files : Everything in lib/docbook/docbook |
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| 218 | |
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| 219 | |
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| 220 | Docbook styler guide |
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| 221 | -------------------- |
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| 222 | An extension to docbook created by Dawid Weiss which simplifies |
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| 223 | file inclusion and building from ant. |
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| 224 | |
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| 225 | More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en |
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| 226 | Version : 2004_06_22-21_12 |
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| 227 | License : docbook.styler.guide.txt |
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| 228 | Files : Everything in lib/docbook except the 'docbook' subdirectory |
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| 229 | |
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| 230 | |
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| 231 | Affymetrix Fusion SDK |
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| 232 | --------------------- |
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| 233 | Package for reading various Affymetrix file formats. |
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| 234 | |
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| 235 | More info: http://www.affymetrix.com/support/developer/fusion/index.affx |
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| 236 | Version : 1.09 |
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| 237 | License : LGPL (lgpl.txt) |
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| 238 | Files : AffxFusion.jar |
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| 239 | |
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| 240 | TAR file support |
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| 241 | ---------------- |
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| 242 | Package for reading and writing TAR files. |
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| 243 | |
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| 244 | More info: http://www.trustice.com/java/tar/ |
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| 245 | Version : 2.5 |
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| 246 | License : tar.license.txt |
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| 247 | Files : tar.jar |
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| 248 | |
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| 249 | BZIP file support |
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| 250 | ----------------- |
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| 251 | Package for reading and writing BZIP files. |
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| 252 | |
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| 253 | More info: http://www.kohsuke.org/bzip2/ |
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| 254 | Version : unknown |
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| 255 | License : Apache software license (apache.license.txt) |
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| 256 | Files : bzip2.jar |
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| 257 | |
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| 258 | |
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| 259 | |
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