Ignore:
Timestamp:
Jun 8, 2005, 4:05:52 PM (18 years ago)
Author:
Nicklas Nordborg
Message:

Major update to the documentation structure to prepare for the
upcoming documentation project

Location:
trunk/doc/specifications/core
Files:
15 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/specifications/core/accesscontrol.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
    2 
    3 <!-- $Id$ -->
    4 
     2<!--
     3  $Id$
     4
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
     8
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: Access control</title>
     28    <title>BASE - Core specification - Access control</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21     Access control</h1>
     41  <h1>Access control</h1>
    2242
    2343  <div class="abstract">
     
    3353    <li><a href="#role">Role-based access</a>
    3454    <li><a href="#project">Project-based access</a>
    35     <li><a href="../../api/develop/net/sf/basedb/core/data/doc-files/authentication.html">Implementation overview</a>
    36       (another document)
    3755    </ol>
     56   
     57    <b>See also</b><br>
     58    <ul>
     59    <li><a href="../../development/overview/data/authentication.html">Implementation overview</a>
     60    </ul>
    3861
    3962    <p class="authors">
  • trunk/doc/specifications/core/annotations.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
     2<!--
     3  $Id$
    24
    3 <!-- $Id$ -->
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
    48
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: Annotations</title>
     28    <title>BASE - Core specification - Annotations</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21      Annotations</h1>
     41  <h1>Annotations</h1>
    2242
    2343  <div class="abstract">
     
    3252    <li><a href="#types">Annotation types</a>
    3353    <li><a href="#ontologies">Standard ontologies</a>
    34 <!--
    35     <li><a href="../../api/develop/net/sf/basedb/core/data/doc-files/annotations.html">Implementation overview</a>
    36       (another document)
    37 -->
    3854    </ol>
     55   
     56    <b>See also</b><br>
     57    <ul>
     58    <li><a href="../../development/overview/data/annotations.html">Implementation overview</a>
     59    </ul>
    3960
    4061    <p class="authors">
  • trunk/doc/specifications/core/arraylims.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
    2 
    3 <!-- $Id$ -->
    4 
     2<!--
     3  $Id$
     4
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
     8
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: Array LIMS</title>
     28    <title>BASE - Core specification - Array LIMS</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21     Array LIMS</h1>
     41  <h1>Array LIMS</h1>
    2242
    2343  <div class="abstract">
     
    3757    <li><a href="#arraybatch">Array batch</a>
    3858    <li><a href="#arrayslide">Array slide</a>
    39 <!--
    40     <li><a href="../../api/develop/net/sf/basedb/core/data/doc-files/lims_plates.html">Implementation overview - plates</a>
    41       (another document)
    42     <li><a href="../../api/develop/net/sf/basedb/core/doc-files/lims_arrays.html">Implementation overview - arrays</a>
    43       (another document)
    44 -->
    4559    </ol>
     60   
     61    <b>See also</b><br>
     62    <ul>
     63    <li><a href="../../development/overview/data/plates.html">Implementation overview - plates</a>
     64    <li><a href="../../development/overview/data/slides.html">Implementation overview - slides</a>
     65    </ul>
    4666
    4767    <p class="authors">
  • trunk/doc/specifications/core/authentication.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
    2 
    3 <!-- $Id$ -->
    4 
     2<!--
     3  $Id$
     4
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
     8
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: User authentication and management</title>
     28    <title>BASE - Core specification - User authentication and management</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21     User authentication and management</h1>
     41  <h1>User authentication and management</h1>
    2242
    2343  <div class="abstract">
     
    3353    <li><a href="#group">Group management</a>
    3454    <li><a href="#role">Role management</a>
    35     <li><a href="../../api/develop/net/sf/basedb/core/data/doc-files/authentication.html">Implementation overview</a>
    36       (another document)
    3755    </ol>
     56   
     57    <b>See also</b><br>
     58    <ul>
     59    <li><a href="../../development/overview/data/authentication.html">Implementation overview</a>
     60    </ul>
    3861
    3962    <p class="authors">
  • trunk/doc/specifications/core/biomaterials.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
     2<!--
     3  $Id$
    24
    3 <!-- $Id$ -->
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
    48
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: Biomaterials</title>
     28    <title>BASE - Core specification - Biomaterials</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21      Biomaterials</h1>
     41  <h1>Biomaterials</h1>
    2242
    2343  <div class="abstract">
     
    3050    <ol>
    3151    <li><a href="#biomaterials">Biomaterials</a>
    32 <!--
    33     <li><a href="../../api/develop/net/sf/basedb/core/data/doc-files/biomaterials.html">Implementation overview</a>
    34       (another document)
    35 -->
    3652    </ol>
     53   
     54    <b>See also</b><br>
     55    <ul>
     56    <li><a href="../../development/overview/data/biomaterial.html">Implementation overview</a>
     57    </ul>
    3758
    3859    <p class="authors">
  • trunk/doc/specifications/core/defaultdata.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
    2 
    3 <!-- $Id$ -->
    4 
     2<!--
     3  $Id$
     4
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
     8
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: Default data for a new installations</title>
     28    <title>BASE - Core specification - Default data for a new installations</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21     Default data for a new installations</h1>
     41  <h1>Default data for a new installations</h1>
    2242
    2343  <div class="abstract">
  • trunk/doc/specifications/core/experiments.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
    2 
    3 <!-- $Id$ -->
    4 
     2<!--
     3  $Id$
     4
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
     8
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: Experiments and analysis</title>
     28    <title>BASE - Core specification - Experiments and analysis</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21     Experiments and analysis</h1>
     41  <h1>Experiments and analysis</h1>
    2242
    2343  <div class="abstract">
  • trunk/doc/specifications/core/fileupload.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
    2 
    3 <!-- $Id$ -->
    4 
     2<!--
     3  $Id$
     4
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
     8
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: File upload and disk quota</title>
     28    <title>BASE - Core specification - File upload and disk quota</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21      File upload and disk quota</h1>
     41  <h1>File upload and disk quota</h1>
    2242
    2343  <div class="abstract">
     
    3252    <li><a href="#secondary">Secondary storage</a>
    3353    <li><a href="#quota">Disk quota</a>
    34 <!--
    35     <li><a href="../../api/develop/net/sf/basedb/core/data/doc-files/files.html">Implementation overview - files and directories</a>
    36       (another document)
    37     <li><a href="../../api/develop/net/sf/basedb/core/data/doc-files/quota.html">Implementation overview - quota</a>
    38       (another document)
    39 -->
    4054    </ol>
     55
     56    <b>See also</b><br>
     57    <ul>
     58    <li><a href="../../development/overview/data/files.html">Implementation overview - files</a>
     59    <li><a href="../../development/overview/data/quota.html">Implementation overview - quota</a>
     60    </ul>
    4161
    4262    <p class="authors">
  • trunk/doc/specifications/core/hybridizations.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
    2 
    3 <!-- $Id$ -->
    4 
     2<!--
     3  $Id$
     4
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
     8
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: Hybridizations and raw data</title>
     28    <title>BASE - Core specification - Hybridizations and raw data</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21      Hybridizations and raw data</h1>
     41  <h1>Hybridizations and raw data</h1>
    2242
    2343  <div class="abstract">
     
    3454    <li><a href="#rawdata">Raw data</a>
    3555    <li><a href="#spotimages">Spot images</a>
    36 <!--
    37     <li><a href="../../api/develop/net/sf/basedb/core/data/doc-files/hybridizations.html">Implementation overview</a>
    38       (another document)
    39 -->
    4056    </ol>
     57   
     58    <b>See also</b><br>
     59    <ul>
     60    <li><a href="../../development/overview/data/hybridizations.html">Implementation overview</a>
     61    </ul>
    4162
    4263    <p class="authors">
  • trunk/doc/specifications/core/importexport.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
     2<!--
     3  $Id$
    24
    3 <!-- $Id$ -->
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
    48
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: Data import and export</title>
     28    <title>BASE - Core specification - Data import and export</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21     Data import and export</h1>
     41  <h1>Data import and export</h1>
    2242
    2343  <div class="abstract">
  • trunk/doc/specifications/core/index.html

    r190 r729  
    1 
    21<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
    3 
    4 <!-- $Id$ -->
    5 
     2<!--
     3  $Id$
     4
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
     8
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    626<html>
    727  <head>
    8     <title>BASE 2.0 - Core specification</title>
     28    <title>BASE - Core specification</title>
    929  <link rel=stylesheet type="text/css" href="../../styles.css">
    1030  </head>
    1131<body>
    1232<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     33  <a href="../../index.html">BASE</a>
    1434  <img src="../../next.gif">
    1535  Core specification
    1636</div>
    1737
    18   <h1>BASE 2.0 - Core specification</h1>
     38  <h1>Core specification</h1>
    1939
    2040  <div class="abstract">
  • trunk/doc/specifications/core/jobqueue.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
     2<!--
     3  $Id$
    24
    3 <!-- $Id$ -->
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
    48
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: Job controller / queue system</title>
     28    <title>BASE - Core specification - Job controller / queue system</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21     Job controller / queue system</h1>
     41  <h1>Job controller / queue system</h1>
    2242
    2343  <div class="abstract">
  • trunk/doc/specifications/core/protocols.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
     2<!--
     3  $Id$
    24
    3 <!-- $Id$ -->
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
    48
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: Protocols and hardware / software</title>
     28    <title>BASE - Core specification - Protocols and hardware / software</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21      Protocols and hardware / software</h1>
     41  <h1>Protocols and hardware / software</h1>
    2242
    2343  <div class="abstract">
     
    3252    <li><a href="#hardware">Hardware</a>
    3353    <li><a href="#software">Software</a>
    34 <!--
    35     <li><a href="../../api/develop/net/sf/basedb/core/data/doc-files/protocols.html">Implementation overview</a>
    36       (another document)
    37 -->
    3854    </ol>
     55   
     56    <b>See also</b><br>
     57    <ul>
     58    <li><a href="../../development/overview/data/wares.html">Implementation overview - hardware and software</a>
     59    <li><a href="../../development/overview/data/protocols.html">Implementation overview - protocols</a>
     60    </ul>
    3961
    4062    <p class="authors">
  • trunk/doc/specifications/core/reporters.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
     2<!--
     3  $Id$
    24
    3 <!-- $Id$ -->
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
    48
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: Reporters</title>
     28    <title>BASE - Core specification - Reporters</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21      Reporters</h1>
     41  <h1>Reporters</h1>
    2242
    2343  <div class="abstract">
     
    3050    <ol>
    3151    <li><a href="#reporters">Reporters</a>
    32 <!--
    33     <li><a href="../../api/develop/net/sf/basedb/core/data/doc-files/reporters.html">Implementation overview</a>
    34       (another document)
    35 -->
    3652    </ol>
     53   
     54    <b>See also</b><br>
     55    <ul>
     56    <li><a href="../../development/overview/data/reporters.html">Implementation overview</a>
     57    </ul>
    3758
    3859    <p class="authors">
  • trunk/doc/specifications/core/sessionsettings.html

    r190 r729  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
     2<!--
     3  $Id$
    24
    3 <!-- $Id$ -->
     5  BioArray Software Environment (BASE) - http://base.thep.lu.se/
     6  Copyright (C) 2002-2004 Lao Saal, Carl Troein,
     7  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
    48
     9  This file is part of BASE.
     10
     11  BASE is free software; you can redistribute it and/or
     12  modify it under the terms of the GNU General Public License
     13  as published by the Free Software Foundation; either version 2
     14  of the License, or (at your option) any later version.
     15
     16  BASE is distributed in the hope that it will be useful,
     17  but WITHOUT ANY WARRANTY; without even the implied warranty of
     18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     19  GNU General Public License for more details.
     20
     21  You should have received a copy of the GNU General Public License
     22  along with this program; if not, write to the Free Software
     23  Foundation, Inc., 59 Temple Place - Suite 330,
     24  Boston, MA  02111-1307, USA.
     25-->
    526<html>
    627  <head>
    7     <title>BASE 2.0 - Core specification: Sessions and application settings</title>
     28    <title>BASE - Core specification - Sessions and application settings</title>
    829  <link rel=stylesheet type="text/css" href="../../styles.css">
    930  </head>
     
    1132
    1233<div class="navigation">
    13   <a href="../../index.html">BASE 2.0</a>
     34  <a href="../../index.html">BASE</a>
    1435  <img src="../../next.gif">
    1536  <a href="index.html">Core specification</a>
     
    1839</div>
    1940
    20   <h1>BASE 2.0 - Core specification:<br>
    21     Sessions and application settings</h1>
     41  <h1>Sessions and application settings</h1>
    2242
    2343  <div class="abstract">
     
    3151    <li><a href="#session">Sessions</a>
    3252    <li><a href="#settings">Settings</a>
    33     <li><a href="../../api/develop/net/sf/basedb/core/data/doc-files/clients.html">Implementation overview</a>
    34       (another document)
    3553    </ol>
     54   
     55    <b>See also</b><br>
     56    <ul>
     57    <li><a href="../../development/overview/data/clients.html">Implementation overview</a>
     58    </ul>
    3659
    3760    <p class="authors">
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