| 1 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> |
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| 2 | <!-- |
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| 3 | $Id: protocols.html 4509 2008-09-11 20:01:44Z jari $ |
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| 4 | |
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| 5 | Copyright (C) 2005 Jari Hakkinen, Nicklas Nordborg |
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| 6 | Copyright (C) 2006 Jari Hakkinen |
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| 7 | |
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| 8 | This file is part of BASE - BioArray Software Environment. |
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| 9 | Available at http://base.thep.lu.se/ |
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| 10 | |
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| 11 | BASE is free software; you can redistribute it and/or |
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| 12 | modify it under the terms of the GNU General Public License |
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| 13 | as published by the Free Software Foundation; either version 3 |
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| 14 | of the License, or (at your option) any later version. |
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| 15 | |
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| 16 | BASE is distributed in the hope that it will be useful, |
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| 17 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 18 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 19 | GNU General Public License for more details. |
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| 20 | |
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| 21 | You should have received a copy of the GNU General Public License |
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| 22 | along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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| 23 | --> |
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| 24 | <html> |
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| 25 | <head> |
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| 26 | <title>BASE - Core specification - Protocols and hardware / software</title> |
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| 27 | <link rel=stylesheet type="text/css" href="../../styles.css"> |
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| 28 | </head> |
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| 29 | <body> |
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| 30 | |
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| 31 | <div class="navigation"> |
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| 32 | <a href="../../index.html">BASE</a> |
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| 33 | <img src="../../next.gif"> |
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| 34 | <a href="index.html">Core specification</a> |
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| 35 | <img src="../../next.gif"> |
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| 36 | Protocols and hardware / software |
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| 37 | </div> |
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| 38 | |
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| 39 | <h1>Protocols and hardware / software</h1> |
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| 40 | |
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| 41 | <div class="abstract"> |
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| 42 | <p> |
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| 43 | This document covers the details of how information about |
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| 44 | protocols, hardware and software is handled by BASE. |
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| 45 | </p> |
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| 46 | |
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| 47 | <b>Contents</b><br> |
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| 48 | <ol> |
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| 49 | <li><a href="#protocols">Protocols</a> |
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| 50 | <li><a href="#hardware">Hardware</a> |
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| 51 | <li><a href="#software">Software</a> |
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| 52 | </ol> |
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| 53 | |
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| 54 | <b>See also</b><br> |
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| 55 | <ul> |
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| 56 | <li><a href="../../development/overview/data/wares.html">Implementation overview - hardware and software</a> |
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| 57 | <li><a href="../../development/overview/data/protocols.html">Implementation overview - protocols</a> |
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| 58 | </ul> |
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| 59 | |
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| 60 | <p class="authors"> |
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| 61 | <b>Last updated:</b> $Date: 2008-09-11 20:01:44 +0000 (Thu, 11 Sep 2008) $ |
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| 62 | </p> |
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| 63 | </div> |
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| 64 | |
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| 65 | <a name="protocols"> |
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| 66 | <h2>1. Protocols</h2> |
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| 67 | </a> |
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| 68 | |
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| 69 | <ol> |
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| 70 | <li>A protocol describes a standardized procedure for doing something. |
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| 71 | <li>There are multiple types of protocols, corresponding to different |
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| 72 | tables or actions in BASE. Some protocol types (mostly concerning |
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| 73 | biomaterials) are system protocol types, required to exist and |
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| 74 | not be modified by users. More protocol types can be created as |
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| 75 | needed. |
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| 76 | <li>The standard protocol types are: |
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| 77 | sampling, extraction, labeling, pooling, hybridization, printing, |
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| 78 | scanning, feature extraction. |
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| 79 | <li>Custom protocol types are needed to describe user-defined events |
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| 80 | in the array LIMS. |
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| 81 | <li>A protocol is of a single protocol type. |
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| 82 | <li class="invalid">A protocol may be annotated. |
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| 83 | <li>A single file may be attached to a protocol. |
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| 84 | <li class="question invalid">[implementation note] There should be a dummy protocol |
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| 85 | "none" for each system protocol type. |
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| 86 | </ol> |
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| 87 | |
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| 88 | |
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| 89 | <a name="hardware"> |
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| 90 | <h2>2. Hardware</h2> |
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| 91 | </a> |
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| 92 | |
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| 93 | <ol> |
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| 94 | <li>A hardware item represents a physical piece of hardware. |
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| 95 | <li>There are different types of hardware. So far the only |
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| 96 | type is scanner. |
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| 97 | </ol> |
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| 98 | |
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| 99 | |
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| 100 | <a name="software"> |
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| 101 | <h2>3. Software</h2> |
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| 102 | </a> |
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| 103 | |
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| 104 | <ol> |
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| 105 | <li>There is one type of software: feature extraction software. |
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| 106 | <li>The software item describes a particular software version. |
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| 107 | </ol> |
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| 108 | |
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| 109 | |
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| 110 | </body> |
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| 111 | </html> |
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