Changeset 4395
- Timestamp:
- Aug 15, 2008, 1:10:59 PM (15 years ago)
- Location:
- trunk/doc
- Files:
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- 2 edited
- 1 moved
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historical/getting_started.html (moved) (moved from trunk/doc/user/getting_started.html)
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src/docbook/userdoc/overview.xml (modified) (1 diff)
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test/index.html (modified) (1 diff)
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trunk/doc/src/docbook/userdoc/overview.xml
r3892 r4395 3 3 "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" 4 4 "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> 5 <!-- 6 $Id$ 7 8 Copyright (C) 2007 Nicklas Nordborg, Martin Svensson 9 10 This file is part of BASE - BioArray Software Environment. 11 Available at http://base.thep.lu.se/ 12 13 BASE is free software; you can redistribute it and/or 14 modify it under the terms of the GNU General Public License 15 as published by the Free Software Foundation; either version 2 16 of the License, or (at your option) any later version. 17 18 BASE is distributed in the hope that it will be useful, 19 but WITHOUT ANY WARRANTY; without even the implied warranty of 20 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 21 GNU General Public License for more details. 22 23 You should have received a copy of the GNU General Public License 24 along with this program; if not, write to the Free Software 25 Foundation, Inc., 59 Temple Place - Suite 330, 26 Boston, MA 02111-1307, USA. 27 --> 28 5 <!-- 6 $Id$ Copyright (C) 2007 Nicklas Nordborg, Martin 7 Svensson This file is part of BASE - BioArray Software Environment. Available at 8 http://base.thep.lu.se/ BASE is free software; you can redistribute it and/or modify it under the 9 terms of the GNU General Public License as published by the Free Software Foundation; either 10 version 2 of the License, or (at your option) any later version. BASE is distributed in the hope 11 that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of 12 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more 13 details. You should have received a copy of the GNU General Public License along with this 14 program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, 15 MA 02111-1307, USA. 16 --> 29 17 <chapter id="userdoc_overview" chunked="0"> 30 18 <?dbhtml dir="overview"?> 31 19 <title>Overview of user documentation</title> 32 <para> 33 The 'User documentation' part is quite extensive and covers everything from how to login on a 34 BASE2 server and find your way through the program, to working with experiments and doing 35 some useful analysis. The intention with this chapter is to give an overview of the 36 following chapters so it will be easier for you to know where to look for certain 37 information in case you don't want to read the whole part from the beginning to the end. 38 </para> 39 20 <para> The 'User documentation' part is quite extensive and covers everything from how to login on 21 a BASE2 server and find your way through the program, to working with experiments and doing some 22 useful analysis. The intention with this chapter is to give an overview of the following chapters 23 so it will be easier for you to know where to look for certain information in case you don't want 24 to read the whole part from the beginning to the end.</para> 40 25 <sect1 id="userdoc_overview.environment"> 41 26 <title>Working environment</title> 42 <para> 43 Before you start working with any big experiment or project in BASE it could be a good 44 idea to get to know the environment and perhaps personalize some behavior and appearance 45 of the program. When this is done your daily work in BASE will be much easier and you 46 will feel more comfortable working with the program. 47 </para> 48 49 <para> 50 Most of the things that have to do with the working environment are gathered in one 51 chapter, where the first subsection, 52 <xref linkend="webclient.introduction" />, 53 gives a good guidance how to start using BASE including a general explanation 54 how to navigate your way through the program. 55 </para> 56 27 <para> Before you start working with any big experiment or project in BASE it could be a good idea 28 to get to know the environment and perhaps personalize some behavior and appearance of the 29 program. When this is done your daily work in BASE will be much easier and you will feel more 30 comfortable working with the program.</para> 31 <para> 32 Most of the things that have to do with the working environment are gathered in one chapter, 33 where the first subsection, 34 <xref linkend="webclient.introduction" /> 35 , gives a good guidance how to start using BASE including a general explanation how to navigate 36 your way through the program. 37 </para> 57 38 <para> 58 39 The second subsection, 59 <xref linkend="webclient.configuration" />, 60 describes how to personlize BASE with contact information, preferences and changing 61 password. The preferences are for instance some appearance like date format, text size 62 or the look of the toolbar buttons. 63 </para> 64 40 <xref linkend="webclient.configuration" /> 41 , describes how to personlize BASE with contact information, preferences and changing password. 42 The preferences are for instance some appearance like date format, text size or the look of the 43 toolbar buttons. 44 </para> 65 45 <para> 66 46 The last two subsections, 67 47 <xref linkend="webclient.items" /> 68 48 and 69 <xref linkend="webclient.itemlist" />, 70 in the webclient chapter explains how to work with BASE. No matter what you 71 are going to do the user interface contains a lot of common functions that 72 works the same everywhere. For example, how to list and search for items, 73 how to create new items and modify and delete existing items. Subsequent 74 chapters with detailed information about each type of item will usually 75 not include descriptions of the common functionality. 49 <xref linkend="webclient.itemlist" /> 50 , in the webclient chapter explains how to work with BASE. No matter what you are going to do the 51 user interface contains a lot of common functions that works the same everywhere. For example, 52 how to list and search for items, how to create new items and modify and delete existing items. 53 Subsequent chapters with detailed information about each type of item will usually not include 54 descriptions of the common functionality. 76 55 </para> 77 56 </sect1> 78 79 57 <sect1 id="userdoc_overview.start2work"> 80 58 <title>Start working with BASE</title> 81 59 <para> 82 There are some working principles that need to be understood by all users in BASE. These 83 concern the permission system and how to get the workflow to move on without any 84 disturbance caused by insufficient permissions. The key is to work in projects, which 85 is covered in detail in <xref linkend="project_permission" />. 86 </para> 87 <para> 88 Understanding the permission system and how to work in projects will not only make it 89 more simple for you to work in BASE but also for your co-workers who want access to your 90 data. 91 </para> 92 <para> 93 The next thing to do is to add some relevant 94 data to work with. Most of the different items can be created manually from the 95 web client, but some items and data must be imported from files. Before importing a file, 96 it has to be uploaded on the BASE-server's filesystem. 60 There are some working principles that need to be understood by all users in BASE. These concern 61 the permission system and how to get the workflow to move on without any disturbance caused by 62 insufficient permissions. The key is to work in projects, which is covered in detail in 63 <xref linkend="project_permission" /> 64 . 65 </para> 66 <para> 67 Understanding the permission system and how to work in projects will not only make it more 68 simple for you to work in BASE but also for your co-workers who want access to your data. 69 </para> 70 <para> 71 The next thing to do is to add some relevant data to work with. Most of the different items can 72 be created manually from the web client, but some items and data must be imported from files. 73 Before importing a file, it has to be uploaded on the BASE-server's filesystem. 97 74 <xref linkend="file_system" /> 98 75 gives you information about the server's file system and how to upload the files. 99 76 </para> 100 101 <para> 77 <para> 78 <xref linkend="import_export_data" /> 79 explains how the import is done. This chapter also covers how the data later on can be exported 80 from the database back into files, often simple text files or xml files. 81 </para> 82 <para> 83 Each different item has it's own section in this part of the documentation, where more 84 specific information and also some screen shots can be found. Go back to the table of contents 85 for this part and look up the item you want to know more about. 86 </para> 87 88 89 <sect2 id="userdoc_overview.start2work.getgoing"> 90 <title>Get going</title> 91 <para> 92 This description will guide you from the initiating tasks of creating the first account to 93 running an analysis plug-in. Most of the steps below ends with a reference to somewhere in the 94 documentation where more information can be found. 95 </para> 102 96 103 <xref linkend="import_export_data" /> 104 explains how the import is done. This chapter also covers how the data later on 105 can be exported from the database back into files, often simple text files or xml files. 106 </para> 107 108 <para> 109 Each different item has it's own section in this part of the documentation, where more specific 110 information and also some screen shots can be found. Go back to the table 111 of contents for this part and look up the item you want to know more about. 112 </para> 97 <sect3 id="userdoc_overview.start2work.getgoing.administrative"> 98 <title>Administrative tasks</title> 99 <para> 100 Most of the tasks in this section require more privileges than the normal user 101 credentials. As always, there are many ways to do things so steps presented here is the path 102 to get going with BASE as fast as possible without creating havoc in future use of the BASE 103 server. 104 </para> 105 <orderedlist> 106 <listitem> 107 <para> 108 Log in as 109 <prompt>root</prompt> 110 using the password you set during BASE initialization. Create an account and give it the 111 administrator-role. Switch user to the new admin account and use this for all future 112 administrative tasks. 113 </para> 114 <note> 115 <para> 116 The root-account should only be used to create the first administrator account and 117 nothing else. 118 </para> 119 </note> 120 </listitem> 121 <listitem> 122 <para> 123 First thing to do, when logged in as administrator, is to create other user-accounts 124 and give them appropriate roles, most of them should be assigned to the User-role. 125 </para> 126 <para> 127 Information related to user-accounts can be found at 128 <xref linkend="user_administration" /> 129 . 130 </para> 131 </listitem> 132 <listitem> 133 <para> 134 Next step for you as an administrator is to import reporter-map and corresponding reporters 135 to BASE. For import of Genepix data you can use the 136 <prompt>Reporter importer</prompt> 137 plug-in and 138 <prompt>Reporter map importer</prompt> 139 plug-in that come with BASE. Go to 140 <menuchoice> 141 <guimenuitem>Array LIMS</guimenuitem> 142 <guimenuitem>Array designs</guimenuitem> 143 </menuchoice> 144 or 145 <menuchoice> 146 <guimenuitem>View</guimenuitem> 147 <guimenuitem>Reporters</guimenuitem> 148 </menuchoice> 149 respectively and start the import from there. You can read more about data-import in 150 <xref linkend="import_export_data" /> 151 </para> 152 </listitem> 153 </orderedlist> 154 </sect3> 155 <sect3 id="userdoc_overview.start2work.getgoing.user"> 156 <title>User tasks</title> 157 <para> 158 A normal user is not allowed to add array design, reporter information, and a lot of 159 other information to BASE. The reason for this is that a lot of information should only exist 160 as one copy in the database. For example, reporters should only exist in one copy because 161 everyone uses the same reporters. There is no need to store several copies of the same array 162 design. 163 </para> 164 <para> 165 A user will normally upload experimental data to BASE for import into the database. To be 166 able to import the data, the array design which is used, must be available in BASE at import 167 time. If the array design is not available, a user with the proper credential must add the 168 array design to BASE. 169 </para> 170 <orderedlist> 171 <listitem> 172 <para> 173 The first thing for an user to do is creating a project to work in and set this as 174 <prompt>active project</prompt> 175 . This should be done before any other items are created. 176 <xref linkend="project_permission.projects" /> 177 tell you more how working in project can help you and your co-workers. 178 </para> 179 </listitem> 180 <listitem> 181 <para> 182 Next step is to create raw bioassays and up-load raw data to BASE. This is done in the raw 183 bioassay section.( 184 <menuchoice> 185 <guimenuitem>View</guimenuitem> 186 <guimenuitem>Raw bioassays</guimenuitem> 187 </menuchoice> 188 ) . More information see 189 <xref linkend="experiments_analysis.rawbioassay" /> 190 </para> 191 </listitem> 192 <listitem> 193 <para> 194 Now when there are data to work with, you can create your first experiment. You reach the 195 experiment section through the menu 196 <menuchoice> 197 <guimenuitem>View</guimenuitem> 198 <guimenuitem>Experiments</guimenuitem> 199 </menuchoice> 200 Further reading in 201 <xref linkend="experiments_analysis.experiments" /> 202 </para> 203 </listitem> 204 <listitem> 205 <orderedlist> 206 <listitem> 207 <para> 208 The analysis often starts with the creation of a root bioassay set. Open the recently 209 created experiment and go to the 210 <guilabel>Bioassay sets</guilabel> 211 tab. Click on the 212 <guibutton>New root bioassay set</guibutton> 213 button to start the creation. 214 </para> 215 </listitem> 216 <listitem> 217 <para> 218 With a root bioassay set you can now continue your analysis with different kinds of 219 analysis plug-in. To the right of the each listed bioassay set is a set of icons for the 220 actions that can be performed. 221 <xref linkend="experiments_analysis.analysis" /> 222 goes to the bottom of analysis in BASE. 223 </para> 224 </listitem> 225 </orderedlist> 226 </listitem> 227 </orderedlist> 228 <para> 229 This concludes the short step-by-step get going text. Far from all functionallity in BASE 230 has been convered here. E.g. nothing about LIMS or biomaterials have been mentioned. But you 231 should now at least be familiar with getting to that point when it is possible to do some 232 analysis. 233 </para> 234 </sect3> 235 </sect2> 113 236 </sect1> 114 237 </chapter> -
trunk/doc/test/index.html
r4394 r4395 56 56 <ol> 57 57 <li><a href="performance/index.html">Performance tests</a>: 58 Test one item/aspect at a time</li>58 Test the performance of BASE</li> 59 59 <li><a href="roles/index.html">Roles</a>: Big test for checking that the predefined 60 60 roles has correct permissions and can do their work as intended. This test goes
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