source: trunk/doc/drafts/doc.txt @ 3146

Last change on this file since 3146 was 3146, checked in by Martin Svensson, 16 years ago

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1
2==========
3* Overview
4==========
5
6- Why use BASE
7  - Low cost
8  - Opensource/GNU-GPL 
9  - Easy to use
10  - Plugin interface
11  - All experiment information in one place
12  - Handles massive amount of data
13  - Coop.s
14   
15- Overview of BASE
16  - Terminology used in BASE / real world
17  - Pre-knowledge
18    - user
19    - admin
20
21====================
22* User documentation
23====================
24
25- How to use this document
26
27- GUI configuration
28  - Introduction
29    - Menu bar
30    - Tool bar
31    - Ctrl/alt/shift - click
32  - List pages
33    - Filters
34    - Table configuration
35      - Hits/page
36      - Column config
37  - View pages
38    - Listed parent/child items
39
40- Projects and the permission system
41  - Introduction
42    - How it works in an users point of view
43  - Share items
44  - The active project
45  - Project
46    - Project managing
47    - Items overview
48
49- File upload/File system
50  - Introduction
51    - Where are the files physically stored
52  - Upload file before use
53  - File managing
54    - New directory
55    - Uploadfile
56    - Edit file
57    - Delete/Restore
58    - Move offline
59    - Move directory
60
61- Reporters
62  - Introduction
63  - Reporter managing
64    - New/Edit
65    - Delete/Restore
66    - Reporter lists 
67
68- Annotations
69  - Introduction
70  - Types
71  - Categories   
72
73- Array LIMS
74  - Plates
75    - Introduction
76  - Array designs and slides
77    - Introduction
78    - Designs   
79      - Features
80    - Slides
81      - Batch
82      - Create multiple
83
84- Biomaterials
85  - Biosources
86  - Samples
87  - Extracts
88  - Labeled extracts
89  - Hybridizations
90
91- Experiments and analysis
92  - Scans and images
93  - Raw bioassays
94  - Experiments
95  - Raw data types
96    - Affymetrix data
97  - Creating a root bioassayset
98  - Filtering
99  - Normalization
100  - Running a plugin
101    - Messages
102  - Plot tool
103  - Experiment overview
104  - Experiment explorer
105  - Using MeV
106 
107- Import and export of data
108
109=====================
110* Admin documentation
111=====================
112
113- Installation and upgrade
114  - Requirements
115    - MySQL, settings, options, etc.
116    - Postgres, settings, options, etc.
117  - Configuration
118    - Raw data types
119    - Extended properties
120    - base.config reference
121    - other configuration files (log4j.properities, web.xml, etc.)
122  - Job agents
123    - jobagent.properties reference
124    - jobagent.sh reference
125 
126- Installing plugins
127  - Plugin configurations
128    - "Test with file" feature for creating import configurations
129  - BASE 1 plugins
130  - Core plugins and configurations
131
132- Adding users, groups, roles
133  - Projects and the permission system
134  - The default roles: admin, power user, user and guest
135  - Quota
136
137
138=========================
139* Developer documentation
140=========================
141- Overview of BASE2
142
143- Plugin developer
144  - How to organize your plugin project
145    - With Ant
146    - With Eclipse
147    - Packaging and installing the plugin
148  - The Plugin API
149    - Interfaces
150    - Asking for parameters
151      - Using custom JSP pages for parameters
152  - Import plugins
153    - Autodetecting importer
154    - The AbstractFlatFileImporter superclass
155  - Export plugins
156    - Immediate download of exported data
157  - Analysis plugins
158  - Other plugins
159    - Authentication plugins
160    - Secondary file storage plugins
161    - File unpacker plugins
162  - Example plugins (with download)
163
164- API overview (how to use and code examples)
165  - Database schema (Data layer API)
166  - The Core API
167  - The Query API
168  - Analysis and the Dynamic and Batch API
169  - Other useful classes and methods
170
171- Javadoc
172     
173- Core developer reference
174  - Important procedures
175  - Publishing a new release
176  - Subversion / building BASE
177  - Coding rules and guidelines
178    - Development process
179    - General coding style guidelines
180    - Data-layer rules
181    - Item-class rules
182    - Batch-class rules
183    - Test-class rules
184  - Internals of the Core API
185    - Authentication and sessions
186    - Access permissions
187    - Data validation
188    - Transaction handling
189    - Create/read/write/delete operations
190    - Batch operations
191    - Quota
192    - Plugin execution / job queue
193
194=======
195* Index
196=======
197
198
199
200
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