source: trunk/doc/drafts/doc.txt @ 3161

Last change on this file since 3161 was 3161, checked in by Martin Svensson, 16 years ago

Added "id" attribute to each part and chapter in the docbook book.
Changed the TOC to only be 2 levels deep at all places(book, part, chapter etc).
Correct a misspelling in the documentation plan.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 5.6 KB
Line 
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  - Handles massive amount of data
12  - All experiment information in one place
13  - Coop.s
14   
15- Overview of BASE
16  - Terminology used in BASE / real world
17  - Pre-knowledge
18    - For users
19    - For admin
20
21====================
22* User documentation
23====================
24
25- How to use this document
26
27- GUI
28  - Introduction
29    - Help texts
30    - Menu bar
31    - Tool bar
32    - Ctrl/alt/shift - click
33  - Configuration
34  - Main page
35    - News
36  - List pages
37    - Filters
38    - Table configuration
39      - Hits/page
40      - Column config
41  - View pages
42    - Listed parent, child items, annotations etc.
43
44- Projects and the permission system
45  - Introduction
46    - How it works (in an users point of view)
47    - Permissions on an item
48  - Share items
49  - The active project
50  - Project
51    - Project management
52    - Items overview
53   
54- Trashcan
55  - Introduction
56  - Manage deleted items
57
58- File upload/File system
59  - Introduction
60    - Where are the files physically stored
61  - Upload file before use
62  - File management
63    - New directory
64    - Uploadfile
65    - Edit file
66    - Delete/Restore
67    - Move offline
68    - Move directory
69
70- Reporters
71  - Introduction
72  - Reporter management
73    - New/Edit
74    - Delete/Restore
75    - Reporter lists 
76
77- Annotations
78  - Introduction
79    - Inherited
80  - Types
81    - management
82      - New/edit
83      - Delete/Restore
84  - Categories
85    - Management
86      - New/edit
87      - Delete/Restore
88
89- Protocols
90  - Types
91    - Protocol type management
92  - Protocol management
93    - Parameters
94
95- Hardware
96  - Types
97  - Hardware management
98
99- Software
100  - Types
101  - Software management
102
103- Array LIMS
104  - Plates
105    - Introduction
106    - Plate types
107    - Plate mappings
108      - Merge
109    - Plate management
110      - Wells
111      - Events
112 
113  - Array designs and slides
114    - Introduction
115    - Designs   
116      - Features
117    - Slides
118      - Batch
119      - Slide management
120        - Create multiple new
121
122- Biomaterials
123  - Introduction
124    - Workflow
125    - Create children   
126    - Biomaterial event
127  - Biosources
128    - Biosource management
129      - Create/Edit
130      - Delete/Restore
131  - Samples
132    - Sample management
133      - Create/Edit
134        - Pool
135      - Delete/Restore
136  - Extracts
137    - Extract management
138      - Create/Edit
139        - Pool
140      - Delete/Restore
141  - Labeled extracts
142    - Labels
143      - Label management
144    - Labeled extract management
145      - Create/Edit
146        - Pool
147      - Delete/Restore   
148  - Hybridizations
149    - Hybridization management
150      - Create/Edit
151      - Delete/Restore 
152
153- Experiments and analysis
154  - Scans and images
155    - Scan management
156      - image management
157  - Raw bioassays
158    - Create spot images
159    - Raw data
160  - Experiments
161  - Raw data types
162    - Affymetrix data
163  - Creating a root bioassayset
164  - Bioassayset
165    - Overview plots
166  - Filtering
167    - Formulas
168      - Formula management
169  - Normalization
170  - Running a (analysis?)plugin
171    - Messages
172  - Plot tool
173    - Scatter plot
174    - Histogram plot
175  - Experiment overview
176    - Validation of an experiment
177      - Options
178  - Experiment explorer
179    - Reporter view
180    - Reporter search
181  - Using MeV
182 
183- Import and export of data
184  - Import
185    - Plugins
186      - Auto detect
187    - File Format
188      - Auto detect
189  - Export
190    - Table exporter
191
192=====================
193* Admin documentation
194=====================
195
196- Installation and upgrade
197  - Requirements
198    - MySQL, settings, options, etc.
199    - Postgres, settings, options, etc.
200  - Configuration
201    - Raw data types
202    - Extended properties
203    - base.config reference
204    - other configuration files (log4j.properities, web.xml, etc.)
205  - Job agents
206    - jobagent.properties reference
207    - jobagent.sh reference
208 
209- Installing plugins
210  - Plugin configurations
211    - "Test with file" feature for creating import configurations
212  - BASE 1 plugins
213  - Core plugins and configurations
214
215- Adding users, groups, roles
216  - Projects and the permission system
217  - The default roles: admin, power user, user and guest
218  - Quota
219
220
221=========================
222* Developer documentation
223=========================
224- Overview of BASE2
225
226- Plugin developer
227  - How to organize your plugin project
228    - With Ant
229    - With Eclipse
230    - Packaging and installing the plugin
231  - The Plugin API
232    - Interfaces
233    - Asking for parameters
234      - Using custom JSP pages for parameters
235  - Import plugins
236    - Autodetecting importer
237    - The AbstractFlatFileImporter superclass
238  - Export plugins
239    - Immediate download of exported data
240  - Analysis plugins
241  - Other plugins
242    - Authentication plugins
243    - Secondary file storage plugins
244    - File unpacker plugins
245  - Example plugins (with download)
246
247- API overview (how to use and code examples)
248  - Database schema (Data layer API)
249  - The Core API
250  - The Query API
251  - Analysis and the Dynamic and Batch API
252  - Other useful classes and methods
253
254- Javadoc
255     
256- Core developer reference
257  - Important procedures
258  - Publishing a new release
259  - Subversion / building BASE
260  - Coding rules and guidelines
261    - Development process
262    - General coding style guidelines
263    - API changes and backwards compatibility
264    - Data-layer rules
265    - Item-class rules
266    - Batch-class rules
267    - Test-class rules
268  - Internals of the Core API
269    - Authentication and sessions
270    - Access permissions
271    - Data validation
272    - Transaction handling
273    - Create/read/write/delete operations
274    - Batch operations
275    - Quota
276    - Plugin execution / job queue
277
278=======
279* Index
280=======
281
282
283
284
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