source: trunk/doc/drafts/doc.txt @ 3148

Last change on this file since 3148 was 3148, checked in by Martin Svensson, 16 years ago

Contents of documentation

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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  - 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  - Congifuration
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  - Hardware management
97
98- Software
99  - Software management
100
101- Array LIMS
102  - Plates
103    - Introduction
104    - Plate types
105    - Plate mappings
106      - Merge
107    - Plate management
108      - Wells
109      - Events
110 
111  - Array designs and slides
112    - Introduction
113    - Designs   
114      - Features
115    - Slides
116      - Batch
117      - Slide management
118        - Create multiple new
119
120- Biomaterials
121  - Introduction
122    - Workflow
123    - Create children   
124    - Biomaterial event
125  - Biosources
126    - Biosource management
127      - Create/Edit
128      - Delete/Restore
129  - Samples
130    - Sample management
131      - Create/Edit
132        - Pool
133      - Delete/Restore
134  - Extracts
135    - Extract management
136      - Create/Edit
137        - Pool
138      - Delete/Restore
139  - Labeled extracts
140    - Labels
141      - Label management
142    - Labeled extract management
143      - Create/Edit
144        - Pool
145      - Delete/Restore   
146  - Hybridizations
147    - Hybridization management
148      - Create/Edit
149      - Delete/Restore 
150
151- Experiments and analysis
152  - Scans and images
153    - Scan management
154      - image management
155  - Raw bioassays
156  - Experiments
157  - Raw data types
158    - Affymetrix data
159  - Creating a root bioassayset
160  - Bioassayset
161    - Overview plots
162  - Filtering
163    - Formulas
164      - Formula management
165  - Normalization
166  - Running a (analysis?)plugin
167    - Messages
168  - Plot tool
169    - Scatter plot
170    - Histogram plot
171  - Experiment overview
172    - Validation of an experiment
173      - Options
174  - Experiment explorer
175    - Reporter view
176    - Reporter search
177  - Using MeV
178 
179- Import and export of data
180  - Import
181    - Plugins
182      - Auto detect
183    - File Format
184      - Auto detect
185  - Export
186    - Table exporter
187
188=====================
189* Admin documentation
190=====================
191
192- Installation and upgrade
193  - Requirements
194    - MySQL, settings, options, etc.
195    - Postgres, settings, options, etc.
196  - Configuration
197    - Raw data types
198    - Extended properties
199    - base.config reference
200    - other configuration files (log4j.properities, web.xml, etc.)
201  - Job agents
202    - jobagent.properties reference
203    - jobagent.sh reference
204 
205- Installing plugins
206  - Plugin configurations
207    - "Test with file" feature for creating import configurations
208  - BASE 1 plugins
209  - Core plugins and configurations
210
211- Adding users, groups, roles
212  - Projects and the permission system
213  - The default roles: admin, power user, user and guest
214  - Quota
215
216
217=========================
218* Developer documentation
219=========================
220- Overview of BASE2
221
222- Plugin developer
223  - How to organize your plugin project
224    - With Ant
225    - With Eclipse
226    - Packaging and installing the plugin
227  - The Plugin API
228    - Interfaces
229    - Asking for parameters
230      - Using custom JSP pages for parameters
231  - Import plugins
232    - Autodetecting importer
233    - The AbstractFlatFileImporter superclass
234  - Export plugins
235    - Immediate download of exported data
236  - Analysis plugins
237  - Other plugins
238    - Authentication plugins
239    - Secondary file storage plugins
240    - File unpacker plugins
241  - Example plugins (with download)
242
243- API overview (how to use and code examples)
244  - Database schema (Data layer API)
245  - The Core API
246  - The Query API
247  - Analysis and the Dynamic and Batch API
248  - Other useful classes and methods
249
250- Javadoc
251     
252- Core developer reference
253  - Important procedures
254  - Publishing a new release
255  - Subversion / building BASE
256  - Coding rules and guidelines
257    - Development process
258    - General coding style guidelines
259    - Data-layer rules
260    - Item-class rules
261    - Batch-class rules
262    - Test-class rules
263  - Internals of the Core API
264    - Authentication and sessions
265    - Access permissions
266    - Data validation
267    - Transaction handling
268    - Create/read/write/delete operations
269    - Batch operations
270    - Quota
271    - Plugin execution / job queue
272
273=======
274* Index
275=======
276
277
278
279
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