source: trunk/doc/drafts/doc.txt @ 3173

Last change on this file since 3173 was 3173, checked in by Martin Svensson, 16 years ago

Added a job chapter in the documentation

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 5.6 KB
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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  - 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- Jobs
71
72- Reporters
73  - Introduction
74  - Reporter management
75    - New/Edit
76    - Delete/Restore
77    - Reporter lists 
78
79- Annotations
80  - Introduction
81    - Inherited
82  - Types
83    - management
84      - New/edit
85      - Delete/Restore
86  - Categories
87    - Management
88      - New/edit
89      - Delete/Restore
90
91- Protocols
92  - Types
93    - Protocol type management
94  - Protocol management
95    - Parameters
96
97- Hardware
98  - Types
99  - Hardware management
100
101- Software
102  - Types
103  - Software management
104
105- Array LIMS
106  - Plates
107    - Introduction
108    - Plate types
109    - Plate mappings
110      - Merge
111    - Plate management
112      - Wells
113      - Events
114 
115  - Array designs and slides
116    - Introduction
117    - Designs   
118      - Features
119    - Slides
120      - Batch
121      - Slide management
122        - Create multiple new
123
124- Biomaterials
125  - Introduction
126    - Workflow
127    - Create children   
128    - Biomaterial event
129  - Biosources
130    - Biosource management
131      - Create/Edit
132      - Delete/Restore
133  - Samples
134    - Sample management
135      - Create/Edit
136        - Pool
137      - Delete/Restore
138  - Extracts
139    - Extract management
140      - Create/Edit
141        - Pool
142      - Delete/Restore
143  - Labeled extracts
144    - Labels
145      - Label management
146    - Labeled extract management
147      - Create/Edit
148        - Pool
149      - Delete/Restore   
150  - Hybridizations
151    - Hybridization management
152      - Create/Edit
153      - Delete/Restore 
154
155- Experiments and analysis
156  - Scans and images
157    - Scan management
158      - image management
159  - Raw bioassays
160    - Create spot images
161    - Raw data
162  - Experiments
163  - Raw data types
164    - Affymetrix data
165  - Creating a root bioassayset
166  - Bioassayset
167    - Overview plots
168  - Filtering
169    - Formulas
170      - Formula management
171  - Normalization
172  - Running a (analysis?)plugin
173    - Messages
174  - Plot tool
175    - Scatter plot
176    - Histogram plot
177  - Experiment overview
178    - Validation of an experiment
179      - Options
180  - Experiment explorer
181    - Reporter view
182    - Reporter search
183  - Using MeV
184 
185- Import and export of data
186  - Import
187    - Plugins
188      - Auto detect
189    - File Format
190      - Auto detect
191  - Export
192    - Table exporter
193
194=====================
195* Admin documentation
196=====================
197
198- Installation and upgrade
199  - Requirements
200    - MySQL, settings, options, etc.
201    - Postgres, settings, options, etc.
202  - Configuration
203    - Raw data types
204    - Extended properties
205    - base.config reference
206    - other configuration files (log4j.properities, web.xml, etc.)
207  - Job agents
208    - jobagent.properties reference
209    - jobagent.sh reference
210 
211- Installing plugins
212  - Plugin configurations
213    - "Test with file" feature for creating import configurations
214  - BASE 1 plugins
215  - Core plugins and configurations
216
217- Adding users, groups, roles
218  - Projects and the permission system
219  - The default roles: admin, power user, user and guest
220  - Quota
221
222
223=========================
224* Developer documentation
225=========================
226- Overview of BASE2
227
228- Plugin developer
229  - How to organize your plugin project
230    - With Ant
231    - With Eclipse
232    - Packaging and installing the plugin
233  - The Plugin API
234    - Interfaces
235    - Asking for parameters
236      - Using custom JSP pages for parameters
237  - Import plugins
238    - Autodetecting importer
239    - The AbstractFlatFileImporter superclass
240  - Export plugins
241    - Immediate download of exported data
242  - Analysis plugins
243  - Other plugins
244    - Authentication plugins
245    - Secondary file storage plugins
246    - File unpacker plugins
247  - Example plugins (with download)
248
249- API overview (how to use and code examples)
250  - Database schema (Data layer API)
251  - The Core API
252  - The Query API
253  - Analysis and the Dynamic and Batch API
254  - Other useful classes and methods
255
256- Javadoc
257     
258- Core developer reference
259  - Important procedures
260  - Publishing a new release
261  - Subversion / building BASE
262  - Coding rules and guidelines
263    - Development process
264    - General coding style guidelines
265    - API changes and backwards compatibility
266    - Data-layer rules
267    - Item-class rules
268    - Batch-class rules
269    - Test-class rules
270  - Internals of the Core API
271    - Authentication and sessions
272    - Access permissions
273    - Data validation
274    - Transaction handling
275    - Create/read/write/delete operations
276    - Batch operations
277    - Quota
278    - Plugin execution / job queue
279
280=======
281* Index
282=======
283
284
285
286
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