Skip to content

Commit dfd604d

Browse files
heuermhandreasprlic
heuermh
authored and
andreasprlic
committed
Change to wiki page
1 parent 051b2c0 commit dfd604d

File tree

2 files changed

+100
-21
lines changed

2 files changed

+100
-21
lines changed

‎_wikis/BOSC2008_Abstract.md‎

Lines changed: 63 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -121,6 +121,9 @@ for manipulating sequences and 3D structures,
121121

122122
and powerful analysis and statistical routines.
123123

124+
BioJava is available freely under the terms of version 2.1 of the GNU
125+
Lesser General Public License (LGPL) from <http://biojava.org/>.
126+
124127
Here we present the latest BioJava release (version 1.6, released on 13
125128
Apr 2008) which provides improvements in the packages for phylogenetic
126129
trees, processing PDB files, and genetic algorithms.
@@ -156,25 +159,57 @@ framework with modules for performing many common bioinformatics tasks.
156159

157160
As a free and open-source project, BioJava is developed by volunteers
158161
coordinated by the Open Bioinformatics Foundation (OBF) and is one of
159-
several Bio\* toolkits (Mangalam, 2002).
160-
161-
...48 contributors via commits, X mailing list subscribers, X wiki
162-
contributors.
163-
164-
All code is distributed under version 2.1 of the GNU Lesser General
165-
Public License (LGPL) license (Free Software Foundation, Inc., 1999).
162+
several Bio\* toolkits (Mangalam, 2002). Over the past eight years, the
163+
BioJava has brought together nearly fifty different code contributors,
164+
hundreds of mailing list subscribers, and several wiki contributors. All
165+
code is distributed under version 2.1 of the GNU Lesser General Public
166+
License (LGPL) license (Free Software Foundation, Inc., 1999). All wiki
167+
documentation is made available online under version 1.2 of the GNU Free
168+
Documentation License (Free Software Foundation, Inc., 2000).
166169

167170
BioJava has been used in a number of real-world applications, including
168171
Bioclipse (Spjuth et al., 2007), BioWeka (Gewehr et al., 2007),
169-
Cytoscape (Shannon et al., 2003), and Taverna (Hull et al, 2006), and
170-
over 50 published studies. A list of these can be found on the BioJava
171-
website.
172+
Cytoscape (Shannon et al., 2003), and Taverna (Oinn et al., 2004), and
173+
been referenced in over 50 published studies. A list of these can be
174+
found on the BioJava website.
175+
176+
The latest BioJava release (version 1.6, released on 13 Apr 2008) offers
177+
more functionality and stability over the previous official releases.
178+
The phylogenomics package was improved and expanded by our 2007 Google
179+
Summer of Code (GSOC'07) student Boh-Yun Lee. It now contains
180+
fully-functional Nexus and Phylip parsers, and tools for calculating
181+
UPGMA and Neighbour Joining, Jukes-Kantor and Kimura Two Parameter, and
182+
MP. The PDB file parser was improved by Jules Jacobsen for better
183+
dealing with PDB header records. Andreas Dräger provided several patches
184+
for improving the Genetic Algorithm modules. The version 1.6 release
185+
also contains numerous bug fixes and documentation improvements.
186+
187+
As a mature project, BioJava faces several challenges:
188+
189+
how one deals with a large established code base
190+
191+
what happens when committers move on, get married, have kids, etc.
192+
193+
how difficult it is to deprecate and remove existing code
194+
195+
evolutionary vs. revolutionary changes [1]
172196

173-
...version 1.6.
197+
the "second system" problem [2]
174198

175-
...docs/wiki.
199+
To this end...
176200

177-
...what it means to be a mature FOSS project.
201+
the BioJava3 use case & refactoring/redesign criteria gathering process
202+
203+
At least one prior attempt, while technically sufficient, was unable to
204+
garner community support.
205+
206+
<http://biojava.org/wiki/BioJava3_Proposal>
207+
208+
<http://biojava.org/wiki/Talk:BioJava3_Proposal>
209+
210+
<http://biojava.org/wiki/BioJava3_Design>
211+
212+
<http://www.derkholm.net/svn/repos/bjv2/website/docs/index.html>
178213

179214
#### References
180215

@@ -184,6 +219,13 @@ Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T.
184219
Taverna: a tool for building and running workflows of services. Nucleic
185220
Acids Res. 2006 Jul 1;34(Web Server issue):W729-32.
186221

222+
or
223+
224+
Oinn,T., Addis,M., Ferris,J., Marvin,D., Greenwood,M., Carver,T.,
225+
Pocock,M.R., Wipat,A. and Li,P. (2004) Taverna: a tool for the
226+
composition and enactment of bioinformatics workflows. Bioinformatics,
227+
20, 3045–3054.
228+
187229
Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J,
188230
Murray-Rust P, Steinbeck C, Wikberg JE. Bioclipse: an open source
189231
workbench for chemo- and bioinformatics. BMC Bioinformatics. 2007 Feb
@@ -198,6 +240,10 @@ BioWeka—extending the Weka framework for bioinformatics Jan E.
198240
Gewehr \*,{dagger}, Martin Szugat {dagger} and Ralf Zimmer
199241
Bioinformatics 2007 23(5):651-653; <doi:10.1093/bioinformatics/btl671>
200242

243+
Free Software Foundation, Inc. (2000) GNU Free Documentation License,
244+
version 1.2, <http://www.gnu.org/licenses/fdl-1.2.html>, accessed 10 May
245+
2008
246+
201247
Free Software Foundation, Inc. (1999) GNU Lesser General Public License,
202248
version 2.1, <http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html>,
203249
accessed 10 May 2008
@@ -320,3 +366,7 @@ Update references to "open source" with "free and open source". Link to
320366
FOSS page on wikipedia?
321367

322368
DengueInfo link on BioJavaInside is broken.
369+
370+
BioJava in Anger is now on the wiki (so under FDL?) but has a separate
371+
vague Copyright section, see
372+
<http://biojava.org/wiki/BioJava:CookBook#Copyright>

‎_wikis/BOSC2008_Abstract.mediawiki‎

Lines changed: 37 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -127,6 +127,7 @@ for manipulating sequences and 3D structures,
127127

128128
and powerful analysis and statistical routines.
129129

130+
BioJava is available freely under the terms of version 2.1 of the GNU Lesser General Public License (LGPL) from http://biojava.org/.
130131

131132
Here we present the latest BioJava release (version 1.6, released on 13 Apr 2008) which provides improvements in the packages for phylogenetic trees, processing PDB files, and genetic algorithms.
132133

@@ -145,23 +146,40 @@ Holland, R.C.G.<sup>1</sup>, Down, T.<sup>2</sup>, Pocock, M.<sup>3</sup>, Prlic
145146
BioJava was conceived in 1999 by Thomas Down and Matthew Pocock as an API to simplify bioinformatics software development using Java (Pocock et al., 2000). It has since then evolved to become a fully-featured framework with modules for performing many common bioinformatics tasks.
146147

147148

148-
As a free and open-source project, BioJava is developed by volunteers coordinated by the Open Bioinformatics Foundation (OBF) and is one of several Bio* toolkits (Mangalam, 2002).
149+
As a free and open-source project, BioJava is developed by volunteers coordinated by the Open Bioinformatics Foundation (OBF) and is one of several Bio* toolkits (Mangalam, 2002). Over the past eight years, the BioJava has brought together nearly fifty different code contributors, hundreds of mailing list subscribers, and several wiki contributors. All code is distributed under version 2.1 of the GNU Lesser General Public License (LGPL) license (Free Software Foundation, Inc., 1999). All wiki documentation is made available online under version 1.2 of the GNU Free Documentation License (Free Software Foundation, Inc., 2000).
149150

150-
...48 contributors via commits, X mailing list subscribers, X wiki contributors.
151151

152-
All code is distributed under version 2.1 of the GNU Lesser General Public License (LGPL) license (Free Software Foundation, Inc., 1999).
152+
BioJava has been used in a number of real-world applications, including Bioclipse (Spjuth et al., 2007), BioWeka (Gewehr et al., 2007), Cytoscape (Shannon et al., 2003), and Taverna (Oinn et al., 2004), and been referenced in over 50 published studies. A list of these can be found on the BioJava website.
153153

154154

155-
BioJava has been used in a number of real-world applications, including Bioclipse (Spjuth et al., 2007), BioWeka (Gewehr et al., 2007), Cytoscape (Shannon et al., 2003), and Taverna (Hull et al, 2006), and over 50 published studies. A list of these can be found on the BioJava website.
155+
The latest BioJava release (version 1.6, released on 13 Apr 2008) offers more functionality and stability over the previous official releases. The phylogenomics package was improved and expanded by our 2007 Google Summer of Code (GSOC'07) student Boh-Yun Lee. It now contains fully-functional Nexus and Phylip parsers, and tools for calculating UPGMA and Neighbour Joining, Jukes-Kantor and Kimura Two Parameter, and MP. The PDB file parser was improved by Jules Jacobsen for better dealing with PDB header records. Andreas Dräger provided several patches for improving the Genetic Algorithm modules. The version 1.6 release also contains numerous bug fixes and documentation improvements.
156156

157157

158-
...version 1.6.
158+
As a mature project, BioJava faces several challenges:
159159

160+
how one deals with a large established code base
160161

161-
...docs/wiki.
162+
what happens when committers move on, get married, have kids, etc.
162163

164+
how difficult it is to deprecate and remove existing code
163165

164-
...what it means to be a mature FOSS project.
166+
evolutionary vs. revolutionary changes [1]
167+
168+
the "second system" problem [2]
169+
170+
To this end...
171+
172+
the BioJava3 use case & refactoring/redesign criteria gathering process
173+
174+
At least one prior attempt, while technically sufficient, was unable to garner community support.
175+
176+
http://biojava.org/wiki/BioJava3_Proposal
177+
178+
http://biojava.org/wiki/Talk:BioJava3_Proposal
179+
180+
http://biojava.org/wiki/BioJava3_Design
181+
182+
http://www.derkholm.net/svn/repos/bjv2/website/docs/index.html
165183

166184

167185
====References====
@@ -172,6 +190,13 @@ Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T.
172190
Taverna: a tool for building and running workflows of services.
173191
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W729-32.
174192

193+
or
194+
195+
Oinn,T., Addis,M., Ferris,J., Marvin,D., Greenwood,M., Carver,T.,
196+
Pocock,M.R., Wipat,A. and Li,P. (2004) Taverna: a tool for the
197+
composition and enactment of bioinformatics workflows.
198+
Bioinformatics, 20, 3045–3054.
199+
175200
Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JE.
176201
Bioclipse: an open source workbench for chemo- and bioinformatics. BMC Bioinformatics. 2007 Feb 22;8:59.
177202

@@ -183,6 +208,8 @@ BioWeka—extending the Weka framework for bioinformatics
183208
Jan E. Gewehr *,{dagger}, Martin Szugat {dagger} and Ralf Zimmer
184209
Bioinformatics 2007 23(5):651-653; doi:10.1093/bioinformatics/btl671
185210

211+
Free Software Foundation, Inc. (2000) GNU Free Documentation License, version 1.2, http://www.gnu.org/licenses/fdl-1.2.html, accessed 10 May 2008
212+
186213
Free Software Foundation, Inc. (1999) GNU Lesser General Public License, version 2.1, http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html, accessed 10 May 2008
187214

188215
Mangalam, H. (2002) The Bio* toolkits – a brief overview. Brief Bioinform., 3, 396-302
@@ -306,4 +333,6 @@ Clarify reference to LGPL.
306333

307334
Update references to "open source" with "free and open source". Link to FOSS page on wikipedia?
308335

309-
DengueInfo link on BioJavaInside is broken.
336+
DengueInfo link on BioJavaInside is broken.
337+
338+
BioJava in Anger is now on the wiki (so under FDL?) but has a separate vague Copyright section, see http://biojava.org/wiki/BioJava:CookBook#Copyright

0 commit comments

Comments
 (0)