biojava
diff --git a/‎_wikis/BOSC2008_Abstract.md‎
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@@ -15,55 +15,75 @@ BOSC2008 Abstract
 
 #### Author \#1
 
-**Name:**
+**Name:** Michael Heuer
 
-**Organization:**
+**Organization:** Harbinger Partners, Inc.
 
-**Country:**
+**Country:** USA
 
 **Email:**
 
-#### Author \#2
+**Additional Authors:**
 
-**Name:**
+Richard Holland
 
-**Organization:**
+Eagle Genomics Ltd.
 
-**Country:**
+UK
 
-**Email:**
+Thomas Down
 
-#### Author \#3
+Wellcome Trust/Cancer Research UK Gurdon Institute
 
-**Name:**
+UK
 
-**Organization:**
+Matthew Pocock
 
-**Country:**
+University Newcastle Upon Tyne
 
-**Email:**
+UK
 
-#### Author \#4
+Andreas Prlic
 
-**Name:**
+Wellcome Trust Sanger Institute
 
-**Organization:**
+UK
 
-**Country:**
+David Huen
 
-**Email:**
+University of Cambridge
 
-#### Author \#5
+UK
 
-**Name:**
+Keith James
 
-**Organization:**
+Wellcome Trust Sanger Institute
 
-**Country:**
+UK
 
-**Email:**
+Sylvain Foisy
 
-**Additional Authors:**
+Laboratory in Genetics and Genomic Medicine of Inflammation
+
+Canada
+
+Andreas Dräger
+
+Eberhard Karls University Tübingen
+
+Germany
+
+Andy Yates
+
+European Bioinformatics Institute (EMBL-EBI)
+
+UK
+
+Mark Schreiber
+
+Novartis Institute for Tropical Diseases
+
+Singapore
 
 ### Contact Author
 
@@ -77,8 +97,6 @@ BOSC2008 Abstract
 
 Bio \* Open Source Project Updates
 
-Lightning Talks ?
-
 ### Content
 
 **Keywords:**
@@ -88,55 +106,102 @@ alignment protein structure phylogenetic trees
 
 **Abstract:**
 
-The small Abstract text should be a summary, while the longer abstract
-should provide more details, including the open-source license
-requirement details.
+BioJava is a mature free and open-source project that provides a
+framework for processing biological data.
 
-Copied from BioJavaBioinformatics.odt
-[1](http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-paper?rev=4751)
-abstract summary with minor revision:
+BioJava provides tools/packages/modules/components
 
-BioJava is a mature Open Source project that provides a framework for
-processing of biological data. BioJava provides tools for parsing common
-file formats, manipulating sequences and 3D structures. Powerful
-analysis and statistical routines enable the rapid bioinformatics
-application development in the Java programming language
-[[2](http://java.sun.com)](http://java.sun.com). 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.
+for parsing common file formats,
 
-The second sentence needs further revision, an additional clause
-perhaps.
+for manipulating sequences and 3D structures,
 
-**Paper:**
+and powerful analysis and statistical routines.
 
-Full-length abstracts are limited to one page with one inch (2.5 cm)
-margins on the top, sides, and bottom. The full-length abstract should
-include the title, authors, and affiliations.
+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.
 
-I have added myself to the author's list from the application note near
-the end. Hopefully this is reasonable to the other authors.
+**Paper:**
 
 BioJava Project Update
 
 Holland, R.C.G.<sup>1</sup>, Down, T.<sup>2</sup>, Pocock,
 M.<sup>3</sup>, Prlic, A.<sup>4</sup>, Huen D.<sup>5</sup>, James
 K.<sup>4</sup>, Foisy, S.<sup>6</sup>, Dräger, A.<sup>7</sup>, Yates,
-A.<sup>1</sup>, Heuer M.<sup>8</sup>, and Schreiber, M.J.<sup>9</sup>
+A.<sup>8</sup>, Heuer M.<sup>9</sup>, and Schreiber, M.J.<sup>10</sup>
 
-<sup>1</sup> European Bioinformatics Institute (EMBL-EBI), Genome
-Campus, Hinxton, Cambridgeshire CB10 1SD, UK <sup>2</sup> Wellcome
+<sup>1</sup> Eagle Genomics Ltd., Cambridge, UK <sup>2</sup> Wellcome
 Trust/Cancer Research UK Gurdon Institute, Cambridge CB2 1QN, UK
 <sup>3</sup> University Newcaste Upon Tyne, Newcastle Upon Tyne, NE1
 7RU, UK <sup>4</sup> Wellcome Trust Sanger Institute, Genome Campus,
 Hinxton, Cambridgeshire CB10 1SA, UK <sup>5</sup> Department of
 Genetics, University of Cambridge, Cambridge CB2 3EH, UK <sup>6</sup>
 Laboratory in Genetics and Genomic Medicine of Inflammation, Montreal,
 Canada. <sup>7</sup> Eberhard Karls University Tübingen, Center for
-Bioinformatics (ZBIT), Germany <sup>8</sup> Harbinger Partners, Inc.,
-St. Paul, Minnesota, USA <sup>9</sup> Novartis Institute for Tropical
-Diseases, 10 Biopolis Road, Chromos \#05-01, Singapore 138670
+Bioinformatics (ZBIT), Germany <sup>8</sup> European Bioinformatics
+Institute (EMBL-EBI), Genome Campus, Hinxton, Cambridgeshire CB10 1SD,
+UK <sup>9</sup> Harbinger Partners, Inc., St. Paul, Minnesota, USA
+<sup>10</sup> Novartis Institute for Tropical Diseases, 10 Biopolis
+Road, Chromos \#05-01, Singapore 138670
+
+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.
+
+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).
+
+...48 contributors via commits, X mailing list subscribers, X wiki
+contributors.
+
+All code is distributed under version 2.1 of the GNU Lesser General
+Public License (LGPL) license (Free Software Foundation, Inc., 1999).
+
+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.
+
+...version 1.6.
+
+...docs/wiki.
+
+...what it means to be a mature FOSS project.
+
+#### References
+
+Needs cleanup.
+
+Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T.
+Taverna: a tool for building and running workflows of services. Nucleic
+Acids Res. 2006 Jul 1;34(Web Server issue):W729-32.
+
+Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J,
+Murray-Rust P, Steinbeck C, Wikberg JE. Bioclipse: an open source
+workbench for chemo- and bioinformatics. BMC Bioinformatics. 2007 Feb
+22;8:59.
+
+Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N,
+Schwikowski B, Ideker T. Cytoscape: a software environment for
+integrated models of biomolecular interaction networks. Genome Research
+2003 Nov; 13(11):2498-504
+
+BioWeka—extending the Weka framework for bioinformatics Jan E.
+Gewehr \*,{dagger}, Martin Szugat {dagger} and Ralf Zimmer
+Bioinformatics 2007 23(5):651-653; <doi:10.1093/bioinformatics/btl671>
+
+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
+
+Mangalam, H. (2002) The Bio\* toolkits – a brief overview. Brief
+Bioinform., 3, 396-302
+
+Pocock, M, Down, T, Hubbard, T (2000) BioJava: Open Source Components
+for Bioinformatics. ACM SIGBIO Newsletter 20(2), 10-12
 
 Notes
 -----
@@ -178,7 +243,7 @@ From
 
 181,197 lines of code in "biojava-live/trunk"
 
-Estimated effort using COCOMO [3](http://en.wikipedia.org/wiki/COCOMO)
+Estimated effort using COCOMO [1](http://en.wikipedia.org/wiki/COCOMO)
 metric: 47 Person Years
 
 48 contributors (committers with at least one commit to cvs and/or
@@ -241,3 +306,12 @@ There is a BioJava group on LinkedIn:
 Developers of the BioJava open-source bioinformatics project.
 
 Not sure how to link to it though.
+
+**Wiki edits for later**
+
+Clarify reference to LGPL.
+
+Update references to "open source" with "free and open source". Link to
+FOSS page on wikipedia?
+
+DengueInfo link on BioJavaInside is broken.