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Fixing the markdown
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_wiki/Current_events.md

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@@ -128,14 +128,14 @@ fixes and improvements.
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New Features:
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`- new Genbank writer`
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`- new parser for Karyotype file from UCSC`
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`- new parser for Gene locations from UCSC `
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`- new parser for Gene names file from genenames.org`
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`- new module for Cox regression code for survival analysis`
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`- new calculation of accessible surface area (ASA)`
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`- new module for parsing .OBO files (ontologies)`
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`- improved representation of SCOP and Berkeley-SCOP classifications`
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- new Genbank writer
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- new parser for Karyotype file from UCSC
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- new parser for Gene locations from UCSC
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- new parser for Gene names file from genenames.org
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- new module for Cox regression code for survival analysis
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- new calculation of accessible surface area (ASA)
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- new module for parsing .OBO files (ontologies)
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- improved representation of SCOP and Berkeley-SCOP classifications
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For a detailed comparison see here:
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<https://github.com/biojava/biojava/compare/biojava-3.0.7>...biojava-3.0.8
@@ -163,11 +163,11 @@ BioJava 3.0.7 was released on September 23rd and is available from
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new features:
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`- added a basic genbank parser `
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`- fixed a problem when translating codons with N`
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`- now can infer bonds in protein structures`
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`- added support to parse mmcif records for organism and expression system`
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`- many small bug fixes and improvements`
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- added a basic genbank parser
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- fixed a problem when translating codons with N
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- now can infer bonds in protein structures
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- added support to parse mmcif records for organism and expression system
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- many small bug fixes and improvements
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BioJava Legacy 1.8.4 released
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-----------------------------
@@ -180,9 +180,9 @@ repository at
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New Features:
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`- We moved our development to Github`
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`- Minor improvements to the sequencing module`
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`- Build/release fixes`
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- We moved our development to Github
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- Minor improvements to the sequencing module
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- Build/release fixes
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BioJava 3.0.6 released
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----------------------
@@ -194,8 +194,8 @@ BioJava 3.0.6 was released on July 15th 2013 and is available from
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New Features:
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`- We moved our development to Github.`
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`- many bug fixes and minor improvements`
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- We moved our development to Github.
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- many bug fixes and minor improvements
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BioJava moves to Github
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-----------------------
@@ -214,10 +214,10 @@ BioJava 3.0.5 was released on Nov 30th 2012 and is available from
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New Features:
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`- New parser for CATH classification`
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`- New parser for Stockholm file format`
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`- Significantly improved representation of biological assemblies of protein structures. Now can re-create biological assembly from asymmetric unit`
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`- Several bug fixes.`
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- New parser for CATH classification
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- New parser for Stockholm file format
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- Significantly improved representation of biological assemblies of protein structures. Now can re-create biological assembly from asymmetric unit
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- Several bug fixes.
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BioJava 2012 paper published
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----------------------------
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BioJava 3.0.2 adds new modules and enhances the capabilities of BioJava:
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`- biojava3-aa-prop: This new module allows the calculation of physico chemical and other properties of protein sequences.`
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`- biojava3-protein-disorder: A new module for the prediction of disordered regions in proteins. It based on a Java implementation of the RONN predictor.`
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- biojava3-aa-prop: This new module allows the calculation of physico chemical and other properties of protein sequences.
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- biojava3-protein-disorder: A new module for the prediction of disordered regions in proteins. It based on a Java implementation of the RONN predictor.
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Other noteworthy improvements:
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`- protein-structure: Improved handling of protein domains: Now with better support for SCOP. New functionality for automated prediction of protein domains, based on Protein Domain Parser.`
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`- Improvements and bug fixes in several modules.`
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- protein-structure: Improved handling of protein domains: Now with better support for SCOP. New functionality for automated prediction of protein domains, based on Protein Domain Parser.
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- Improvements and bug fixes in several modules.
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Currently, up to 8 different people are making commits per month. This
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gives an indication how active Biojava is being developed. The two new

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