/* Improve structural alignment datastructures to support topology-independent alignments */

sbliven · andreasprlic · commit 3ad597baa890 · 2016-04-09T10:59:44.000-07:00
diff --git a/_wikis/Google_Summer_of_Code_2013.md b/_wikis/Google_Summer_of_Code_2013.md
@@ -47,6 +47,36 @@ integrate them as a whole or cannibalize them and extract something
 useful on its own. You are more than welcome to optimize and improve the
 code while porting it to BioJava as you see fit.
 
+#### Improve structural alignment datastructures to support topology-independent alignments
+
+BioJava contains a number of algorithms for aligning protein structures.
+In the most general case, an alignment consists of a mapping between
+residues of two (or more) proteins. However, for historical and
+performance reasons alignments are stored as linear, sorted arrays. This
+makes it difficult to express cases where the order of aligned residues
+differs between the two proteins. For instance, storing the following
+alignment requires some creative work-arounds:
+
+` 123456`  
+` 456123`
+
+Additionally, the class to store structural alignments (AFPChain)
+contains a number of unneccessary, poorly documented, or
+algorithm-specific parameters which should be removed or refactored.
+
+Your challenge is to propose and implement a data structure for storing
+structure alignments which
+
+-   Is flexible enough to store topology-independent alignments
+-   Efficiently utilizes memory
+-   Has good performance for common tasks
+
+This project requires an understanding of basic data structures and
+performance considerations. A successful proposal should consider not
+only the new data structure, but also suggest a plan for integrating it
+into existing methods, particularly in the biojava3-structure and
+biojava3-structure-gui modules.
+
 Previous Years
 --------------
 
diff --git a/_wikis/Google_Summer_of_Code_2013.mediawiki b/_wikis/Google_Summer_of_Code_2013.mediawiki
@@ -23,6 +23,22 @@ Please send your proposals to the BioJava dev mailing list early, so we can disc
 
 P.S. Actually you are not limited to the old versions of BioJava, there are plenty of small little known Java projects in the Bioinformatics field which can be of interest to a wider user community. You can integrate them as a whole or cannibalize them and extract something useful on its own. You are more than welcome to optimize and improve the code while porting it to BioJava as you see fit.
 
+==== Improve structural alignment datastructures to support topology-independent alignments ====
+
+BioJava contains a number of algorithms for aligning protein structures. In the most general case, an alignment consists of a mapping between residues of two (or more) proteins. However, for historical and performance reasons alignments are stored as linear, sorted arrays. This makes it difficult to express cases where the order of aligned residues differs between the two proteins. For instance, storing the following alignment requires some creative work-arounds:
+
+  123456
+  456123
+
+Additionally, the class to store structural alignments (AFPChain) contains a number of unneccessary, poorly documented, or algorithm-specific parameters which should be removed or refactored.
+
+Your challenge is to propose and implement a data structure for storing structure alignments which
+* Is flexible enough to store topology-independent alignments
+* Efficiently utilizes memory
+* Has good performance for common tasks
+
+This project requires an understanding of basic data structures and performance considerations. A successful proposal should consider not only the new data structure, but also suggest a plan for integrating it into existing methods, particularly in the biojava3-structure and biojava3-structure-gui modules.
+
 == Previous Years ==
 
 [[Google Summer of Code 2012]]
