We have implemented the repressilator circuit and a Turing pattern circuit in
Eugene. We have documented issues we found with Eugene in Problem1/eugene.pdf.
We have implemented a Java application which can convert a subset of BioPAX to
SBOL2. The source and readme can be found in the Problem2 directory.
ran out of time sorry :-(
We have modified both the SBOL Stack and JBEI ICE. Our modified version of JBEI-ICE supports annotated SBOL2 support, which is a major improvement over the existing SBOL implementation (which serialized SBOL1 and converted it to SBOL2). Our modified version of the SBOL Stack features federation of queries to JBEI-ICE registry instances, meaning queries to the SBOL Stack can now incorporate data from ICE.
A list of modified files can be found in the README files in the respective
directories under Problem4.