On Reverse Engineering and Decompilation

This chapter examines reverse engineering and the decompilation of computer programs, both of which are highly regulated under the current copyright regime. It begins with a practical overview of reverse engineering and decompilation of software, focusing on types of reverse engineering prevalent in the software industry, the various stages of reverse engineering, and the motivation and methods for reverse engineering. It then looks at the reasons for and benefits of decompilation, which is a category of reverse engineering, and examines software interoperability. At this stage the chapter considers what EU and US copyright laws say about decompilation, with particular emphasis on the role that the idea-expression dichotomy plays in decompilation scenarios. It also discusses the problem of entitlement with respect to intellectual property rules, and more specifically in the case of decompilation of computer programs. It provides a critical evaluation of Article 6 of the Software Directive in enabling decompilation in order to achieve interoperability. The chapter concludes with a commentary on reverse engineering in the cloud environment under copyright law.

TopHat-Recondition: A post-processor for TopHat unmapped reads

Summary: TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format - the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct format implementation is paramount for software interoperability and correct analysis. However, TopHat writes its unmapped reads in a way that is not compatible with other software that implements the SAM/BAM format. We have developed TopHat-Recondition, a post-processor for TopHat unmapped reads that restores read information in the proper format. TopHat-Recondition thus enables downstream software to process the plethora of BAM files written by TopHat. Availability and implementation: TopHat-Recondition is implemented in Python using the Pysam library and is freely available under a 2-clause BSD license on GitHub: https://github.com/cbrueffer/tophat-recondition. Contact: [email protected], [email protected]