Dynamically Typed Languages

The languages discussed in this special issue have a long history, which is perhaps why some have had several different names over the years. One such language is Lisp, the second-oldest programming language. For years, many somewhat dismissively described languages such as Lisp as "scripting languages." Today, we more commonly refer to them as dynamically typed languages, typified by Python and Ruby, and their impact is arguably greater than ever. This issue highlights the practical uses of such languages and shows how they're frequently a vehicle for innovation in the development sphere. This article is part of a special issue on dynamically typed languages

Traits at Work: the design of a new trait-based stream library

International audienceRecent years saw the development of a composition mechanism called Traits. Traits are pure units of behavior that can be composed to form classes or other traits. The trait composition mechanism is an alternative to multiple or mixin inheritance in which the composer has full control over the trait composition. To evaluate the expressiveness of traits, some hierarchies were refactored, showing code reuse. However, such large refactorings, while valuable, may not exhibit all possible composition problems, since the hierarchies were previously expressed using single inheritance and following certain patterns. This paper presents our work on designing and implementing a new trait-based stream library named Nile. It evaluates how far traits enable reuse, what problems can be encountered when building a library using traits from scratch and compares the traits solution to alternative composition mechanisms. Nile's core allows the de?nition of compact collection and ?le streaming libraries as well as the implementation of a backward-compatible new stream library. Nile method size shows a reduction of 40% compared to the Squeak equivalent. The possibility to reuse the same set of traits to implement two distinct libraries is a concrete illustration of trait reuse capability

A communication profiler to optimize embedded resource usage

While the number of cores in both embedded MultiProcessor Systems-on-Chip and general purpose processors keeps rising, on-chip communication becomes more and more important. In order to write efficient programs for these architectures, it is therefore necessary to have a good idea of the communication behavior of an application. We present a communication profiler that extracts this behavior from compiled sequential C/C++ programs, and constructs a dynamic dataflow graph at the level of major functional blocks. In contrast to existing methods of measuring inter-program communication, our tool automatically generates the program's dataflow graph and is less demanding for the developer. It can also be used to view differences between program phases (such as different video frames), which allows both input- and phase-specific optimizations to be made. We also look at how this information can subsequently be used to guide the effort of parallelizing the application, to co-design the software, memory hierarchy and communication hardware, and to provide new sources of communication-related runtime optimizations

Multithreaded variant calling in elPrep 5

We present elPrep 5, which updates the elPrep framework for processing sequencing alignment/map files with variant calling. elPrep 5 can now execute the full pipeline described by the GATK Best Practices for variant calling, which consists of PCR and optical duplicate marking, sorting by coordinate order, base quality score recalibration, and variant calling using the haplotype caller algorithm. elPrep 5 produces identical BAM and VCF output as GATK4 while significantly reducing the runtime by parallelizing and merging the execution of the pipeline steps. Our benchmarks show that elPrep 5 speeds up the runtime of the variant calling pipeline by a factor 8-16x on both whole-exome and whole-genome data while using the same hardware resources as GATK4. This makes elPrep 5 a suitable drop-in replacement for GATK4 when faster execution times are needed

Synchronising Changes to Design and Implementation using a Declarative Meta-Programming Language

When developing software systems, the relation between design and implementation is typically left unspecified. As a result design or implementation can be modified independently of each other, and a modification of either one does not leave any trace in the other. The practical result of this is a number of well-known problems such as drift and erosion, documentation maintenance problems or round-trip engineering trouble. To solve these problems we propose to make the relation between design and implementation explicit by expressing design as a logic meta-program over implementation. This is the cornerstone for building a complete synchronisation framework that allows one to synchronise changes to design and implementation