Motivation: Synthetic biology is typified by developing novel genetic constructs from the assembly of reusable synthetic DNA parts, which contain one or more features such as promoters, ribosome binding sites, coding sequences and terminators. PartsGenie is introduced to facilitate the computational design of such synthetic biology parts, bridging the gap between optimization tools for the design of novel parts, the representation of such parts in community-developed data standards such as Synthetic Biology Open Language, and their sharing in journal-recommended data repositories. Consisting of a drag-and-drop web interface, a number of DNA optimization algorithms, and an interface to the well-used data repository JBEI ICE, PartsGenie facilitates the design, optimization and dissemination of reusable synthetic biology parts through an integrated application. Availability and implementation: PartsGenie is freely available at https://parts.synbiochem.co.uk.

Scientific workflows management systems are increasingly used by scientists to specify complex data processing pipelines. Workflows are represented using a graph structure, where nodes represent tasks and links represent the dataflow. However, the complexity of workflow structures is increasing over time, reducing the rate of scientific workflows reuse. Here, we introduce DistillFlow, a tool based on effective methods for workflow design, with a focus on the Taverna model. DistillFlow is able to detect "anti-patterns" in the structure of workflows (idiomatic forms that lead to over-complicated design) and replace them with different patterns to reduce the workflow's overall structural complexity. Rewriting workflows in this way is beneficial both in terms of user experience and workflow maintenance.

BACKGROUND: Scientific workflows management systems are increasingly used to specify and manage bioinformatics experiments. Their programming model appeals to bioinformaticians, who can use them to easily specify complex data processing pipelines. Such a model is underpinned by a graph structure, where nodes represent bioinformatics tasks and links represent the dataflow. The complexity of such graph structures is increasing over time, with possible impacts on scientific workflows reuse. In this work, we propose effective methods for workflow design, with a focus on the Taverna model. We argue that one of the contributing factors for the difficulties in reuse is the presence of "anti-patterns", a term broadly used in program design, to indicate the use of idiomatic forms that lead to over-complicated design. The main contribution of this work is a method for automatically detecting such anti-patterns, and replacing them with different patterns which result in a reduction in the workflow's overall structural complexity. Rewriting workflows in this way will be beneficial both in terms of user experience (easier design and maintenance), and in terms of operational efficiency (easier to manage, and sometimes to exploit the latent parallelism amongst the tasks). RESULTS: We have conducted a thorough study of the workflows structures available in Taverna, with the aim of finding out workflow fragments whose structure could be made simpler without altering the workflow semantics. We provide four contributions. Firstly, we identify a set of anti-patterns that contribute to the structural workflow complexity. Secondly, we design a series of refactoring transformations to replace each anti-pattern by a new semantically-equivalent pattern with less redundancy and simplified structure. Thirdly, we introduce a distilling algorithm that takes in a workflow and produces a distilled semantically-equivalent workflow. Lastly, we provide an implementation of our refactoring approach that we evaluate on both the public Taverna workflows and on a private collection of workflows from the BioVel project. CONCLUSION: We have designed and implemented an approach to improving workflow structure by way of rewriting preserving workflow semantics. Future work includes considering our refactoring approach during the phase of workflow design and proposing guidelines for designing distilled workflows.

BACKGROUND: The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. RESULTS: The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. CONCLUSIONS: Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers.

There seems to be a general consensus on the crucial role metadata can play for enhancing the functionalities of scientific workflows systems, e.g., workflow and service discovery, composition and provenance browsing, among others. However, in most cases their management is under-specified, if not left unaddressed at all. A step in this direction, the main contribution of the work presented in this paper is an overview of metadata and their management in the Taverna workflow system. In Taverna, we consider metadata to be a first class citizen in the system, in the sense that we fully cover their life cycle from their creation, through their use and curation until their eventual removal. We present the main steps of this cycle and present the models used for metadata specification. In doing so, we distinguish two classes of metadata: metadata that describe workflow related entities, such as services, workflows and sub- workflows, and metadata that describe workflow executions, also known as workflow provenance.

Recently, there has been considerable interest in asynchronous design techniques, particularly at the chip level. New compositional approaches, such as Sutherland's micropipeline design philosophy, have greatly assisted development. However, sophisticated CAD systems for such specialized asynchronous systems are not yet widely available, hampering the development of asynchronous design. The Rainbow asynchronous design framework is based upon a high-level multi-view design representation for micropipelines. The system contains a collection of formally based design representation and support tools. The Green sub-language supports textual/schematic static dataflow descriptions. Yellow is an imperative, control-flow parallel language, with an Ada-like rendezvous. Tables allow concise definition of combined functional and dataflow control blocks. The sub-languages have common sets of data expressions, functions and types. The formal semantics for the Rainbow sub-languages is defined via a specialized process term language called APA, producing a compact, direct semantic representation with little unnecessary encoding. APA has micropipeline primitives, uses rich structured actions and anextended Ada-like rendezvous as its atomic communication. These features enable the semantics to be defined at a suitable high level of abstraction, i.e. micropipelines. The semantic representation acts as a basis for formal analysis tools, with the aim of extending their tractability. The Rainbow design system contains textual and graphical editors for design entry, and compilation and simulation tools, supporting animation of schematics. State generation tools provide an interface to external formal analysis systems. Rainbow currently incorporates a novel on-the-fly CTL* model checker. The MARBLE asynchronous bus design from the AMULET3 microprocessor is used as an example.

A process algebraic foundation has been developed for formal analysis of synchronous hardware designs represented through the commercially available hardware design language, ELLA. An underlying semantic foundation, based on input/output trace sets, is presented first through the use of state machines. Such a representation enables direct application of standard, fully automated trace equivalence checking tools. However, to overcome the computational limitations imposed by such analysis methods, the input/output trace semantics is represented through a synchronous process algebra, EPA. Primitive processes in EPA denote the behaviour of primitive hardware components, such as delays or multiplexers, with composition operators corresponding to the different ways in which behaviours may be built. Of particular significance is the parallel composition operator which captures the machinery for building networks from other components/networks. Actions in EPA are structured and signify the state of input and output signals. This structure, however, is abstracted by developing an algebra for the actions. In particular, parallel composition on processes neatly lifts to a special (synchronous) product operation on actions. The EPA representation forms a good basis for semi-automated high-level symbolic manipulation and reasoning tools. First, the original design structure can be maintained, thus easing the problems of user level feedback from tools. Secondly, the application of EPA to ELLA enables a deterministic finite automation form for EPA terms. This provides a route to tractable symbolic verification and simulation, using a state evolution method to establish strong bisimulation properties. The method has been successfully applied to classes of unbounded state space systems.