Structured Composition of Dataflow and Control-Flow for Reusable and Robust Scientific Workflows

Data-centric scientific workflows are often modeled as dataflow process networks. The simplicity of the dataflow framework facilitates workflow design, analysis, and optimization. However, some workflow tasks are particularly ''control-flow intensive'', e.g., procedures to make workflows more fault-tolerant and adaptive in an unreliable, distributed computing environment. Modeling complex control-flow directly within a dataflow framework often leads to overly complicated workflows that are hard to comprehend, reuse, schedule, and maintain. In this paper, we develop a framework that allows a structured embedding of control-flow intensive subtasks within dataflow process networks. In this way, we can seamlessly handle complex control-flows without sacrificing the benefits of dataflow. We build upon a flexible actor-oriented modeling and design approach and extend it with (actor) frames and (workflow) templates. A frame is a placeholder for an (existing or planned) collection of components with similar function and signature. A template partially specifies the behavior of a subworkflow by leaving ''holes'' (i.e., frames) in the subworkflow definition. Taken together, these abstraction mechanisms facilitate the separation and structured re-combination of control-flow and dataflow in scientific workflow applications. We illustrate our approach with a real-world scientific workflow from the astrophysics domain. This data-intensive workflow requires remote execution and file transfer in a semi-reliable environment. For such work-flows, we propose a 3-layered architecture: The top-level, typically a dataflow process network, includes Generic Data Transfer (GDT) frames and Generic remote eXecution (GX) frames. At the second level, the user can specialize the behavior of these generic components by embedding a suitable template (here: transducer templates for control-flow intensive tasks). At the third level, frames inside the transducer template are specialized by embedding the desired implementation. Our approach yields workflows that are more robust (fault-tolerance strategies can be define by control-flow driven transducer templates) and at the same time more reuseable, since the embedding of frames and templates yields more structured and modular workflows

Drug repositioning and indication discovery using description logics

Drug repositioning is the discovery of new indications for approved or failed drugs. This practice is commonly done within the drug discovery process in order to adjust or expand the application line of an active molecule. Nowadays, an increasing number of computational methodologies aim at predicting repositioning opportunities in an automated fashion. Some approaches rely on the direct physical interaction between molecules and protein targets (docking) and some methods consider more abstract descriptors, such as a gene expression signature, in order to characterise the potential pharmacological action of a drug (Chapter 1). On a fundamental level, repositioning opportunities exist because drugs perturb multiple biological entities, (on and off-targets) themselves involved in multiple biological processes. Therefore, a drug can play multiple roles or exhibit various mode of actions responsible for its pharmacology. The work done for my thesis aims at characterising these various modes and mechanisms of action for approved drugs, using a mathematical framework called description logics. In this regard, I first specify how living organisms can be compared to complex black box machines and how this analogy can help to capture biomedical knowledge using description logics (Chapter 2). Secondly, the theory is implemented in the Functional Therapeutic Chemical Classification System (FTC - https://www.ebi.ac.uk/chembl/ftc/), a resource defining over 20,000 new categories representing the modes and mechanisms of action of approved drugs. The FTC also indexes over 1,000 approved drugs, which have been classified into the mode of action categories using automated reasoning. The FTC is evaluated against a gold standard, the Anatomical Therapeutic Chemical Classification System (ATC), in order to characterise its quality and content (Chapter 3). Finally, from the information available in the FTC, a series of drug repositioning hypotheses were generated and made publicly available via a web application (https://www.ebi.ac.uk/chembl/research/ftc-hypotheses). A subset of the hypotheses related to the cardiovascular hypertension as well as for Alzheimer’s disease are further discussed in more details, as an example of an application (Chapter 4). The work performed illustrates how new valuable biomedical knowledge can be automatically generated by integrating and leveraging the content of publicly available resources using description logics and automated reasoning. The newly created classification (FTC) is a first attempt to formally and systematically characterise the function or role of approved drugs using the concept of mode of action. The open hypotheses derived from the resource are available to the community to analyse and design further experiments.This work was supported by the European Molecular Biology Laboratory (EMBL)

The decentered translation of management ideas:Attending to the conditioning flow of everyday work practices

Based on a study of Lean management practices at the Swedish Migration Board, we develop a novel theoretical understanding of the translation of management ideas. We show how translation, rather than being reduced to a network of human intentions and actions governing the transformation of organizational practices, can instead be understood as a historically contingent, situated flow of mundane everyday work practices through which social and material translators simultaneously become translated, conditioned to be and act in certain ways. We show how prior actor-centric accounts of translation of management ideas can be understood as performative consequences of a conceptual vocabulary inherited from Callon and Latour. Contrasting this, the non-actor-centric vocabulary of social anthropologist Tim Ingold allows us to background the intentional human actor and foreground the flow of mundane, situated practices. In adopting this vocabulary, we capture how the flow of practices conditions subjects and objects to become enacted as well as act, and develop an understanding of translation as occurring within, rather than distinct from, these practices. In essence, our novel view of translation emphasizes how management ideas are radically unstable, and subject to alteration through the flow of practices rather than as a result of deliberate implementation efforts

Proceedings of the 12th International Conference on Digital Preservation

The 12th International Conference on Digital Preservation (iPRES) was held on November 2-6, 2015 in Chapel Hill, North Carolina, USA. There were 327 delegates from 22 countries. The program included 12 long papers, 15 short papers, 33 posters, 3 demos, 6 workshops, 3 tutorials and 5 panels, as well as several interactive sessions and a Digital Preservation Showcase