A notation and system for expressing and executing cleanly typed workflows on messy scientific data (original) (raw)
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International Journal of Systematic and Evolutionary Microbiology
Background/context A preprint is a scholarly manuscript posted by the author(s) in an openly accessible platform, usually before or in parallel with the peer review process. While the sharing of manuscripts via preprint platforms has been common in some disciplines (such as physics and mathematics) for many years, uptake in other disciplines traditionally had been low, possibly influenced by differences in research culture and strong opposition by some journal publishers [1]. The landscape has evolved rapidly in other fields in recent years, however, thanks to the launch of additional, discipline-specific preprint platforms and increased support by funders and initiatives such as ASAPBio [2, 3]. Why use preprints? Preprint servers provide researchers with a platform to disseminate their work quickly and broadly, in a shorter timeframe than that needed at a peer-reviewed journal. Researchers can establish precedence and may be able to obtain feedback before (or, sometimes, in parallel with) peer review at a journal and from a wider audience than the two or three reviewers traditionally involved in reviewing manuscripts. The availability of preprints can also facilitate interactions between researchers working on similar areas or projects, and may help foster collaboration between groups. Some funders allow inclusion of preprints in grant applications [4] and thus, posting work as a preprint can help authors to provide evidence of research productivity. Preprint platforms do not currently incur submission fees and, thus, provide a free service to both authors and readers. The long-term sustainability of this business model is an open question, although some feel that the operational costs can be offset via grants and partnerships with other parties [5]. Some preprint platforms provide features where readers can publicly log comments, critiques and suggestions. Even if commenting features are not available, readers can contact the researchers directly. Authors may then use the feedback from the preprint posting to revise their manuscript before submission to a journal, or in addition to the reviewer comments from traditional peer review. From an editor's perspective, preprint platforms can also provide opportunities to scout upcoming work and invite the submission of suitable manuscripts to their journal. Preprint servers and journals may also enter partnerships to facilitate easy submission of preprint papers to a participating journal; bioRxiv is a recent example of a preprint server entering such a scheme with some journals to facilitate the direct transfer of papers posted as a preprint on their server.
Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science
Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science, 2013
This paper identifies the high value to researchers in many disciplines of having web-based graphical editors for scientific workflows and draws attention to two technological transitions: good quality editors can now run in a browser and workflow enactment systems are emerging that manage multiple workflow languages and support multi-lingual workflows. We contend that this provides a unique opportunity to introduce multi-lingual graphical workflow editors which in turn would yield substantial benefits: workflow users would find it easier to share and combine methods encoded in multiple workflow languages, the common framework would stimulate conceptual convergence and increased workflow component sharing, and the many workflow communities could share a substantial part of the effort of delivering good quality graphical workflow editors in browsers. The paper examines whether such a common framework is feasible and presents an initial design for a web-based editor, tested with a pre...
Second Call for Papers – Extended Submission Period | ISCH Annual Conference 2015
Time is all-around us, as an invisible but always present frame of our existence: we live in time, we change and learn to adapt to its fluidity, and we organize our life and our relations with othersfrom daily agendas to life projectsdepending on Time. Even if Time is a physical reality, our impossibility to perceive it by senses generated a multitude of cultural solution, that in fact transformed Time in probably the most culturally mediated physical dimension of the reality. Across cultures, measuring, structuring, explaining and valuing time takes various forms, from language to technology, from mythology to arts, politics, philosophy, ideology or rituals. History itself, as an intellectual demarche, is ultimately a reflection about time and its variables. Equally perceived with personal and social instruments and concepts, awareness of time is a universal cultural fact, but time and its representations, use and value may vary from one culture to another, and from that perspective we are ourselves products of time.
Computer-Assisted Scientific Workflow Design
Journal of Grid Computing, 2013
HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.