15 papers · ranked by Valyu relevance
Stephen R Piccolo, Zachary E Ence, Elizabeth C Anderson, Jeffrey T Chang + 3 more
'Jeffrey T Chang' 'Andrea H Bild' 'C Daniela Robles-Espinoza' 'Aleksandra M Walczak'] Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using…
Adam A Hunter, Andrew B Macgregor, Tamas O Szabo, Crispin A Wellington + 1 more
'Crispin A Wellington' 'Matthew I Bellgard'] Background There is a significant demand for creating pipelines or workflows in the life science discipline that chain a number of discrete compute and data intensive analysis tasks into sophisticated analysis procedures. This need has led to the development of general as…
Mohamed Abouelhoda, Shadi Alaa Issa, Moustafa Ghanem
Background Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and…
Shadi A. Issa, Romeo Kienzler, Mohamed El-Kalioby, Peter J. Tonellato + 3 more
'Peter J. Tonellato' 'Dennis Wall' 'Rémy Bruggmann' 'Mohamed Abouelhoda'] Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or…
Luis de la Garza, Johannes Veit, Andras Szolek, Marc Röttig + 4 more
'Stephan Aiche' 'Sandra Gesing' 'Knut Reinert' 'Oliver Kohlbacher'] Background Reproducibility is one of the tenets of the scientific method. Scientific experiments often comprise complex data flows, selection of adequate parameters, and analysis and visualization of intermediate and end results. Breaking down the…
Ezio Bartocci, Flavio Corradini, Emanuela Merelli, Lorenzo Scortichini
'Lorenzo Scortichini'] Background An in-silico experiment can be naturally specified as a workflow of activities implementing, in a standardized environment, the process of data and control analysis. A workflow has the advantage to be reproducible, traceable and compositional by reusing other workflows. In order to…
Daniel J.B. Clarke, John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino + 38 more
'Giacomo B. Marino' 'Anna I. Byrd' 'Mano R. Maurya' 'Sumana Srinivasan' 'Keyang Yu' 'Varduhi Petrosyan' 'Matthew E. Roth' 'Miroslav Milinkov' 'Charles Hadley King' 'Jeet Kiran Vora' 'Jonathon Keeney' 'Christopher Nemarich' 'William Khan' 'Alexander Lachmann' 'Nasheath Ahmed' 'Alexandra Agris' 'Juncheng Pan' 'Srinivasan…
Hirotaka Suetake, Tomoya Tanjo, Manabu Ishii, Bruno P. Kinoshita + 10 more
'Takeshi Fujino' 'Tsuyoshi Hachiya' 'Yuichi Kodama' 'Takatomo Fujisawa' 'Osamu Ogasawara' 'Atsushi Shimizu' 'Masanori Arita' 'Tsukasa Fukusato' 'Takeo Igarashi' 'Tazro Ohta'] The increased demand for efficient computation in data analysis encourages researchers in biomedical science to use workflow systems. Workflow…
Vojtech Huser, Luke V Rasmussen, Ryan Oberg, Justin B Starren
Background Workflow engine technology represents a new class of software with the ability to graphically model step-based knowledge. We present application of this novel technology to the domain of clinical decision support. Successful implementation of decision support within an electronic health record (EHR) remains…
Alexandre Melo, Alessandra Faria-Campos, Daiane Mariele DeLaat, Rodrigo Keller + 2 more
'Rodrigo Keller' 'Vinícius Abreu' 'Sérgio Campos'] Background The need to manage large amounts of data is a clear demand for laboratories nowadays. The use of Laboratory Information Management Systems (LIMS) to achieve this is growing each day. A LIMS is a complex computational system used to manage laboratory data…
Hanqi Li, Xianhui Liu, Weidong Zhao, Claudia Campolo
In recent years, cloud-native technology has become popular among Internet companies. Microservice architecture solves the complexity problem for multiple service methods by decomposing a single application so that each service can be independently developed, independently deployed, and independently expanded. At the…
Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen + 10 more
In recent years, the volumes of data to be analyzed, as well as the complexity of that analysis, across many scientific fields (from genomics through to exoplanet exploration) have increased massively. As a consequence, workflows (abstract representations of data flow between multiple analytic tools) have become a core…
Luciano V Araújo, Simon Malkowski, Kelly R Braghetto, Maria R Passos-Bueno + 3 more
'Maria R Passos-Bueno' 'Mayana Zatz' 'Calton Pu' 'João E Ferreira'] Background Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for…
Georgios Kontonatsios, Ioannis Korkontzelos, BalaKrishna Kolluru, Paul Thompson + 1 more
'Paul Thompson' 'Sophia Ananiadou'] Background U-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows. U-Compare contains a large library of components that are tuned to the biomedical domain. Users can rapidly develop biomedical text mining workflows by…
Anna Hristoskova, Vangelis Sakkalis, Giorgos Zacharioudakis, Manolis Tsiknakis + 1 more
'Manolis Tsiknakis' 'Filip De Turck'] A major challenge related to caring for patients with chronic conditions is the early detection of exacerbations of the disease. Medical personnel should be contacted immediately in order to intervene in time before an acute state is reached, ensuring patient safety. This paper…