14 papers · ranked by Valyu relevance
Michael Kotliar, Andrey V Kartashov, Artem Barski
Modern biomedical research has seen a remarkable increase in the production and computational analysis of large datasets, leading to an urgent need to share standardized analytical techniques. However, of the >100 computational workflow systems used in biomedical research, most define their own specifications for…
Mahnoor Zulfiqar, Michael R. Crusoe, Birgitta König-Ries, Christoph Steinbeck + 3 more
Scientific workflows facilitate the automation of data analysis tasks by integrating various software and tools executed in a particular order. To enable transparency and reusability in workflows, it is essential to implement the FAIR principles. Here, we describe our experiences implementing the FAIR principles for…
Farah Zaib Khan, Stian Soiland-Reyes, Richard O Sinnott, Andrew Lonie + 2 more
Amongst the many big data domains, genomics is considered the most demanding with respect to all stages of the data lifecycle, including acquisition, storage, distribution, and analysis . Because genomic data are growing at an unprecedented rate due to improved sequencing technologies and reduced cost, it is currently…
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…
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…
Amruta Kale, Ziheng Sun, Xiaogang Ma
Computational workflows are widely used in data analysis, enabling automated tracking of steps and storage of provenance information, leading to innovation and decision-making in the scientific community. However, the growing popularity of workflows has raised concerns about reproducibility and reusability which can…
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…
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…
Michael Jackson, Kostas Kavoussanakis, Edward W. J. Wallace, Francis Ouellette
'Francis Ouellette'] Workflow management systems represent, manage, and execute multistep computational analyses and offer many benefits to bioinformaticians. They provide a common language for describing analysis workflows, contributing to reproducibility and to building libraries of reusable components. They can…
Alastair P. Droop
Summary: The Sun Grid Engine (SGE) high-performance computing batch queueing system is commonly used in bioinformatics analysis. Creating re-usable scripts for the SGE is a common challenge. The qsubsec template language and interpreter described here allow researchers to easily create generic template definitions that…
Alessandro Maccagnan, Mauro Riva, Erika Feltrin, Barbara Simionati + 3 more
'Tullio Vardanega' 'Giorgio Valle' 'Nicola Cannata'] Background Laboratory protocols in life sciences tend to be written in natural language, with negative consequences on repeatability, distribution and automation of scientific experiments. Formalization of knowledge is becoming popular in science. In the case of…
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…
Alexander Garcia Castro, Samuel Thoraval, Leyla J Garcia, Mark A Ragan
'Mark A Ragan'] Background Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite 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…