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Bioinformatics Meets User-Centred Design: A Perspective

Katrina Pavelin, Jennifer A. Cham, Paula de Matos, Cath Brooksbank, Graham Cameron, Christoph Steinbeck, Philip E. Bourne
2012 PLoS Computational Biology  
Designers have a saying Citation: Pavelin K, Cham JA, de Matos P, Brooksbank C, Cameron G, et al. (2012) Bioinformatics Meets User-Centred Design: A Perspective. PLoS Comput Biol 8(7): e1002554.  ...  In this paper, we explore the need for a user-centred design (UCD) strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI.  ...  Figure 1 . 1 An overview of the user-centred design process. User-centred design focuses on the needs of the user, ensuring that the end product is fit for purpose.  ... 
doi:10.1371/journal.pcbi.1002554 pmid:22807660 pmcid:PMC3395592 fatcat:i6fxb4wdqbbarntag4362do6au

The Development of Data Infrastructures for eHealth: A Socio-Technical Perspective

Jenny Ure, Rob Procter, Yu-wei Lin, Mark Hartswood, Stuart Anderson, Sharon Lloyd, Joanna Wardlaw, Horacio Gonzalez-Velez, Kate Ho
2009 Journal of the AIS  
These experiences problematize the "one size fits all" model initially adopted by HealthGrids, and highlight the need for design and development strategies that are able to engage with local needs and  ...  We link these problems to contradictions between underlying assumptions about data as a commodity whose reuse is not compromised when it is extracted from the context in which it has been captured, and  ...  the ESRC UK National Centre for e-Social Science for funding the Agenda Setting workshop on ontology building.  ... 
doi:10.17705/1jais.00197 fatcat:2krfg3i23fb4zagl73im5fr2je

Bioinformatics Education--Perspectives and Challenges out of Africa

O. Tastan Bishop, E. F. Adebiyi, A. M. Alzohairy, D. Everett, K. Ghedira, A. Ghouila, J. Kumuthini, N. J. Mulder, S. Panji, H.-G. Patterton
2014 Briefings in Bioinformatics  
The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of virtually  ...  This dearth of bioinformatics expertise has had a knock-on effect on the establishment of many modern high-throughput projects at African institutes, including the comprehensive and systematic analysis  ...  Internshipprograms: Internship programs are designed to train students in a specific area of bioinformatics.  ... 
doi:10.1093/bib/bbu022 pmid:24990350 pmcid:PMC4364068 fatcat:jdq7jhwcsbbozbtvqzmgxohkgq

Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective [chapter]

T.K. Attwood, A. Gisel, N-E. Eriksson, E. Bongcam-Rudloff
2011 Bioinformatics - Trends and Methodologies  
Building on the ongoing sequencing work, this advance set the scene for an exciting new era in which structure determination took centre stage in our quest to understand the biophysical mechanisms that  ...  Interestingly, Smith spoke here of 'biology informatics', not bioinformatics; and the NCBI was a 'center for biotechnology information', not a bioinformatics centre.  ...  www.intechopen.comConcepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective .  ... 
doi:10.5772/23535 fatcat:dwe4umftd5anrfobkciktbmg3m

A Bioinformatics Perspective on Proteomics: Data Storage, Analysis, and Integration

Andreas Kremer, Reinhard Schneider, Georg C. Terstappen
2005 Bioscience Reports  
The field of proteomics is advancing rapidly as a result of powerful new technologies and proteomics experiments yield a vast and increasing amount of information.  ...  This review will shed light on recent steps towards the generation of a common standard in proteomics data storage and integration, but is not meant to be a comprehensive overview of all available databases  ...  The term proteome was first introduced by Marc Wilkins 10 years ago during a proteomics meeting in Siena (Italy) to describe the set of proteins encoded and expressed by the genome.  ... 
doi:10.1007/s10540-005-2850-4 pmid:16222422 fatcat:wwsnrzha45dshmu3wiipdbg2ca

Next-generation sequencing for cancer diagnostics: a practical perspective

Cliff Meldrum, Maria A Doyle, Richard W Tothill
2011 Clinical biochemist reviews  
Targeted DNA enrichment methods allow even higher genome throughput at a reduced cost per sample.  ...  The sensitivity, speed and reduced cost per sample make it a highly attractive platform compared to other sequencing modalities.  ...  Acknowledgements We would like to thank Dr Alison Trainer and Associate Professor Alex Dobrovic at the Peter MacCallum Cancer Centre for their helpful comments on the manuscript and Derek Campbell and  ... 
pmid:22147957 pmcid:PMC3219767 fatcat:kf3jnkl67zektcliim2bfqst3e

The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics

Paula de Matos, Jennifer A Cham, Hong Cao, Rafael Alcántara, Francis Rowland, Rodrigo Lopez, Christoph Steinbeck
2013 BMC Bioinformatics  
User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software  ...  To achieve this, you must characterise users' requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios.  ...  user-centred design process used during the project.  ... 
doi:10.1186/1471-2105-14-103 pmid:23514033 pmcid:PMC3623738 fatcat:lq4k3fmy45fsdmf5c7vjhxdt6u

The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects

Alexie Papanicolaou
2016 F1000Research  
The most reliable genome projects are the ones created as part of an active research program and designed to address specific questions but their life extends past publication.  ...  In turn, genomics is underpinned by a reference sequence and ancillary information created by so-called "genome projects".  ...  A reliable and user-friendly IT platform for dissemination is the most effective way to reduce the bioinformatic bottleneck that is manifesting in many labs.  ... 
doi:10.12688/f1000research.7559.1 pmid:27006757 pmcid:PMC4798206 fatcat:4vqpcreekbaj7myobrllpzg54i

Participatory programming and the scope of mutual responsibility

Catherine Letondal, Wendy E. Mackay
2004 Proceedings of the eighth conference on Participatory design Artful integration: interweaving media, materials and practices - PDC 04  
We introduce participatory programming, which integrates participatory design and end-user programming, and examine how it acts as a medium for forging scientific ideas.  ...  We first describe the history of these activities and how they have created the beginnings of a participatory design culture.  ...  We want to reduce the need for tailoring through user-centred methods at design time.  ... 
doi:10.1145/1011870.1011875 dblp:conf/pdc/LetondalM04 fatcat:7bxmtc33ozdubcamasje2wwvfa

Implementation of a workflow for publishing citeable environmental data: successes, challenges and opportunities from a data centre perspective

Kathryn A. Harrison, Daniel G. Wright, Philip Trembath
2016 International Journal on Digital Libraries  
Here we describe a workflow for publishing citeable data in 18 the context of the environmental sciencesan area spanning many domains and generating 19 a vast array of heterogeneous data products.  ...  In 26 conclusion, whilst data centres may have the infrastructure, tools, resources and processes 27 available to publish citeable datasets, further work is required before large-scale uptake of 28 the  ...  from a data centre perspective 248 The motivation for requesting a DOI for data deposited with EIDC has varied over time.  ... 
doi:10.1007/s00799-016-0175-5 fatcat:6iqohutzbnccxoegpnx7fqrhey

Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned

Gerald Li, Peter Bankhead, Philip D Dunne, Paul G O'Reilly, Jacqueline A James, Manuel Salto-Tellez, Peter W Hamilton, Darragh G McArt
2016 Briefings in Bioinformatics  
more detailed perspective.  ...  Along the way, we stress that integromics is not just a set of tools, but rather a cohesive paradigm for how modern bioinformatics can be enhanced.  ...  with a solid foundation across a broad range of topics such as advanced bioinformatics, database design, tissue imaging and integromics.  ... 
doi:10.1093/bib/bbw044 pmid:27255914 pmcid:PMC5862317 fatcat:q7wew3armjejrbfunjhcjhrt5e

The history of pathology informatics: A global perspective

Seung Park, AnilV Parwani, RaymondD Aller, Lech Banach, MichaelJ Becich, Stephan Borkenfeld, AlexisB Carter, BruceA Friedman, MarcialGarcia Rojo, Andrew Georgiou, Gian Kayser, Klaus Kayser (+6 others)
2013 Journal of Pathology Informatics  
The history of pathology informatics in different countries is a tale with many dimensions.  ...  Major drivers in the field included the need for pathologists to comply with national standards for health information technology and telepathology applications to meet the scarcity of pathology services  ...  Matsumura, A. Kamataki, Y. Miura, and M. Uzuki for help in researching and editing the Asia section of this monograph. Marcial Garcia Rojo gratefully acknowledges Dr.  ... 
doi:10.4103/2153-3539.112689 pmid:23869286 pmcid:PMC3714902 fatcat:ppr3pdk42neprathb2wathiwbe

Modelling biological complexity: a physical scientist's perspective

Peter V. Coveney, Philip W. Fowler
2005 Journal of the Royal Society Interface  
From the perspective of a physical scientist, it is especially interesting to examine how the differing weights given to philosophies of science in the physical and biological sciences impact the application  ...  These modelling methods are expected to bring numerous benefits to biology, for example, the properties of a system could be studied over a wider range of length-and time-scales, a key aim of systems biology  ...  Access to the US TeraGrid and LeMieux located at Pittsburgh Supercomputing Centre were provided through NSF (USA) NRAC and PACI grants MCA04N014 and ASC030006P, respectively.  ... 
doi:10.1098/rsif.2005.0045 pmid:16849185 pmcid:PMC1578273 fatcat:4mm2adaewjdc7aofcfddbmknqm

Pharmaceutical information: A 30-year perspective on the literature

David Bawden, Lyn Robinson
2011 Annual Review of Information Science and Technology  
The 'scientist' information producer/user group is a very broad one.  ...  The review shows the pharmaceutical subject domain to be particularly information intensive, with a complex communication chain, involving a notably varied set of producers and users of information, and  ...  new drug from a perspective in the 1980s, and Snow (2008) gave a picture of the extensive communication aspects of the drug development process thirty years later.  ... 
doi:10.1002/aris.2011.1440450109 fatcat:qirsfglp35f3xpiyz6hf6f2ude

Prospects of library use data integration in campus information systems: A glocalized perspective

Stavroula Sant-Geronikolou, Daniel Martínez-Ávila
2019 El Profesional de la Informacion  
European Bioinformatics Institute (EMBL-EBI).  ...  In the evening, there's a dinner at Exeter College with the Centre for Islamic Studies, whose board is meeting in Oxford.  ...  resource like the Business and IP Centre.  ... 
doi:10.3145/epi.2019.jul.10 fatcat:npfl66vxa5fpxhxe5u4epgmhjq
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