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Capturing and supporting contexts for scientific data sharing via the biological sciences collaboratory

George Chin, Carina S. Lansing
2004 Proceedings of the 2004 ACM conference on Computer supported cooperative work - CSCW '04  
Under development at the Pacific Northwest National Laboratory, the Biological Sciences Collaboratory (BSC) enables the sharing of biological data and analyses through diverse capabilities such as metadata  ...  Today, a movement is afoot within the scientific computing community to shift "collaboratory" development from traditional tool-centric approaches to more data-centric ones.  ...  ACKNOWLEDGMENTS The research described in this paper was conducted under the Laboratory-Directed Research and Development (LDRD) Program at the Pacific Northwest National Laboratory, a multiprogram national  ... 
doi:10.1145/1031607.1031677 dblp:conf/cscw/ChinL04 fatcat:pgwhxmj7czghxm5ineaocldqsu

A Review of "Scientific Collaboration on the Internet"

Kalpana Shankar
2012 The Information Society  
The chapters of the book are organized in six parts: the contemporary collaboratory vision; perspectives on distributed, collaborative science; physical sciences; biological and health sciences; earth  ...  to the "science of collaboratories" that is the heart of this project.  ... 
doi:10.1080/01972243.2012.670034 fatcat:q6h5efltivbgdc6ad6vppctaia

Expectations for a scientific collaboratory

Diane H. Sonnenwald
2003 Proceedings of the 2003 international ACM SIGGROUP conference on Supporting group work - GROUP '03  
In the past decade, a number of scientific collaboratories have emerged, yet adoption of scientific collaboratories remains limited.  ...  These results both confirm existing knowledge and raise new issues for the design and evaluation of collaboratories.  ...  , Mary Whitton and others worked on the developed the single-user nM and nM collaboratory.  ... 
doi:10.1145/958169.958171 fatcat:xygl36g7ird2ncz5imjee355lm

Expectations for a scientific collaboratory

Diane H. Sonnenwald
2003 Proceedings of the 2003 international ACM SIGGROUP conference on Supporting group work - GROUP '03  
In the past decade, a number of scientific collaboratories have emerged, yet adoption of scientific collaboratories remains limited.  ...  These results both confirm existing knowledge and raise new issues for the design and evaluation of collaboratories.  ...  , Mary Whitton and others worked on the developed the single-user nM and nM collaboratory.  ... 
doi:10.1145/958160.958171 dblp:conf/group/Sonnenwald03 fatcat:2td7x65ntrgo5da7szyvtvt2w4

Incorporating collaboratory concepts into informatics in support of translational interdisciplinary biomedical research

E LEE, D MCDONALD, N ANDERSON, P TARCZYHORNOCH
2009 International Journal of Medical Informatics  
We, therefore, undertook a cross cutting study of science and engineering collaboratories to identify emergent themes.  ...  There is, however, a growing body of literature on the study and fostering of collaboration in fields such as computer supported cooperative work (CSCW) and information science (IS).  ...  Acknowledgments The authors would like to thank and acknowledge NIH NLM Training Grant (5 T15 LM007442-05) and NIH CTSA Grant (08 URR 025014A) for providing the funding to support parts of this work.  ... 
doi:10.1016/j.ijmedinf.2008.06.011 pmid:18706852 pmcid:PMC2606933 fatcat:xvc5d2dr6rcldhj2chxygtc7ti

Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory

Carole Goble, Stian Soiland-Reyes, Finn Bacall, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Simone Leo, Luca Pireddu, Laura Rodriguez-Navas, José Mª Fernández, Salvador Capella-Gutierrez (+5 others)
2021 Zenodo  
EOSC-Life brings together 13 of the Life Science 'ESFRI' research infrastructures to create an open, digital and collaborative space for biological and medical research.  ...  The collaboratory aims to provide a framework for researchers and workflow specialists to use and reuse workflows.  ...  This work has received funding from the European Commission's Horizon 2020 research and innovation programme under grant agreement numbers 824087 (EOSC-Life) and 823830 (BioExcel-2) and is supported by  ... 
doi:10.5281/zenodo.4605654 fatcat:z746zwknrjenxbn45t2hqwpuwq

How Collaboratories Affect Scientists from Developing Countries [chapter]

Airong Luo, Judith S. Olson
2008 Scientific Collaboration on the Internet  
The Chinese government also imposes strict restrictions on exporting materials related to biological research.  ...  Data Collection From the nearly two hundred collaboratories identified by the Science of Collaboratories project (see the introduction to this volume), we found eight that had participants from developing  ... 
doi:10.7551/mitpress/9780262151207.003.0021 fatcat:jnvlkhaplfbhjgqksrev2xxvdm

Initial Experiences in Developing a Chronologically Organized Digital Library for Continuing Education in Biodefense

Donna M. D'Alessandro, Michael P. D'Alessandro
2005 D-Lib Magazine  
BiodefenseEducation.org was also enrolled in the leading Internet general and health-sciences specific search engines and directories.  ...  The third strength of our technique is the key role played by the BiodefenseEducation.org curators, who have expertise in library science, medical informatics, medicine, and education.  ... 
doi:10.1045/april2005-dalessandro fatcat:qfcxfkgnebhf5gzah67tq5uvci

Cyberinfrastructure as a Platform to Facilitate Effective Collaboration between Institutions and Support Collaboratories

Eric Coulter, Jeremy Fischer, Barbara Hallock, Richard Knepper, Dave Lifka, JP Navarro, Marlon Pierce, Craig Stewart
2016 Proceedings of the 2016 ACM on SIGUCCS Annual Conference - SIGUCCS '16  
Currently XCI provides toolkits and training, and collaborates with organizations such as ACI-REF, XSEDE Campus Champions, and the Open Science Grid to identify tools and best practices that support the  ...  The XSEDE Community Infrastructure (XCI) group assists campuses in using their own resources and promotes the sharing of those resources in order to create collaboratories improving use of the nation's  ...  Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation or Pervasive Technology  ... 
doi:10.1145/2974927.2974962 dblp:conf/siguccs/CoulterFHKLNPS16 fatcat:s3kt7morknawvppsovtat6jrvq

Addressing the digital divide in contemporary biology: Lessons from teaching UNIX [article]

Serghei Mangul, Lana Martin, Alexander Hoffmann, Matteo Pellegrini, Eleazar Eskin
2017 bioRxiv   pre-print
Researchers in the biomedical sciences increasingly rely on applications that lack a graphical interface and require inputting code that, such as UNIX.  ...  Scientists who are not trained in computer science face an enormous challenge in analyzing the high-throughput data their research groups generate.  ...  Active engagement in analyzing the data they generate is essential to advancing interdisciplinary research in the biological sciences.  ... 
doi:10.1101/122424 fatcat:5weq2vz2zfgy5i736dflos7vhq

Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX

Serghei Mangul, Lana S. Martin, Alexander Hoffmann, Matteo Pellegrini, Eleazar Eskin
2017 Trends in Biotechnology  
Active engagement in analyzing the data they generate is essential to advancing interdisciplinary research in the biological sciences.  ...  We developed a publically available resource with workshop materials at: https://qcb.ucla.edu/collaboratory/workshops/collaboratory-workshop-1/ peer-reviewed) is the author/funder.  ... 
doi:10.1016/j.tibtech.2017.06.007 pmid:28720283 fatcat:6f2xhw3bhzeodcrrnojmmhdtce

The Collaboratory for Structural Nanobiology

Alvaro M. Gonzalez-Ibanez, Fernando Gonzalez-Nilo, Raul Cachau
2009 Biophysical Journal  
assay using full-length and truncation mutants of the SNARE proteins: syntaxin-1A, SNAP-25B and synaptobrevin, which have 0-4 cysteines.  ...  With this assay we are able to quantitatively measure the number of cysteine residues modified in reactions such as palmitoylation and oxidation. This assay is as sim-  ...  Nanobiotechnology is the field of science focused on the design, synthesis, characterization and application of nanomaterials and nanodevices to biological and biomedical problems.  ... 
doi:10.1016/j.bpj.2008.12.151 fatcat:eggvkdvivvfideb2hl7caxpkpq

Scientific collaboratories in higher education: exploring learning style preferences and perceptions of technology

Diane H. Sonnenwald, Bin Li
2003 British Journal of Educational Technology  
, compatibility and complexity of the collaboratory system.  ...  We conducted a repeated-measures study that provided data regarding social interaction learning styles and perceptions of a scientific collaboratory system from 40 university science students working face-to-face  ...  Acknowledgments Our thanks to: Chris Wiesen for guidance regarding the statistical analysis in this paper; the study participants; Martin Guthold and Richard Superfine for their natural science expertise  ... 
doi:10.1111/1467-8535.00339 fatcat:c4wqfrkxabdx3dlbm6vir5d6qy

Computational Science and Engineering On-line: an integrated web-based environment for multi-scale modelling of complex reaction systems

Thanh N. Truong, Tom Cook, Manohar Nayak, Chaiwoot Boonyasiriwat, Le-Thuy T. Tran, Shaowen Zhang
2004 Molecular Physics  
We present a development of an integrated extendable web-based environment called Computational Science and Engineering On-line (CSEO) to include different fields of computational science.  ...  Work is in progress to allow CSEO accessing resources from the computing grids using the Globus technology. CSEO can be accessed at http://cseo.net. It can also be hosted at different mirror sites.  ...  Another example is the Research Collaboratory for Structural Bioinformatics, which provides access to databases of biological structures and tools for determining and analysing these structures and the  ... 
doi:10.1080/00268970310001649392 fatcat:hhwy2srfabhvhahmnnzjgtzjz4
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