Author: buildbot
Date: Thu Jun 23 15:11:24 2016
New Revision: 991261
Log:
Staging update by buildbot for taverna
Modified:
websites/staging/taverna/trunk/cgi-bin/ (props changed)
websites/staging/taverna/trunk/content/ (props changed)
websites/staging/taverna/trunk/content/community/publications.html
websites/staging/taverna/trunk/content/community/references.html
Propchange: websites/staging/taverna/trunk/cgi-bin/
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Propchange: websites/staging/taverna/trunk/content/
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Modified: websites/staging/taverna/trunk/content/community/publications.html
==============================================================================
--- websites/staging/taverna/trunk/content/community/publications.html
(original)
+++ websites/staging/taverna/trunk/content/community/publications.html Thu Jun
23 15:11:24 2016
@@ -197,16 +197,33 @@ At: <a href="http://provenanceweek.org/2
<a href="http://provenanceweek.org/2016/p3yl/papers/paper_86.pdf";>[pdf]</a>
<a href="http://provenanceweek.org/2016/p3yl/slides/slide_86.pdf";>[slide]</a>
<a href="https://github.com/stain/2016-provweek-tavernaprov/";>[source]</a></p>
+<p>Pinar Alper (2016)
+<strong>Towards harnessing computational workflow provenance for experiment
reporting</strong>
+PhD thesis.
+<a
href="https://www.escholar.manchester.ac.uk/api/datastream?publicationPid=uk-ac-man-scw:300560&datastreamId=FULL-TEXT.PDF";>[pdf]</a>
+<a
href="https://www.escholar.manchester.ac.uk/uk-ac-man-scw:300560";>[escholar]</a></p>
<h3 id="2015">2015<a class="headerlink" href="#2015" title="Permanent
link">¶</a></h3>
+<p>Rudolf Mayer, Andreas Rauber (2015):
+<strong>A Quantitative Study on the Re-executability of Publicly Shared
Scientific Workflows</strong>
+At <em>2015 IEEE 11th International Conference on e-Science (e-Science)</em>.
+<a
href="http://dx.doi.org/10.1109/eScience.2015.58";>doi:10.1109/eScience.2015.58</a>
+<a
href="http://www.ifs.tuwien.ac.at/~mayer/publications/pdf/may_escience15_workflows.pdf";>[pdf]</a></p>
<h3 id="2014">2014<a class="headerlink" href="#2014" title="Permanent
link">¶</a></h3>
<p>Sarah Cohen-Boulakia, Jiuqiang Chen, Paolo Missier, Carole A. Goble, Alan
R. Williams, Christine Froidevaux. (2014).
<strong>Distilling structure in Taverna scientific workflows: a refactoring
approach.</strong>
In: <em>BMC Bioinformatics</em>, 15(suppl 1).
<a
href="http://dx.doi.org/10.1186/1471-2105-15-S1-S12";>doi:10.1186/1471-2105-15-S1-S12</a></p>
-<!---
-The above link is broken as of 1/20/16; it worked on 1/18/16. GN
---->
-
+<p>Pinar Alper (2014):
+<strong>Re-thinking Workflow Provenance against Data-Oriented Investigation
Lifecycle</strong>
+Technical report.
+<a
href="https://www.escholar.manchester.ac.uk/api/datastream?publicationPid=uk-ac-man-scw:224895&datastreamId=FULL-TEXT.PDF";>[pdf]</a>
+<a
href="https://www.escholar.manchester.ac.uk/uk-ac-man-scw:224895";>[escholar]</a></p>
+<p>Judicaël Ribault, Gregory Zacharewicz (2014):
+<strong>Time-based orchestration of workflow, interoperability with
G-Devs/Hla</strong>
+In: <em>Journal of Computational Science</em> <strong>10</strong> 126-136.
+<a
href="http://dx.doi.org/10.1016/j.jocs.2014.07.002";>doi:10.1016/j.jocs.2014.07.002</a>
+<a
href="https://www.researchgate.net/publication/264498536_Time-Based_Orchestration_Of_Workflow_Interoperability_With_G-DevsHla";>[researchgate]</a>
+<a
href="https://www.researchgate.net/profile/Gregory_Zacharewicz/publication/264498536_Time-Based_Orchestration_Of_Workflow_Interoperability_With_G-DevsHla/links/54d1eecf0cf28959aa7bcf52.pdf?inViewer=0&pdfJsDownload=0&origin=publication_detail";>[pdf]</a></p>
<h3 id="2013">2013<a class="headerlink" href="#2013" title="Permanent
link">¶</a></h3>
<p>Anja Le Blanc, John Brooke, Donal Fellows, Marco Soldati, David
Pérez-Suárez, Alessandro Marassi, Andrej Santin. (2013).
<strong>Workflows for heliophysics.</strong>
Modified: websites/staging/taverna/trunk/content/community/references.html
==============================================================================
--- websites/staging/taverna/trunk/content/community/references.html (original)
+++ websites/staging/taverna/trunk/content/community/references.html Thu Jun 23
15:11:24 2016
@@ -185,9 +185,14 @@ h2:hover > .headerlink, h3:hover > .head
See also <a href="/community/publications">publications</a> and <a
href="/community/cite">how to cite Taverna</a>.</em></p>
<p><em>Please suggest an <a href="/community/edit">edit</a> of the website to
add or correct a publication listing.</em></p>
<h2 id="2016">2016<a class="headerlink" href="#2016" title="Permanent
link">¶</a></h2>
-<p>Arzu Tugce Guler, Cathelijn J. F. Waaijer, Magnus Palmblad. (2016).
<strong>Scientific workflows for
-bibliometrics.</strong> In: <em>Scientometrics</em>. Advance online
publication, 15 February 2016.
+<p>Arzu Tugce Guler, Cathelijn J. F. Waaijer, Magnus Palmblad. (2016):
+<strong>Scientific workflows for bibliometrics.</strong>
+In: <em>Scientometrics</em>. <strong>107</strong>(2) 385-Ì£398.
<a
href="http://dx.doi.org/10.1007/s11192-016-1885-6";>doi:10.1007/s11192-016-1885-6</a>.</p>
+<p>H Munir, A Benjamin, JW Allwood, WB Dunn, S He, GB Nash, HM McGettrick
(2016):
+<strong>A1.18â
Mesenchymal stem cells lose their immuno-protective effects
upon changes in their local microenvironment</strong>
+In: <em>Annals of the Rheumatic Diseases</em> 2016 <strong>75</strong>(A8).
+<a
href="http://dx.doi.org/10.1136/annrheumdis-2016-209124.18";>doi:10.1136/annrheumdis-2016-209124.18</a></p>
<h2 id="2015">2015<a class="headerlink" href="#2015" title="Permanent
link">¶</a></h2>
<p>Khalid Belhajjame, Jun Zhao, Daniel Garijo, Matthew Gamble, Kristina
Hettne, Raúl Palma,
Eleni Mina, Oscar Corcho, José Manuel Gómez-Pérez, Sean
Bechhofer,
@@ -199,6 +204,45 @@ In: <em>Journal of Web Semantics: Scence
<strong>Scientific workflow optimization for improved peptide and protein
identification.</strong>
In: <em>BMC Bioinformatics</em> 16(1): 1-13.
<a
href="http://dx.doi.org/10.1186/s12859-015-0714-x";>doi:10.1186/s12859-015-0714-x</a></p>
+<p>Steve OâHagan, Douglas B. Kell (2015):
+<strong>Software review: the KNIME workflow environment and its applications
in genetic programming and machine learning</strong>.
+In: <em>Genetic Programming and Evolvable Machines</em> <strong>16</strong>(3)
387-391.
+<a
href="http://dx.doi.org/10.1007/s10710-015-9247-3";>doi:10.1007/s10710-015-9247-3</a>
+<a
href="http://www.taverna.org.uk/pages/wp-content/uploads/2015/2015-Hagan-Kell-KNIME-software-review.pdf";>[preprint]</a></p>
+<p>Renato De Giovanni, Alan R. Williams, Vera Hernández Ernst, Robert
Kulawik, Francisco Quevedo Fernandez, Alex R. Hardisty (2015):
+<strong>ENM Components: a new set of web service-based workflow components for
ecological niche modelling</strong>.
+In: <em>Ecography</em> <strong>39</strong>(4).
+<a href="http://dx.doi.org/10.1111/ecog.01552";>doi:10.1111/ecog.01552</a></p>
+<p>Edward Baker, Ben W. Price, S. D. Rycroft1, Jon Hill, Vincent S. Smith
(2015):
+<strong>BioAcoustica: a free and open repository and analysis platform for
bioacoustics</strong>
+In <em>Database</em> <strong>2015</strong>(bav054).
+<a
href="http://dx.doi.org/10.1093/database/bav054";>doi:10.1093/database/bav054</a></p>
+<p>Yassene Mohammed, Christoph H. Borchers (2015):
+<strong>An extensive library of surrogate peptides for all human
proteins</strong>
+<em>Journal of Proteomics</em> <strong>129</strong> 93-97.
+<a
href="http://dx.doi.org/10.1016/j.jprot.2015.07.025";>doi:10.1016/j.jprot.2015.07.025</a>
+<a
href="https://www.researchgate.net/publication/280602358_An_Extensive_Library_of_Surrogate_Peptides_for_all_Human_Proteins";>[researchgate]</a>
+<em>preprint not currently available</em></p>
+<p>Ji Liu, Esther Pacitti, Patrick Valduriez, Marta Mattoso (2015):
+<strong>A Survey of Data-Intensive Scientific Workflow Management</strong>
+In: <em>Journal of Grid Computing</em> <strong>13</strong> 457-493.
+<a
href="http://dx.doi.org/10.1007/s10723-015-9329-8";>doi:10.1007/s10723-015-9329-8</a>
+<a
href="http://www-sop.inria.fr/members/Patrick.Valduriez/pmwiki/Patrick/uploads//Publications/jogc2015";>[pdf]</a>
+<a
href="https://www.researchgate.net/publication/304292492_A_Survey_on_Scheduling_Workflows_in_Cloud_Environment";>[researchgate]</a></p>
+<p>Susana Sánchez Expósito, Pablo MartÃn, Jose Enrique RuÃz, Lourdes
Verdes-Montenegro, Julian Garrido, Raül Sirvent Pardell, Antonio RuÃz Falcó,
Rosa Badia (2015):
+<strong>Web services as building blocks for Science Gateways in
Astrophysics</strong>.
+At: <em>7th International Workshop on Science Gateways (IWSG) 2015</em>
+<a href="http://dx.doi.org/10.1109/IWSG.2015.7";>doi:10.1109/IWSG.2015.7</a>
+<a
href="http://amiga.iaa.es/FCKeditor/UserFiles/File/BuildingBlocks.pdf";>[pdf]</a></p>
+<p>Fabrizio Marozzo, Domenico Talia, Paolo Trunfio (2015):
+<strong>JS4Cloud: script-based workflow programming for scalable data analysis
on cloud platforms</strong>
+In: <em>Concurrency and Computation: Practice and Experience</em>.
<strong>27</strong>(17) 5214â5237.
+<a href="http://dx.doi.org/10.1002/cpe.3563";>doi:10.1002/cpe.3563</a>
+<a
href="https://www.researchgate.net/publication/280971659_JS4Cloud_Script-based_workflow_programming_for_scalable_data_analysis_on_cloud_platforms";>[researchgate]</a></p>
+<p>Jeremy Leipzig (2015):
+<strong>A review of bioinformatic pipeline frameworks</strong>.
+In: <em>Briefings in bioinformatics</em> (2016) 1-7 bbw020.<br />
+<a href="http://dx.doi.org/10.1093/bib/bbw020";>doi:10.1093/bib/bbw020</a></p>
<h2 id="2014">2014<a class="headerlink" href="#2014" title="Permanent
link">¶</a></h2>
<p>Pinar Alper, Carole A Goble, Khalid Belhajjame (2014):
<strong>"On assisting scientific data curation in collection-based dataflows
using labels,"</strong>
@@ -240,7 +284,7 @@ in <em>Big Data (BigData Congress), 2013
<a
href="http://dx.doi.org/10.1109/BigData.Congress.2013.49";>doi:10.1109/BigData.Congress.2013.49</a>
<a
href="http://www.computer.org/csdl/proceedings/bigdatacongress/2013/5006/00/5006a318.pdf";>[pdf]</a></p>
<p>Khalid Belhajjame, Jun Zhao, Daniel Garijo, Aleix Garrido, Stian
Soiland-Reyes, Pinar Alper, Oscar Corcho. (2013).
-<strong>"A workflow PROV-corpus based on Taverna and Wings,"</strong>
+<strong>"A workflow PROV-corpus based on Taverna and Wings."</strong>
in <em>Proceedings of the Joint EDBT/ICDT 2013 Workshops (EDBT'13)</em>,
18–22 Mar 2013: 331–332.
<a
href="http://dx.doi.org/10.1145/2457317.2457376";>doi:10.1145/2457317.2457376</a>
<a
href="http://delicias.dia.fi.upm.es/members/dgarijo/papers/prov-bench-paper.pdf";>[pdf]</a>
@@ -251,7 +295,7 @@ In: <em>Future Generation Computer Syste
<a
href="http://dx.doi.org/10.1016/j.future.2013.09.018";>doi:10.1016/j.future.2013.09.018</a>
<a
href="http://oa.upm.es/21854/1/1-s2_0-S0167739X13001970-main.pdf";>[preprint]</a></p>
<p>Carole Goble, David De Roure and Sean Bechhofer (2013):
-<strong>"Accelerating Scientists’ Knowledge Turns,"</strong>
+<strong>"Accelerating Scientists’ Knowledge Turns."</strong>
in <em>Communications in Computer and Information Science, Vol 348</em>.
Springer, Berlin, 8 June 2013: 3–25.
<a
href="http://dx.doi.org/10.1007/978-3-642-37186-8_1";>doi:10.1007/978-3-642-37186-8_1</a>
<a
href="http://ora.ox.ac.uk/objects/uuid%3A17de32c4-518f-4be6-bf78-1ecd6c761b81";>[preprint
server]</a>
@@ -270,6 +314,12 @@ in <em>Proceedings of the 4th Internatio
<strong>"From workflows to Research Objects: an architecture for preserving
the semantics of science,"</strong>
in <em>Proceedings of the 2nd International Workshop on Linked Science</em>.
<a
href="http://linkedscience.org/wp-content/uploads/2012/05/lisc2012_submission_15.pdf";>[pdf]</a></p>
+<p>Jeroen S. de Bruin, André M. Deelder, Magnus Palmblad (2012):
+<strong>Scientific Workflow Management in Proteomics</strong>
+In: <em>Molecular & Cellular Proteomics</em>
<strong>11</strong>(7):M111.010595
+<a
href="http://dx.doi.org/10.1074/mcp.M111.010595";>doi:10.1074/mcp.M111.010595</a>
+<a href="http://www.ncbi.nlm.nih.gov/pubmed/22411703";>pmid:22411703</a>
+<a href="http://europepmc.org/articles/PMC3394934";>PMC3394934</a></p>
<h2 id="2011">2011<a class="headerlink" href="#2011" title="Permanent
link">¶</a></h2>
<p>R. Bentley, J. Brooke, A. Csillaghy, D. Fellows, A. Le Blanc, M.
Messerotti, D. Perez-Suarez, G. Pierantoni, M. Soldati. (2011).
<strong>"HELIO: Discovery and Analysis of Data in Heliophysics,"</strong>
@@ -301,12 +351,12 @@ in <em>Workflows in Support of Large-Sca
in <em>Proceedings of the 13th International Conference on Extending Database
Technology (EDBT'10)</em>: 299–310.
<a
href="http://dx.doi.org/10.1145/1739041.1739079";>doi:10.1145/1739041.1739079</a></p>
<h2 id="2009">2009<a class="headerlink" href="#2009" title="Permanent
link">¶</a></h2>
-<p>Kahlid Belhajjame, Paolo Missier, Carole Goble. (2009).
+<p>Khalid Belhajjame, Paolo Missier, Carole Goble. (2009).
<strong>"Data Provenance in Scientific Workflows,"</strong>
in <em>Handbook of Research on Computational Grid Technologies for Life
Sciences, Biomedicine, and Healthcare</em>. Hershey, PA: 46–59.
<a
href="http://dx.doi.org/10.4018/978-1-60566-374-6.ch003";>doi:10.4018/978-1-60566-374-6.ch003</a></p>
<p>David De Roure, Carole Goble. (2009).
-<strong>"Lessons from myExperiment: Research Objects for Data Intensive
Research,"</strong>
+<strong>"Lessons from myExperiment: Research Objects for Data Intensive
Research,"</strong>
in <em>eScience Workshop 2009</em>, 15–17 Oct 2009.
<a href="http://eprints.ecs.soton.ac.uk/17744/";>[eprint]</a></p>
<p>David De Roure, Carole Goble. (2009).
