svn commit: r1749918 - in /incubator/taverna/site/trunk/content/community: publications.md references.md

Thu, 23 Jun 2016 08:12:06 -0700 

Author: stain
Date: Thu Jun 23 15:11:11 2016
New Revision: 1749918

URL: http://svn.apache.org/viewvc?rev=1749918&view=rev
Log:
added lots of 2015/2016 Taverna publications

Modified:
    incubator/taverna/site/trunk/content/community/publications.md
    incubator/taverna/site/trunk/content/community/references.md

Modified: incubator/taverna/site/trunk/content/community/publications.md
URL: 
http://svn.apache.org/viewvc/incubator/taverna/site/trunk/content/community/publications.md?rev=1749918&r1=1749917&r2=1749918&view=diff
==============================================================================
--- incubator/taverna/site/trunk/content/community/publications.md (original)
+++ incubator/taverna/site/trunk/content/community/publications.md Thu Jun 23 
15:11:11 2016
@@ -37,9 +37,20 @@ At: [PROV: Three Years Later](http://pro
 [[slide]](http://provenanceweek.org/2016/p3yl/slides/slide_86.pdf)
 [[source]](https://github.com/stain/2016-provweek-tavernaprov/)
 
-### 2015
+Pinar Alper (2016)
+**Towards harnessing computational workflow provenance for experiment 
reporting**
+PhD thesis.
+[[pdf]](https://www.escholar.manchester.ac.uk/api/datastream?publicationPid=uk-ac-man-scw:300560&datastreamId=FULL-TEXT.PDF)
+[[escholar]](https://www.escholar.manchester.ac.uk/uk-ac-man-scw:300560)
+
 
+### 2015
 
+Rudolf Mayer, Andreas Rauber (2015):
+**A Quantitative Study on the Re-executability of Publicly Shared Scientific 
Workflows**
+At _2015 IEEE 11th International Conference on e-Science (e-Science)_.
+[doi:10.1109/eScience.2015.58](http://dx.doi.org/10.1109/eScience.2015.58)
+[[pdf]](http://www.ifs.tuwien.ac.at/~mayer/publications/pdf/may_escience15_workflows.pdf)
 
 ### 2014
 Sarah Cohen-Boulakia, Jiuqiang Chen, Paolo Missier, Carole A. Goble, Alan R. 
Williams, Christine Froidevaux. (2014).
@@ -47,9 +58,19 @@ Sarah Cohen-Boulakia, Jiuqiang Chen, Pao
 In: *BMC Bioinformatics*, 15(suppl 1).
 
[doi:10.1186/1471-2105-15-S1-S12](http://dx.doi.org/10.1186/1471-2105-15-S1-S12)
 
-<!---
-The above link is broken as of 1/20/16; it worked on 1/18/16. GN
---->
+
+Pinar Alper (2014):
+**Re-thinking Workflow Provenance against Data-Oriented Investigation 
Lifecycle**
+Technical report.
+[[pdf]](https://www.escholar.manchester.ac.uk/api/datastream?publicationPid=uk-ac-man-scw:224895&datastreamId=FULL-TEXT.PDF)
+[[escholar]](https://www.escholar.manchester.ac.uk/uk-ac-man-scw:224895)
+
+Judicaël Ribault, Gregory Zacharewicz (2014):
+**Time-based orchestration of workflow, interoperability with G-Devs/Hla**
+In: _Journal of Computational Science_ **10** 126-136.
+[doi:10.1016/j.jocs.2014.07.002](http://dx.doi.org/10.1016/j.jocs.2014.07.002)
+[[researchgate]](https://www.researchgate.net/publication/264498536_Time-Based_Orchestration_Of_Workflow_Interoperability_With_G-DevsHla)
+[[pdf]](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)
 
 ### 2013
 Anja Le Blanc, John Brooke, Donal Fellows, Marco Soldati, David 
P&eacute;rez-Su&aacute;rez, Alessandro Marassi, Andrej Santin. (2013).

Modified: incubator/taverna/site/trunk/content/community/references.md
URL: 
http://svn.apache.org/viewvc/incubator/taverna/site/trunk/content/community/references.md?rev=1749918&r1=1749917&r2=1749918&view=diff
==============================================================================
--- incubator/taverna/site/trunk/content/community/references.md (original)
+++ incubator/taverna/site/trunk/content/community/references.md Thu Jun 23 
15:11:11 2016
@@ -24,10 +24,17 @@ See also [publications](/community/publi
 
 ## 2016
 
-Arzu Tugce Guler, Cathelijn J. F. Waaijer, Magnus Palmblad. (2016). 
**Scientific workflows for
-bibliometrics.** In: *Scientometrics*. Advance online publication, 15 February 
2016.
+Arzu Tugce Guler, Cathelijn J. F. Waaijer, Magnus Palmblad. (2016):
+**Scientific workflows for bibliometrics.**
+In: *Scientometrics*. **107**(2) 385-Ì£398.
 [doi:10.1007/s11192-016-1885-6](http://dx.doi.org/10.1007/s11192-016-1885-6).
 
+
+H Munir, A Benjamin, JW Allwood, WB Dunn, S He, GB Nash, HM McGettrick (2016):
+**A1.18 Mesenchymal stem cells lose their immuno-protective effects upon 
changes in their local microenvironment**
+In: _Annals of the Rheumatic Diseases_ 2016 **75**(A8).
+[doi:10.1136/annrheumdis-2016-209124.18](http://dx.doi.org/10.1136/annrheumdis-2016-209124.18)
+
 ## 2015
 
 Khalid Belhajjame, Jun Zhao, Daniel Garijo, Matthew Gamble, Kristina Hettne, 
Ra&uacute;l Palma,
@@ -42,6 +49,54 @@ Sonja Holl, Yassene Mohammed, Olav Zimme
 In: *BMC Bioinformatics* 16(1): 1-13.
 [doi:10.1186/s12859-015-0714-x](http://dx.doi.org/10.1186/s12859-015-0714-x)
 
+Steve O’Hagan, Douglas B. Kell (2015):
+**Software review: the KNIME workflow environment and its applications in 
genetic programming and machine learning**.
+In: *Genetic Programming and Evolvable Machines* **16**(3) 387-391.
+[doi:10.1007/s10710-015-9247-3](http://dx.doi.org/10.1007/s10710-015-9247-3)
+[[preprint]](http://www.taverna.org.uk/pages/wp-content/uploads/2015/2015-Hagan-Kell-KNIME-software-review.pdf)
+
+Renato De Giovanni, Alan R. Williams, Vera Hernández Ernst, Robert Kulawik, 
Francisco Quevedo Fernandez, Alex R. Hardisty (2015):
+**ENM Components: a new set of web service-based workflow components for 
ecological niche modelling**.
+In: *Ecography* **39**(4).
+[doi:10.1111/ecog.01552](http://dx.doi.org/10.1111/ecog.01552)
+
+Edward Baker, Ben W. Price, S. D. Rycroft1, Jon Hill, Vincent S. Smith (2015):
+**BioAcoustica: a free and open repository and analysis platform for 
bioacoustics**
+In *Database*  **2015**(bav054).
+[doi:10.1093/database/bav054](http://dx.doi.org/10.1093/database/bav054)
+
+Yassene Mohammed, Christoph H. Borchers (2015):
+**An extensive library of surrogate peptides for all human proteins**
+_Journal of Proteomics_ **129** 93-97.
+[doi:10.1016/j.jprot.2015.07.025](http://dx.doi.org/10.1016/j.jprot.2015.07.025)
+[[researchgate]](https://www.researchgate.net/publication/280602358_An_Extensive_Library_of_Surrogate_Peptides_for_all_Human_Proteins)
+_preprint not currently available_
+
+Ji Liu, Esther Pacitti, Patrick Valduriez, Marta Mattoso (2015):
+**A Survey of Data-Intensive Scientific Workflow Management**
+In: _Journal of Grid Computing_ **13** 457-493.
+[doi:10.1007/s10723-015-9329-8](http://dx.doi.org/10.1007/s10723-015-9329-8)
+[[pdf]](http://www-sop.inria.fr/members/Patrick.Valduriez/pmwiki/Patrick/uploads//Publications/jogc2015)
+[[researchgate]](https://www.researchgate.net/publication/304292492_A_Survey_on_Scheduling_Workflows_in_Cloud_Environment)
+
+
+Susana Sánchez Expósito, Pablo Martín, Jose Enrique Ruíz, Lourdes 
Verdes-Montenegro, Julian Garrido, Raül Sirvent Pardell, Antonio Ruíz Falcó, 
Rosa Badia (2015):
+**Web services as building blocks for Science Gateways in Astrophysics**.
+At: _7th International Workshop on Science Gateways (IWSG) 2015_
+[doi:10.1109/IWSG.2015.7](http://dx.doi.org/10.1109/IWSG.2015.7)
+[[pdf]](http://amiga.iaa.es/FCKeditor/UserFiles/File/BuildingBlocks.pdf)
+
+Fabrizio Marozzo, Domenico Talia, Paolo Trunfio (2015):
+**JS4Cloud: script-based workflow programming for scalable data analysis on 
cloud platforms**
+In: _Concurrency and Computation: Practice and Experience_. **27**(17) 
5214–5237.
+[doi:10.1002/cpe.3563](http://dx.doi.org/10.1002/cpe.3563)
+[[researchgate]](https://www.researchgate.net/publication/280971659_JS4Cloud_Script-based_workflow_programming_for_scalable_data_analysis_on_cloud_platforms)
+
+Jeremy Leipzig (2015):
+**A review of bioinformatic pipeline frameworks**.
+In: _Briefings in bioinformatics_ (2016) 1-7 bbw020.  
+[doi:10.1093/bib/bbw020](http://dx.doi.org/10.1093/bib/bbw020)
+
 ## 2014
 
 Pinar Alper, Carole A Goble, Khalid Belhajjame (2014):
@@ -78,6 +133,7 @@ In: *BMC Research Notes*, 7: 740.
 [doi:10.1186/1756-0500-7-740](http://dx.doi.org/10.1186/1756-0500-7-740)
 
 ## 2013
+
 Pinar Alper, Khalid Belhajjame, Carole A. Goble, Pinar Karagoz. (2013).
 **"Enhancing and abstracting scientific workflow provenance for data 
publishing,"**
 in *Proceedings of the Joint EDBT/ICDT 2013 Workshops (EDBT'13)*, 18&ndash;22 
Mar 2013: 313&ndash;318.
@@ -92,12 +148,13 @@ in *Big Data (BigData Congress), 2013 IE
 
[[pdf]](http://www.computer.org/csdl/proceedings/bigdatacongress/2013/5006/00/5006a318.pdf)
 
 Khalid Belhajjame, Jun Zhao, Daniel Garijo, Aleix Garrido, Stian 
Soiland-Reyes, Pinar Alper, Oscar Corcho. (2013).
-**"A workflow PROV-corpus based on Taverna and Wings,"**
+**"A workflow PROV-corpus based on Taverna and Wings."**
 in *Proceedings of the Joint EDBT/ICDT 2013 Workshops (EDBT'13)*, 18&ndash;22 
Mar 2013: 331&ndash;332.
 [doi:10.1145/2457317.2457376](http://dx.doi.org/10.1145/2457317.2457376)
 
[[pdf]](http://delicias.dia.fi.upm.es/members/dgarijo/papers/prov-bench-paper.pdf)
 [[related website]](https://github.com/provbench/Wf4Ever-PROV)
 
+
 Daniel Garijo, Pinar Alper, Khalid Belhajjame, Oscar Corcho, Yolanda Gil, 
Carole Goble. (2013).
 **Common motifs in scientific workflows: An empirical analysis.**
 In: *Future Generation Computer Systems*, 36: 338-351.
@@ -105,13 +162,14 @@ In: *Future Generation Computer Systems*
 [[preprint]](http://oa.upm.es/21854/1/1-s2_0-S0167739X13001970-main.pdf)
 
 Carole Goble, David De Roure and Sean Bechhofer (2013):
-**"Accelerating Scientists&rsquo; Knowledge Turns,"**
+**"Accelerating Scientists&rsquo; Knowledge Turns."**
 in *Communications in Computer and Information Science, Vol 348*.  Springer, 
Berlin, 8 June 2013: 3&ndash;25.
 
[doi:10.1007/978-3-642-37186-8_1](http://dx.doi.org/10.1007/978-3-642-37186-8_1)
 [[preprint 
server]](http://ora.ox.ac.uk/objects/uuid%3A17de32c4-518f-4be6-bf78-1ecd6c761b81)
 [[download 
pdf]](http://ora.ox.ac.uk/objects/uuid:17de32c4-518f-4be6-bf78-1ecd6c761b81/datastreams/ATTACHMENT01).
 
 ## 2012
+
 Kahlid Belhajjame, Oscar Corcho, Daniel Garijo, Jun Zhao, Paolo Missier, David 
Newman, Ra&uacute;l Palma, Sean Bechhofer, Esteban Garc&iacute;a Cuesta, 
Jos&eacute; Manuel G&oacute;mez-P&eacute;rez, Graham Klyne, Kevin Page, Marco 
Roos, Jos&eacute; Ruiz, Stian Soiland-Reyes, Lourdes Verdes-Montenegro, David 
De Roure, Carole Goble. (2012).
 **"Workflow-Centric Research Objects: First Class Citizens in Scholarly 
Discourse,"**
 in *Proceedings of Workshop on the Semantic Publishing (SePublica 2012)*, 28 
May 2012: 1&ndash;12.
@@ -128,6 +186,13 @@ Kevin Page, Ra&uacute;l Palma, Piotr Ho&
 in *Proceedings of the 2nd International Workshop on Linked Science*.
 
[[pdf]](http://linkedscience.org/wp-content/uploads/2012/05/lisc2012_submission_15.pdf)
 
+Jeroen S. de Bruin, André M. Deelder, Magnus Palmblad (2012):
+**Scientific Workflow Management in Proteomics**
+In: *Molecular & Cellular Proteomics* **11**(7):M111.010595
+[doi:10.1074/mcp.M111.010595](http://dx.doi.org/10.1074/mcp.M111.010595)
+[pmid:22411703](http://www.ncbi.nlm.nih.gov/pubmed/22411703)
+[PMC3394934](http://europepmc.org/articles/PMC3394934)
+
 ## 2011
 
 R. Bentley, J. Brooke, A. Csillaghy, D. Fellows, A. Le Blanc, M. Messerotti, 
D. Perez-Suarez, G. Pierantoni, M. Soldati. (2011).
@@ -175,7 +240,7 @@ in *Handbook of Research on Computationa
 
[doi:10.4018/978-1-60566-374-6.ch003](http://dx.doi.org/10.4018/978-1-60566-374-6.ch003)
 
 David De Roure, Carole Goble. (2009).
-**"Lessons from myExperiment: Research Objects for Data Intensive Research,"**
+**"Lessons from myExperiment: Research  Objects for Data Intensive Research,"**
 in *eScience Workshop 2009*, 15&ndash;17 Oct 2009.
 [[eprint]](http://eprints.ecs.soton.ac.uk/17744/)

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