ProCKSI

= Main (Internal) Publications =

This page provides access to all ProCKSI related '''Papers''', '''Posters''', '''Presentations''', '''Demonstrations''', and '''Tutorials'''.br
When adding new publications, please refer to the [wiki:WikiPolicy Wiki Policy] on how files should be named.

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Papers === 2007 ===
'''A.A. Shah, D. Barthel, and N. Krasnogor'''br
Grid and distributed public computing schemes for structural proteomics.br
In P. Thulasiraman, X. He, T. Li-Xu, M. Denko, R.K. Thulasiram, and L.T. Yang, editors, ''Frontiers of High Performance Computing and Networking ISPA 2007 Workshops''.br
Lecture Notes in Computer Science. Springer, Vol.4743, p.424-434, isbn 978-3-540-74766-6, 2007. ( [http://www.springerlink.com/content/90n46423p200502r/ Electronic Edition])([http://dblp.uni-trier.de/rec/bibtex/conf/ispa/ShahBK07 bibtex])

'''A.A. Shah, D. Barthel, and N. Krasnogor'''br
Protein Structure Comparison, Analysis and Clustering: An overview of the ProCKSI Decision Support System.br
''4th International Biotechnology Symposium (IBS 2007)''.br
University of Sindh, Pakistan, Nov.4-8, 2007 (Accepted).

=== 2006 ===
'''D. Barthel, J.D. Hirst, J. Blacewicz, and N. Krasnogor'''br
ProCKSI: A Metaserver for Protein Comparison using Kolmogorov and other Similarity Measures.br
In ''Late Breaking Papers. European Conference on Computational Biology'', 2006.br
Eilat, Israel, 2006. Peer reviewed CDROM publication.

=== 2005 ===
'''D.A. Pelta, N. Krasnogor, C. Bousono-Calzon, J.L. Verdegay, J. Hirst, and E.K. Burke''' ([http://dx.doi.org/10.1016/j.fss.2004.10.017 publisher])br
A fuzzy sets based generalization of contact maps for the overlap of protein structures.br
''Journal of Fuzzy Sets and Systems'', 152(2):103-123, 2005.

'''D.A. Pelta, J.R. Gonzales, and N. Krasnogor'''br
Protein structure comparison through fuzzy contact maps and the universal similarity metric.br
In ''Fourth Conference of the European Society for Fuzzy Logic and Technology and 11 Recontres Francophones sur la Logique Floue et ses Applications (EUSFLAT-LFA'05)'', 1124-1129, Barcelona, Spain, 2005.

=== 2004 ===
'''N. Krasnogor''' ([http://dx.doi.org/10.1023/B:GENP.0000023687.41210.d7 publisher])br
Self-generating metaheuristics in bioinformatics: the protein structure comparison case.br
''Genetic Programming and Evolvable Machines'', 5(2):181-201, 2004.

'''N. Krasnogor and D.A. Pelta''' ([http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/7/1015 publisher])br
Measuring the similarity of protein structures by means of the universal similarity metric.br
''Bioinformatics'', 20(7):1015-1021, 2004.

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Posters === 2007 ===
'''D. Barthel, J.D. Hirst, and N. Krasnogor'''
([source:/Publications/Poster_2007_ECCB06_DanielBarthel.ppt PPT])br
ProCKSi: A Meta-Server for Protein Structure Comparisonbr
European Conference on Computational Biology (ECCB'06), Eilat, Israel

=== 2006 ===
'''D. Barthel, J.D. Hirst, and N. Krasnogor'''
([source:/Publications/Poster_2006_AHM_DanielBarthel.ppt PPT])br
UK e-science - All Hands Meeting (AHM'06), Nottingham, UK

=== 2005 ===
'''D. Barthel, J.D. Hirst, and N. Krasnogor'''
([source:/Publications/Poster_2005_GrantholdersWorkshop_DanielBarthel.ppt PPT])br
Similarity Comparison of Proteinsbr
BBSRC Bioinformatics and e-Science Grantholders Workshop, Manchester, UK

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Presentations === 2007 ===
'''D. Barthel ''' ([attachment:Presentation_2007_ASAP_PPMM_DanielBarthel_v2.pdf PDF], [source:/Publications/Presentation_2007_ASAP_PPMM_DanielBarthel_v2.ppt PPT])br
ProCKSI - !TechTalkbr
ProCKSI and Protein Multiverse Meeting (PPMM'07), Nottingham, UK

'''A.A. Shah ''' ([attachment:Presentation_2007_ASAP_PPMM_AzharAliShah.pdf PDF], [attachment:Presentation_2007_ASAP_PPMM_AzharAliShah.ppt PPT])br
Protein Multiverse on University HPC Grid br
ProCKSI and Protein Multiverse Meeting (PPMM'07), Nottingham, UK

'''D. Barthel ''' ([source:/Publications/Presentation_2007_RAD_DanielBarthel.ppt PPT])br
The ProCKSi-Server: A Decision-Support System for Protein Structure Comparison using Hyper-Heuristicsbr
Research Away Day (RAD'07), Nottingham, UK

'''A.A. Shah ''' ([source:/Publications/Presentation_2007_RAD_AzharAliShah.ppt PPT])br
Grid-enabled Protein Structure Comparison (PSC): architectural design and analysis br
Research Away Day (RAD'07), Nottingham, UK

'''D. Barthel '''
([source:/Publications/Presentation_2007_ASAP_NGDS-Evaluation_DanielBarthel.ppt PPT])br
The ProCKSi-Server: A Decision-Support Meta-Server for Protein Structure Comparison using Hyper-Heuristicsbr
ASAP, Next Generation Decision Support - EPSRC Evaluation, Nottingham, UK

'''D. Barthel '''
([source:/Publications/Presentation_2007_ASAP_NGDS-Workshop1_DanielBarthel.ppt PPT])br
The ProCKSi-Server: A Decision-Support Meta-Server for Protein Structure Comparisonbr
ASAP, Next Generation Decision Support - First Workshop, Nottingham, UK

'''D. Barthel '''
([source:/Publications/Presentation_2007_ASAP_DanielBarthel.ppt PPT])br
The ProCKSi-Server: A Meta-Server for Protein Structure Comparisonbr
ASAP, Group Seminar, Nottingham, UK

'''D. Barthel '''
([source:/Publications/Presentation_2007_ASAP_CASP_DanielBarthel.ppt PPT])br
Evaluating CASP7 - Thoughts and Challengesbr
ASAP, CASP Workshop, Nottingham, UK

'''D. Barthel '''
([source:/Publications/Presentation_2006_CNIO_DanielBarthel.ppt PPT])br
The ProCKSi-Server: A Meta-Server for Protein Comparison using Kolmogorov and other Similarity Measuresbr
CNIO, Group Seminar, Madrid, Spain

=== 2006 ===
'''D. Barthel '''
([source:/Publications/Presentation_2006_EMPW_DanielBarthel.ppt PPT])br
The ProCKSi-Server: A Meta-Server for Protein Comparison using Kolmogorov and other Similarity Measuresbr
East Midlands Proteomics Workshop (EMPW'06), Nottingham, UK

'''P. Widera '''
([source:/Publications/Presentation_2006_EMPW_PawelWidera.pdf PDF])
([source:/Publications/Presentation_2006_EMPW_PawelWidera_src.tar.gz TGZ])br
The MAX-CMO problem and its representationbr
East Midlands Proteomics Workshop (EMPW'06), Nottingham, UK

'''D. Barthel '''
([source:/Publications/Presentation_2006_RAD_DanielBarthel.ppt PPT])br
An Introduction to the ProCKSi-Serverbr
Research Away Day (RAD'06), Nottingham, UK

'''D. Barthel '''
[source:/Publications/Presentation_2006_ASAP_DanielBarthel.ppt PPT])br
Similarity Comparison of Proteins - The ProCKSi-Serverbr
ASAP, Group Seminar, Nottingham, UK

'''D. Barthel '''
([source:/Publications/Presentation_2006_ASAP_CASP_DanielBarthel.ppt PPT])br
CAFASP - An Overview and Comparison with CASP and other Competitionsbr
ASAP, CASP Workshop, Nottingham, UK

'''D. Barthel '''
([source:/Publications/Presentation_2006_SchoolOfChemistry_DanielBarthel.ppt PPT])br
Similarity Comparison of Proteins - The ProCKSi-Serverbr
School of Chemistry, Group Seminar, Nottingham, UK

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Demonstrations === 2006 ===
'''D. Barthel'''
(Part1: [source:/Publications/Demonstration_2006_AHM_Part1_DanielBarthel.ppt PPT], Part2: [source:/Publications/Demonstration_2006_AHM_Part2_DanielBarthel.ppt PPT])br
The ProCKSi-Server: A Meta-Server for Protein Comparison using Kolmogorov and other Similarity Measuresbr
Part1: Overview and Background, Part2: Offline Demonstrationbr
UK e-science - All Hands Meeting (AHM'06), Nottingham, UK '''&'''br
School of Chemistry, Group Seminar, Nottingham, UK

=== 2005 ===
'''D. Barthel, N. Krasnogor'''br
Similarity Comparison of Proteinsbr
BBSRC Bioinformatics and e-Science Grantholders Workshop, Manchester, UK

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Tutorials === 2007 ===
'''D. Barthel '''
([source:/Publications/Presentation_2007_ASAP_JournalClub_DanielBarthel.ppt PPT])br
Total Evidence, Concensus, and Bat Phylogeny: A Distance-Based Approachbr
ASAP, Journal Club, Nottingham, UK

=== 2006 ===
'''D. Barthel'''
([source:/Publications/Tutorial_2006_ASAP_ClusterAnalysis_DanielBarthel.ppt PPT])br
Cluster Analysis and Validationbr
ASAP, Journal Club, Nottingham, UK