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Anonymous, 10/02/2007 04:21 PM

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= Main (Internal) Publications =
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This page provides access to all ProCKSI related '''Papers''', '''Posters''', '''Presentations''', '''Demonstrations''', and '''Tutorials'''.[[br]]
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When adding new publications, please refer to the [wiki:WikiPolicy Wiki Policy] on how files should be named.
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== Papers ==
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=== 2007 ===
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'''A.A. Shah, D. Barthel, and N. Krasnogor'''[[br]]
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Grid and distributed public computing schemes for structural proteomics.[[br]]
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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]]
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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])
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'''A.A. Shah, D. Barthel, and N. Krasnogor'''[[br]]
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Protein Structure Comparison, Analysis and Clustering: An overview of the ProCKSI Decision Support System.[[br]]
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''4th International Biotechnology Symposium (IBS 2007)''.[[br]]
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University of Sindh, Pakistan, Nov.4-8, 2007 (Accepted). 
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=== 2006 ===
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'''D. Barthel, J.D. Hirst, J. Blacewicz, and N. Krasnogor'''[[br]] 
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ProCKSI: A Metaserver for Protein Comparison using Kolmogorov and other Similarity Measures.[[br]]
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In ''Late Breaking Papers. European Conference on Computational Biology'', 2006.[[br]]
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Eilat, Israel, 2006. Peer reviewed CDROM publication.
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=== 2005 ===
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'''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]]
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A fuzzy sets based generalization of contact maps for the overlap of protein structures.[[br]]
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''Journal of Fuzzy Sets and Systems'', 152(2):103-123, 2005.
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'''D.A. Pelta, J.R. Gonzales, and N. Krasnogor'''[[br]]
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Protein structure comparison through fuzzy contact maps and the universal similarity metric.[[br]] 
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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.
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=== 2004 ===
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'''N. Krasnogor''' ([http://dx.doi.org/10.1023/B:GENP.0000023687.41210.d7 publisher])[[br]]
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Self-generating metaheuristics in bioinformatics: the protein structure comparison case.[[br]]
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''Genetic Programming and Evolvable Machines'', 5(2):181-201, 2004.
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'''N. Krasnogor and D.A. Pelta''' ([http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/7/1015 publisher])[[br]]
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Measuring the similarity of protein structures by means of the universal similarity metric.[[br]]
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''Bioinformatics'', 20(7):1015-1021, 2004.
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== Posters ==
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=== 2007 ===
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'''D. Barthel, J.D. Hirst, and N. Krasnogor''' 
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([source:/Publications/Poster_2007_ECCB06_DanielBarthel.ppt PPT])[[br]]
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ProCKSi: A Meta-Server for Protein Structure Comparison[[br]]
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European Conference on Computational Biology (ECCB'06), Eilat, Israel
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=== 2006 ===
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'''D. Barthel, J.D. Hirst, and N. Krasnogor'''
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([source:/Publications/Poster_2006_AHM_DanielBarthel.ppt PPT])[[br]]
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UK e-science - All Hands Meeting (AHM'06), Nottingham, UK
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=== 2005 ===
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'''D. Barthel, J.D. Hirst, and N. Krasnogor'''
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([source:/Publications/Poster_2005_GrantholdersWorkshop_DanielBarthel.ppt PPT])[[br]]
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Similarity Comparison of Proteins[[br]]
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BBSRC Bioinformatics and e-Science Grantholders Workshop, Manchester, UK
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== Presentations ==
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=== 2007 ===
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'''D. Barthel ''' ([attachment:Presentation_2007_ASAP_PPMM_DanielBarthel_v2.pdf PDF], [source:/Publications/Presentation_2007_ASAP_PPMM_DanielBarthel_v2.ppt PPT])[[br]]
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ProCKSI - !TechTalk[[br]]
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ProCKSI and Protein Multiverse Meeting (PPMM'07), Nottingham, UK
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'''A.A. Shah ''' ([attachment:Presentation_2007_ASAP_PPMM_AzharAliShah.pdf PDF], [attachment :Presentation_2007_ASAP_PPMM_AzharAliShah.ppt PPT])[[[br]]
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Protein Multiverse on University HPC Grid [[br]]
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ProCKSI and Protein Multiverse Meeting (PPMM'07), Nottingham, UK
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'''D. Barthel ''' ([source:/Publications/Presentation_2007_RAD_DanielBarthel.ppt PPT])[[br]]
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The ProCKSi-Server: A Decision-Support System for Protein Structure Comparison using Hyper-Heuristics[[br]]
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Research Away Day (RAD'07), Nottingham, UK
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'''D. Barthel '''
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([source:/Publications/Presentation_2007_ASAP_NGDS-Evaluation_DanielBarthel.ppt PPT])[[br]]
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The ProCKSi-Server: A Decision-Support Meta-Server for Protein Structure Comparison using Hyper-Heuristics[[br]]
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ASAP, Next Generation Decision Support -  EPSRC Evaluation, Nottingham, UK
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'''D. Barthel '''
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([source:/Publications/Presentation_2007_ASAP_NGDS-Workshop1_DanielBarthel.ppt PPT])[[br]]
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The ProCKSi-Server: A Decision-Support Meta-Server for Protein Structure Comparison[[br]]
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ASAP, Next Generation Decision Support - First Workshop, Nottingham, UK
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'''D. Barthel '''
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([source:/Publications/Presentation_2007_ASAP_DanielBarthel.ppt PPT])[[br]]
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The ProCKSi-Server: A Meta-Server for Protein Structure Comparison[[br]]
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ASAP, Group Seminar, Nottingham, UK
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'''D. Barthel '''
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([source:/Publications/Presentation_2007_ASAP_CASP_DanielBarthel.ppt PPT])[[br]]
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Evaluating CASP7 - Thoughts and Challenges[[br]]
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ASAP, CASP Workshop, Nottingham, UK
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'''D. Barthel '''
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([source:/Publications/Presentation_2006_CNIO_DanielBarthel.ppt PPT])[[br]]
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The ProCKSi-Server: A Meta-Server for Protein Comparison using Kolmogorov and other Similarity Measures[[br]]
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CNIO, Group Seminar, Madrid, Spain
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=== 2006 ===
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'''D. Barthel '''
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([source:/Publications/Presentation_2006_EMPW_DanielBarthel.ppt PPT])[[br]]
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The ProCKSi-Server: A Meta-Server for Protein Comparison using Kolmogorov and other Similarity Measures[[br]]
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East Midlands Proteomics Workshop (EMPW'06), Nottingham, UK
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'''P. Widera '''
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([source:/Publications/Presentation_2006_EMPW_PawelWidera.pdf PDF])
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([source:/Publications/Presentation_2006_EMPW_PawelWidera_src.tar.gz TGZ])[[br]]
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The MAX-CMO problem and its representation[[br]]
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East Midlands Proteomics Workshop (EMPW'06), Nottingham, UK
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'''D. Barthel '''
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([source:/Publications/Presentation_2006_RAD_DanielBarthel.ppt PPT])[[br]]
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An Introduction to the ProCKSi-Server[[br]]
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Research Away Day (RAD'06), Nottingham, UK
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'''D. Barthel '''
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[source:/Publications/Presentation_2006_ASAP_DanielBarthel.ppt PPT])[[br]]
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Similarity Comparison of Proteins - The ProCKSi-Server[[br]]
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ASAP, Group Seminar, Nottingham, UK
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'''D. Barthel '''
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([source:/Publications/Presentation_2006_ASAP_CASP_DanielBarthel.ppt PPT])[[br]]
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CAFASP - An Overview and Comparison with CASP and other Competitions[[br]]
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ASAP, CASP Workshop, Nottingham, UK
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'''D. Barthel '''
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([source:/Publications/Presentation_2006_SchoolOfChemistry_DanielBarthel.ppt PPT])[[br]]
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Similarity Comparison of Proteins - The ProCKSi-Server[[br]]
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School of Chemistry, Group Seminar, Nottingham, UK
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== Demonstrations ==
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=== 2006 ===
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'''D. Barthel'''
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(Part1: [source:/Publications/Demonstration_2006_AHM_Part1_DanielBarthel.ppt PPT], Part2: [source:/Publications/Demonstration_2006_AHM_Part2_DanielBarthel.ppt PPT])[[br]]
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The ProCKSi-Server: A Meta-Server for Protein Comparison using Kolmogorov and other Similarity Measures[[br]]
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Part1: Overview and Background, Part2: Offline Demonstration[[br]]
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UK e-science - All Hands Meeting (AHM'06), Nottingham, UK '''&'''[[br]] 
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School of Chemistry, Group Seminar, Nottingham, UK
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=== 2005 ===
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'''D. Barthel, N. Krasnogor'''[[br]]
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Similarity Comparison of Proteins[[br]]
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BBSRC Bioinformatics and e-Science Grantholders Workshop, Manchester, UK
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== Tutorials ==
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=== 2007 ===
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'''D. Barthel '''
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([source:/Publications/Presentation_2007_ASAP_JournalClub_DanielBarthel.ppt PPT])[[br]]
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Total Evidence, Concensus, and Bat Phylogeny: A Distance-Based Approach[[br]]
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ASAP, Journal Club, Nottingham, UK
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=== 2006 ===
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'''D. Barthel'''
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([source:/Publications/Tutorial_2006_ASAP_ClusterAnalysis_DanielBarthel.ppt PPT])[[br]]
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Cluster Analysis and Validation[[br]]
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ASAP, Journal Club, Nottingham, UK