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, P. Lukasiak, J. Blacewicz, N. Krasnogor''' ([http://www.bentham.org/cbio/index.htm publisher])[[br]]

Web & Grid Technologies in Bioinformatics, Computational Biology and Systems Biology: A Review. [[br]]

''Current Bioinformatics'', (Accepted).

'''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 Comparison[[br]]

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 Proteins[[br]]

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 - !TechTalk[[br]]

ProCKSI and Protein Multiverse Meeting (PPMM'07), Nottingham, UK

'''A.A. Shah ''' ([attachment:Presentation_2007_ASAP_PPMM_AzharAliShah.pdf PDF], [source:Publications/Presentation_2007_ASAP_PPMM_AzharAliShah.ppt PPT])[[br]]

Protein Multiverse on University HPC Grid [[br]]

ProCKSI and Protein Multiverse Meeting (PPMM'07), Nottingham, UK

'''G. Folino ''' ([attachment:Presentation_2007_ASAP_PPMM_Folino.ppt PPT])[[br]]

ProCKSI - !TechTalk[[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-Heuristics[[br]]

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-Heuristics[[br]]

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 Comparison[[br]]

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 Comparison[[br]]

ASAP, Group Seminar, Nottingham, UK

'''D. Barthel '''

([source:/Publications/Presentation_2007_ASAP_CASP_DanielBarthel.ppt PPT])[[br]]

Evaluating CASP7 - Thoughts and Challenges[[br]]

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 Measures[[br]]

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 Measures[[br]]

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 representation[[br]]

East Midlands Proteomics Workshop (EMPW'06), Nottingham, UK

'''D. Barthel '''

([source:/Publications/Presentation_2006_RAD_DanielBarthel.ppt PPT])[[br]]

An Introduction to the ProCKSi-Server[[br]]

Research Away Day (RAD'06), Nottingham, UK

'''D. Barthel '''

[source:/Publications/Presentation_2006_ASAP_DanielBarthel.ppt PPT])[[br]]

Similarity Comparison of Proteins - The ProCKSi-Server[[br]]

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 Competitions[[br]]

ASAP, CASP Workshop, Nottingham, UK

'''D. Barthel '''

([source:/Publications/Presentation_2006_SchoolOfChemistry_DanielBarthel.ppt PPT])[[br]]

Similarity Comparison of Proteins - The ProCKSi-Server[[br]]

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 Measures[[br]]

Part1: Overview and Background, Part2: Offline Demonstration[[br]]

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 Proteins[[br]]

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 Approach[[br]]

ASAP, Journal Club, Nottingham, UK

=== 2006 ===

'''D. Barthel'''

([source:/Publications/Tutorial_2006_ASAP_ClusterAnalysis_DanielBarthel.ppt PPT])[[br]]

Cluster Analysis and Validation[[br]]

ASAP, Journal Club, Nottingham, UK