DocuPublications » History » Version 36
Version 35 (Anonymous, 10/06/2007 02:00 PM) → Version 36/37 (Anonymous, 10/10/2007 11:19 AM)
= Main (Internal) Publications =
This page provides access to all ProCKSI related ''Papers'', ''Posters'', ''Presentations'', ''Demonstrations'', '''Papers''', '''Posters''', '''Presentations''', '''Demonstrations''', and ''Tutorials'':
* [wiki:DocuPapers Papers]
* [wiki:DocuPosters Posters]
* [wiki:DocuPresentations Presentations]
* [wiki:DocuDemonstrations Demonstrations]
* [wiki:DocuTutorials Tutorials]
'''Tutorials'''.[[br]]
When adding new publications, please refer to the [wiki:WikiPolicy Wiki Policy] on how files should be named.
----
== 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.
----
== 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
----
== 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
----
== 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
----
== 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
This page provides access to all ProCKSI related ''Papers'', ''Posters'', ''Presentations'', ''Demonstrations'', '''Papers''', '''Posters''', '''Presentations''', '''Demonstrations''', and ''Tutorials'':
* [wiki:DocuPapers Papers]
* [wiki:DocuPosters Posters]
* [wiki:DocuPresentations Presentations]
* [wiki:DocuDemonstrations Demonstrations]
* [wiki:DocuTutorials Tutorials]
'''Tutorials'''.[[br]]
When adding new publications, please refer to the [wiki:WikiPolicy Wiki Policy] on how files should be named.
----
== 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.
----
== 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
----
== 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
----
== 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
----
== 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