A Workflow System for Virtual    Screening in Cancer     Chemoprevention Kannas C. C., Achilleos K. G., Antoniou Z., Kalva...
Outline       About LiSIs platform             Objectives             What is LiSIs?             Virtual Screening & Scien...
About LiSIs platformIEEE 12th International Conference on BioInformatics &                                                ...
Objectives       Provide a set of tools to create virtual screening process for       the discovery of novel agents with d...
What is LiSIs?          Life Science Informatics          Scientific Workflow Management System               Computationa...
Virtual Screening & Scientific              Workflow Management Systems        Virtual Screening              Computationa...
Available @ http://lisis.cs.ucy.ac.cy                                                LiSIs platformIEEE 12th International...
Virtual Screening Process                                 Template                                                        ...
Docking Model Preparation                                                             Protein (pdb file)                  ...
Predictive Model Preparation                                                         Chemical                             ...
Predictive Model Preparation                                                          Model                               ...
3rd Party ToolsIEEE 12th International Conference on BioInformatics &                                                     ...
Galaxy       Galaxy is an open, web-based platform for data intensive       biomedical research.       Free public server....
Galaxy Integration Methodology           Galaxy configuration:                Web Server(s) (Handle Users Requests)       ...
RDKit       A collection of cheminformatics and machine-learning       software written in C++ and Python.       The core ...
The R Project       R is a language and environment for statistical computing and       graphics.       R provides a wide ...
AutoDock Vina       AutoDock Vina is a new open-source program for drug       discovery, molecular docking and virtual scr...
Available @ http://lisis.cs.ucy.ac.cy                                  LiSIs platform DemoIEEE 12th International Conferen...
LiSIs platform Live Demo!!!                                                http://lisis.cs.ucy.ac.cyIEEE 12th Internationa...
Concluding Remarks       Fill a current void in chemoprevention, and in general life       sciences, research.       Enabl...
Acknowledgement  Computer Science, UCY                                       Cancer Biology and  Prof. C. S. Pattichis    ...
Questions?IEEE 12th International Conference on BioInformatics &                                                          ...
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Granatum_LiSIs_BIBE_2012_presentation_v4.0

  1. 1. A Workflow System for Virtual Screening in Cancer Chemoprevention Kannas C. C., Achilleos K. G., Antoniou Z., Kalvari I., Kirmitzoglou I., Nicolaou C. A., Promponas V. J., Pattichis C. S. 13th November 2012 IEEE 12th International Conference on BioInformatics & BioEngineering
  2. 2. Outline About LiSIs platform Objectives What is LiSIs? Virtual Screening & Scientific Workflow Management Systems LiSIs platform Virtual Screening Process Template Docking Models Predictive Models 3rd Party Tools The GRANATUM-LiSIs Platform Concluding Remarks Acknowledgement Questions?IEEE 12th International Conference on BioInformatics & 2 13th November 2012BioEngineering
  3. 3. About LiSIs platformIEEE 12th International Conference on BioInformatics & 3 13th November 2012BioEngineering
  4. 4. Objectives Provide a set of tools to create virtual screening process for the discovery of novel agents with desired properties. Provide a set of tools to create data-driven models designed to predict biochemical properties of interest. Provide an environment to create, update, store and share Scientific Workflows, that is accessible via a web interface.IEEE 12th International Conference on BioInformatics & 4 13th November 2012BioEngineering
  5. 5. What is LiSIs? Life Science Informatics Scientific Workflow Management System Computational Environment for Virtual Screening. Cancer Chemoprevention Research Computational Tools borrowed from Drug Discovery Process. GRANATUM project (http://www.granatum.org) Partially funded by the European Commission under the Seventh Framework Programme in the area of Virtual Physiological Human (ICT-2009.5.3).IEEE 12th International Conference on BioInformatics & 5 13th November 2012BioEngineering
  6. 6. Virtual Screening & Scientific Workflow Management Systems Virtual Screening Computational counterpart of biological screening. Goal: decrease the number of compounds physically screened. Scientific Workflow Management Systems (SWMS) Computational environments which facilitate the design and execution of computational experiments (workflows). Known SWMS: Taverna (http://www.taverna.org.uk/) KNIME (http://www.knime.org/ ) Galaxy (http://galaxy.psu.edu/)IEEE 12th International Conference on BioInformatics & 6 13th November 2012BioEngineering
  7. 7. Available @ http://lisis.cs.ucy.ac.cy LiSIs platformIEEE 12th International Conference on BioInformatics & 7 13th November 2012BioEngineering
  8. 8. Virtual Screening Process Template Output Postprocessing •Storage •Visualization •Cleaning •Formatting Processing •Merging •Descriptor Filters •Similarity Search Preprocessing •Substructure Search •File format •Docking Models transformations •Predictive Models •Property Normalizer Input •Descriptors •GRANATUM Calculation platform File •Fragmentation Loader •Coordinates •File Readers Calculation •Protein CleanerIEEE 12th International Conference on BioInformatics & 8 13th November 2012BioEngineering
  9. 9. Docking Model Preparation Protein (pdb file) Add Hydrogens Protein Preparation: Remove H2O Docking Input Model Protein.pdb file Calculate Pocket Process Coordinates Remove water molecules Separate reference Add hydrogen atoms ligand Calculate binding domain coordinates Clean protein from co-crystalized molecule Output Modified protein.pdb fileIEEE 12th International Conference on BioInformatics & 9 13th November 2012BioEngineering
  10. 10. Predictive Model Preparation Chemical data Algorithm Biological •Algorithm data parameters Predictive ModelIEEE 12th International Conference on BioInformatics & 10 13th November 2012BioEngineering
  11. 11. Predictive Model Preparation Model Predictions •Chembl Training •Cross-Validation •Pubchem •Independent •Feature extraction / validation using •Predict biological •Literature selection separate datasets properties of •Various algorithms compounds (kNN, SVM, Random •E.g. Toxicity, ER- Forest, Decision Trees) binding activity Data Model gathering ValidationIEEE 12th International Conference on BioInformatics & 11 13th November 2012BioEngineering
  12. 12. 3rd Party ToolsIEEE 12th International Conference on BioInformatics & 12 13th November 2012BioEngineering
  13. 13. Galaxy Galaxy is an open, web-based platform for data intensive biomedical research. Free public server. Deploy locally. Deploy in a Cluster/Grid environment Deploy in the cloud (CloudMan Amazon EC2). http://galaxy.psu.edu/IEEE 12th International Conference on BioInformatics & 13 13th November 2012BioEngineering
  14. 14. Galaxy Integration Methodology Galaxy configuration: Web Server(s) (Handle Users Requests) Job Manager (Job Management) Job Handler(s) (Job Execution) Galaxy Tools are wrappers around command line applications. Galaxy runs command line jobs at the background.IEEE 12th International Conference on BioInformatics & 14 13th November 2012BioEngineering
  15. 15. RDKit A collection of cheminformatics and machine-learning software written in C++ and Python. The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL- based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches. Features Overview RDKit Home PageIEEE 12th International Conference on BioInformatics & 15 13th November 2012BioEngineering
  16. 16. The R Project R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of Rs strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control. The R ProjectIEEE 12th International Conference on BioInformatics & 16 13th November 2012BioEngineering
  17. 17. AutoDock Vina AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi- core capability, high performance and enhanced accuracy and ease of use. Features: Accuracy Compatibility with AutoDock Tools Ease of Use Flexible Side Chains Some receptor side chains can be chosen to be treated as flexible during docking. Speed AutoDock VinaIEEE 12th International Conference on BioInformatics & 17 13th November 2012BioEngineering
  18. 18. Available @ http://lisis.cs.ucy.ac.cy LiSIs platform DemoIEEE 12th International Conference on BioInformatics & 18 13th November 2012BioEngineering
  19. 19. LiSIs platform Live Demo!!! http://lisis.cs.ucy.ac.cyIEEE 12th International Conference on BioInformatics & 19 13th November 2012BioEngineering
  20. 20. Concluding Remarks Fill a current void in chemoprevention, and in general life sciences, research. Enabling researchers to utilize state of the art computational techniques to search for the discovery of novel agents with desired properties.IEEE 12th International Conference on BioInformatics & 20 13th November 2012BioEngineering
  21. 21. Acknowledgement Computer Science, UCY Cancer Biology and Prof. C. S. Pattichis Chemoprevention C. A. Nicolaou (PhD) laboratory at Department of Biological Sciences, UCY. Z. Antoniou Cancer Chemoprevention K. G. Achilleos and Epigenomics Workgroup Biological Sciences, UCY at German Cancer Research Dr. V. J. Promponas Center. I. Kirmitzoglou Members of the GRANATUM I. Kalvari consortium.IEEE 12th International Conference on BioInformatics & 21 13th November 2012BioEngineering
  22. 22. Questions?IEEE 12th International Conference on BioInformatics & 22 13th November 2012BioEngineering

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