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LiSIs platform
The document discusses the Lisis platform, a scientific workflow management system designed for life sciences research that facilitates tools for virtual screening and model sharing. It highlights the platform's technological underpinnings, including the Galaxy Project, RDKit, R Project, and AutoDock Vina. Additionally, it outlines the processes involved in virtual screening, such as input handling, pre-processing, processing, and post-processing stages.
LiSIs platform
- 1. LiSIs Platform Christos Kannas ZinonasAntoniou Kleio Achilleos 21 June 2013 International Workshop on LiSIs1
- 2. Outline What isLiSIs? What powers LiSIs? Virtual Screening on LiSIs LiSis Tools LiSIs Demo 21 June 2013 International Workshop on LiSIs 2
- 3. Life Sciences Informatics Scientific Workflow Management System for Life Sciences Research Tools for Virtual Screening Create, Use and Share Docking and Property Prediction Models Design, Execute and Share Virtual Screening Workflows 21 June 2013 International Workshop on LiSIs 3
- 4. LiSIs is poweredby: Galaxy Project Scientific Workflow Management System http://galaxyproject.org/ RDKit Cheminformatics and Machine Learning Software http://www.rdkit.org/ The R Project Software environment for statistical computing and graphics http://www.r-project.org/ AutoDock Vina Software for molecular docking http://vina.scripps.edu/ 21 June 2013 International Workshop on LiSIs 4
- 5. Virtual Screening onLiSIs 21 June 2013 International Workshop on LiSIs 5 Input •GRANATUM Platform •Files •Chemical & Biological File Parsing Pre-processing •Descriptor Calculation •Fragmentation •3D Coordinate Calculation •Protein Cleaning Processing •Attribute filter •Similarity filter •Substructure Search •Docking Predictions •Property Predictions Post-processing •Merging Output •Storage •Reporting •File format transformations
- 6. LiSIs Tools 21 June2013 International Workshop on LiSIs 6
- 7. LiSIs Demo http://lisis.cs.ucy.ac.cy 21 June2013 International Workshop on LiSIs 7
- 8. 21 June 2013 InternationalWorkshop on LiSIs 8
Editor's Notes
- #7 Briefly explain the tools.Redirect for Docking and Predictive Models in upcoming presentations.
- #8 Demonstration of LiSIs platform.Show LiSIs/Galaxy features.Explain History vs. Workflow.Show tool usage from Input, Pre-Processing, User Processing, Output Layers.Exclude Docking and Predictive Models.Show Workflow Design, Execution & Sharing.Demo Outline:Import dataset from Shared LibraryParse File (SDF / SMI)Calculate DescriptorsRo5 FilteringCalculate FingerprintsDiversity Filtering on Ro5 Passed CompoundsCreate Output File(s)Workflow Design:Extract Workflow from HistoryEdit & Save WorkflowExecute Workflow on different datasetShow User Data Features.