UGM 2007 Training

Archive of all tasks and demos of the Training day

Structural Search





Trainer: Szabolcs Csepregi





Summary:





1. Searching in the JSP application, exploring thin client architecture


2. Searching in IJC


3. Search features


4. Search options


5. Reaction search





Training demo:


http://www.chemaxon.com/shared/szabolcs/search_training_audio/





References:


Structural Search Using ChemAxon Tools


http://www.chemaxon.com/conf/Structural_Search.ppt (.ppt)


http://www.chemaxon.com/conf/Advanced_structural_searching_using_ChemAxon_tools.pdf (poster format in pdf)


JChem Query guide http://www.chemaxon.com/jchem/doc/user/Query.html


JChem Base web application (JSP) examples: http://www.chemaxon.com/jchem/examples.html

Chemical Terms





Trainer: Zsolt Mohácsi





Summary:





1. Property calculations with Chemical Terms


2. Elements of the Chemical Terms language


3. Filtering with Chemical Terms


4. Match functions in Chemical Terms








Training demo:


http://www.chemaxon.com/shared/zsolt/ugm2007_chemical_terms_training/videos/


(Remaining videos are coming soon.)





References:


Chemical Terms, a Language for Cheminformatics (.ppt) http://www.chemaxon.com/conf/ChemicalTerms.ppt


Chemical Term Language Reference http://www.chemaxon.com/jchem/doc/user/ChemicalTerms.html


Chemical Terms Reference Tables http://www.chemaxon.com/jchem/doc/user/EvaluatorTables.html


Predefined Molecules and Molecule Sets http://www.chemaxon.com/jchem/doc/user/Evaluator_files/mols.smarts

Reactor Training





Trainer: Gyorgy Pirok





Summary:





1. Combinatorial enumeration


Generate a reaction library


2. Reaction Design


Design a reaction and test it with added examples in the Reaction Editor and in the Reaction Wizard





References:





Demo:





Licenses:

Instant JChem Training





Trainer: Tim Dudgeon





Summary:


1. Open the demo data


2. Explore the PubChem demo data


3. Explore the Wombat data


4. Import 'result2.smiles' into IJC


5. Import 'result4.smiles' into IJC


6. Import 'result1.smiles' into IJC


7. Use the 'Schema Editor' to view the database contents


8. Import 'screening_collection.sdf'


9. Build a form


10. Query your data


11. Apply a Standardizer








Training demo:


http://www.chemaxon.com/shared/tim/ugm-training/





Licenses:


Standardizer license is needed to specify non-default standardization in the last exercise

LibMCS Training








Trainer: Miklos Vargyas





Summary:





Maximum Common Substructure clustering of structure sets with Library MCS: Identify diverse sets through; import structure sets and related data into LibraryMCS, fast clustering for initial evaluation, tune parameters to explore clustering outcomes, perform exhaustive clustering with 'best' parameters, select novel scaffolds.





References:





Demo:





Licenses: