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Open-source softwareIndigo
Indigo KNIME nodes
Mikhail Rybalkin
Alexander Saveliev
5th KNIME Users Group Meeting and WorkshopFebruary 2, 2012
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History of Indigo project
BingoOracle, Sql Server, PostgreSQL
Open-source
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
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History of Indigo project
BingoOracle, Sql Server, PostgreSQL
ToolsCanonical SMILES, Rendering,
Decomposition
Open-source
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
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History of Indigo project
BingoOracle, Sql Server, PostgreSQL
IndigoC, Java, Python, C#
Tools
Indigo C++ Core
Open-source
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
![Page 5: Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012](https://reader034.vdocuments.net/reader034/viewer/2022052313/5a8f65437f8b9a78648d98cf/html5/thumbnails/5.jpg)
History of Indigo project
BingoOracle, Sql Server, PostgreSQL
IndigoC, Java, Python, C#
Tools
Indigo C++ Core
KnimeNodes
Open-source
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
![Page 6: Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012](https://reader034.vdocuments.net/reader034/viewer/2022052313/5a8f65437f8b9a78648d98cf/html5/thumbnails/6.jpg)
History of Indigo project
BingoOracle, Sql Server, PostgreSQL
IndigoC, Java, Python, C#
Tools
Indigo C++ Core
KnimeNodes
KetcherJavascript Molecule
Sketcher
Open-source
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
![Page 7: Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012](https://reader034.vdocuments.net/reader034/viewer/2022052313/5a8f65437f8b9a78648d98cf/html5/thumbnails/7.jpg)
History of Indigo project
BingoOracle, Sql Server, PostgreSQL
IndigoC, Java, Python, C#
Tools
Indigo C++ Core
KnimeNodes
KetcherJavascript Molecule
Sketcher
Proprietary projectsMass spectrometry
Molecular dynamics
Sequence processing
High-throughput screening
GPGPU, cluster computing
Image analysys and recognition
Open-source
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
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Why Open Source?
I Bussiness model
I Relationship with the scientific commnity
I Feedback from the commnityI SuggestionsI Testing
I Experience to develop commercial projects
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
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Why Open Source?
I Bussiness model
I Relationship with the scientific commnity
I Feedback from the commnityI SuggestionsI Testing
I Experience to develop commercial projects
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
![Page 10: Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012](https://reader034.vdocuments.net/reader034/viewer/2022052313/5a8f65437f8b9a78648d98cf/html5/thumbnails/10.jpg)
Why Open Source?
I Bussiness model
I Relationship with the scientific commnity
I Feedback from the commnityI SuggestionsI Testing
I Experience to develop commercial projects
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
![Page 11: Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012](https://reader034.vdocuments.net/reader034/viewer/2022052313/5a8f65437f8b9a78648d98cf/html5/thumbnails/11.jpg)
Indigo Nodes (Stable)
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
![Page 12: Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012](https://reader034.vdocuments.net/reader034/viewer/2022052313/5a8f65437f8b9a78648d98cf/html5/thumbnails/12.jpg)
Indigo Nodes (Nightly)
IndigoCombinatorial Chemistry
Combinatorial Reaction EnumerationManipulators
AromatizerAtom Replacer
Bond Replacer
Dearomatizer
Feature RemoverHydrogen Adder
Hydrogen RemoverMolecule Nodes
Component CombinerComponent Separator
Molecule TransformationMurcko ScaffoldR-Group Decomposer
Scaffold FinderSubstructure Match CounterSubstructure Matcher
Molecule Translators
Indigo to MoleculeIndigo to Query MoleculeMolecule to IndigoQuery Molecule to Indigo
PropertiesFingerprint SimilarityIndigo FigerprintMolecule Properties
Valence Checker
Reaction NodesReaction Automapper
Reaction BuilderReaction SplitterSubstructure Matcher
Reaction Translators
Indigo to ReactionIndigo to Query ReactionReaction to IndigoQuery Reaction to Indigo
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
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Functionallity
I Manipulators
Aromatizer Dearomatizer Hydrogen RemoverAtom Replacer Bond Replacer Feature RemoverHydrogen Adder
I Substructure search (Ordinary, Tautomer, Exact)
Parse SMILES
Parse query SMILES
Match tautomer substructure
Molecule to Indigo
Query Moleculeto Indigo
SubstructureMatcher
Parse SMILES
Parse query SMILES
Match tautomer substructure
Molecule to Indigo
Query Moleculeto Indigo
SubstructureMatcher
O
N
Query
O
NH
Highlightedtarget molecule
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
![Page 14: Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012](https://reader034.vdocuments.net/reader034/viewer/2022052313/5a8f65437f8b9a78648d98cf/html5/thumbnails/14.jpg)
Functionallity
I Manipulators
Aromatizer Dearomatizer Hydrogen RemoverAtom Replacer Bond Replacer Feature RemoverHydrogen Adder
I Substructure search (Ordinary, Tautomer, Exact)
Parse SMILES
Parse query SMILES
Match tautomer substructure
Molecule to Indigo
Query Moleculeto Indigo
SubstructureMatcher
Parse SMILES
Parse query SMILES
Match tautomer substructure
Molecule to Indigo
Query Moleculeto Indigo
SubstructureMatcher
O
N
Query
O
NH
Highlightedtarget molecule
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
![Page 15: Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012](https://reader034.vdocuments.net/reader034/viewer/2022052313/5a8f65437f8b9a78648d98cf/html5/thumbnails/15.jpg)
Functionallity (2)
I Scaffold finder and R-Group decomposition
N
N
O
C
R1
R2
R3R4
R5
O* Cl *
O OC
C
*
O OC
C
O* Cl
O*
N
N
*
O N
CN
*
O
C
CO N*
N*'
R1 R2 R3 R4 R5
initial moleculesin SMILES
converter
scaffold detection
R-group decomposition
Table Creator Molecule to Indigo
Scaffold Finder
R-Group Decomposer
converter
scaffold detection
R-group decomposition
Table Creator
Scaffold Finder
R-Group Decomposer
I Indigo Fingerpints
Calculate fingerprints Distance matrix Cluster by Tanimoto distance
View the clusters
Indigo FingerprintDistance MatrixCalculate
Hierarchical Clustering(DistMatrix)
HierarchicalCluster ViewCalculate fingerprints Distance matrix Cluster by Tanimoto distance
View the clusters
Distance MatrixCalculate
Hierarchical Clustering(DistMatrix)
HierarchicalCluster View
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
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Functionallity (2)
I Scaffold finder and R-Group decomposition
N
N
O
C
R1
R2
R3R4
R5
O* Cl *
O OC
C
*
O OC
C
O* Cl
O*
N
N
*
O N
CN
*
O
C
CO N*
N*'
R1 R2 R3 R4 R5
initial moleculesin SMILES
converter
scaffold detection
R-group decomposition
Table Creator Molecule to Indigo
Scaffold Finder
R-Group Decomposer
converter
scaffold detection
R-group decomposition
Table Creator
Scaffold Finder
R-Group Decomposer
I Indigo Fingerpints
Calculate fingerprints Distance matrix Cluster by Tanimoto distance
View the clusters
Indigo FingerprintDistance MatrixCalculate
Hierarchical Clustering(DistMatrix)
HierarchicalCluster ViewCalculate fingerprints Distance matrix Cluster by Tanimoto distance
View the clusters
Distance MatrixCalculate
Hierarchical Clustering(DistMatrix)
HierarchicalCluster View
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
![Page 17: Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012](https://reader034.vdocuments.net/reader034/viewer/2022052313/5a8f65437f8b9a78648d98cf/html5/thumbnails/17.jpg)
Whats New?
I Reaction Support
I Library Enumeration
I Molecule Transformations (Standardization)
Translator
Translator Transformation
Query Reactionto Indigo
Molecule to IndigoMoleculeTransformation
Translator
Translator Transformation
Query Reactionto Indigo
Molecule to IndigoMoleculeTransformation
A2A1 A2A1
R1
OH
O
R1 COOH
CF31
F
1
F
F
CF3
C
O
N
O
O
OH
O
CF3
CF3
F
F F
F
F
F
COOH
O
N
O O
CF3
CF3
Source molecule Transformations Result molecule
I Builder/Splitter Nodes
I InChI, InChIKey (preliminary)
I No dependencies on other packages in RHEL, and Mac OS X
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
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Whats New?
I Reaction Support
I Library Enumeration
I Molecule Transformations (Standardization)
Translator
Translator Transformation
Query Reactionto Indigo
Molecule to IndigoMoleculeTransformation
Translator
Translator Transformation
Query Reactionto Indigo
Molecule to IndigoMoleculeTransformation
A2A1 A2A1
R1
OH
O
R1 COOH
CF31
F
1
F
F
CF3
C
O
N
O
O
OH
O
CF3
CF3
F
F F
F
F
F
COOH
O
N
O O
CF3
CF3
Source molecule Transformations Result molecule
I Builder/Splitter Nodes
I InChI, InChIKey (preliminary)
I No dependencies on other packages in RHEL, and Mac OS X
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
![Page 19: Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012](https://reader034.vdocuments.net/reader034/viewer/2022052313/5a8f65437f8b9a78648d98cf/html5/thumbnails/19.jpg)
Whats New?
I Reaction Support
I Library Enumeration
I Molecule Transformations (Standardization)
Translator
Translator Transformation
Query Reactionto Indigo
Molecule to IndigoMoleculeTransformation
Translator
Translator Transformation
Query Reactionto Indigo
Molecule to IndigoMoleculeTransformation
A2A1 A2A1
R1
OH
O
R1 COOH
CF31
F
1
F
F
CF3
C
O
N
O
O
OH
O
CF3
CF3
F
F F
F
F
F
COOH
O
N
O O
CF3
CF3
Source molecule Transformations Result molecule
I Builder/Splitter Nodes
I InChI, InChIKey (preliminary)
I No dependencies on other packages in RHEL, and Mac OS X
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
![Page 20: Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012](https://reader034.vdocuments.net/reader034/viewer/2022052313/5a8f65437f8b9a78648d98cf/html5/thumbnails/20.jpg)
Friday Community Workshop
I Real workflow examples (by Simon)
I Indigo nodes in-depth
I Planned nodes
I Discussion
Thank you!
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012
![Page 21: Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012](https://reader034.vdocuments.net/reader034/viewer/2022052313/5a8f65437f8b9a78648d98cf/html5/thumbnails/21.jpg)
Friday Community Workshop
I Real workflow examples (by Simon)
I Indigo nodes in-depth
I Planned nodes
I Discussion
Thank you!
Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012