jchem extensions for knime
TRANSCRIPT
JChem Extensions for KNIME
Attila Szabó Takahiro Ohshima
March 2013, Zürich
6th KNIME User Group Meeting
About ChemAxon
• Cheminformatics software – since ’98
• Pharma, biotech, agrochem, academia
• Global sales – USA, Europe, Japan, RoW
Product Overview
Just turned 15 years old
Thank you for your attention!
© 2013 INFOCOM CORPORATION All right reserved. 6th KNIME Users Group Meeting and Workshop
INFOCOM
IT Business company of Teijin Group
Offering wide varieties of IT services & solutions
Head office: Tokyo, JAPAN
Capital: 1.59 billion yen (ca. $15M)
No. of employees:
673 (stand-alone) / 1,188 (consolidated) , as of Mar 31, 2012
Chem & Bio Informatics Department
for life science market in Japan
for more than 25 years
© 2013 INFOCOM CORPORATION All right reserved. 6th KNIME Users Group Meeting and Workshop
JChem Extensions
Extensions of ChemAxon’s tool
for KNIME workflow
Infocom implement it with the
support of ChemAxon
Contains over 90% of ChemAxon's
cheminformatics functionality
© 2013 INFOCOM CORPORATION All right reserved. 6th KNIME Users Group Meeting and Workshop
Database management, Property calculation
Create and connect to both local
and remote database
Insertion, search and retrieval of
structures, create and drop
structure tables
Structure canonicalization
Automatic revision of structures
Almost all calculation plug-in can be
used
© 2013 INFOCOM CORPORATION All right reserved. 6th KNIME Users Group Meeting and Workshop
Virtual reaction enumeration
Sequential or combinatorial mode
Product or reaction output
Hi-lite mapping between reactant
and product
© 2013 INFOCOM CORPORATION All right reserved. 6th KNIME Users Group Meeting and Workshop
Markush structures
Markush enumeration
Markush search
Markush structure generation
R-group Decomposition /
Composition
Markush Viewer
© 2013 INFOCOM CORPORATION All right reserved. 6th KNIME Users Group Meeting and Workshop
JChem for Excel
JC4XL Reader
Reads Excel file created with
JChem For Excel.
JC4XL Writer
Writes JChem For Excel
compatible xlsx file.
© 2013 INFOCOM CORPORATION All right reserved. 6th KNIME Users Group Meeting and Workshop
Marvin Family Nodes and Marvin are FREELY
available in KNIME
What’s new “Marvin Family Nodes”
Marvin Sketch node
Output molecules as multiple
fragments
Output molecule properties that are
added in Marvin Sketch GUI
Marvin View node
Show the colored information
Show the hi-lited points
Filter the hi-lited points
© 2013 INFOCOM CORPORATION All right reserved. 6th KNIME Users Group Meeting and Workshop
Future Plan
JChem Extensions + Parvasive DataRush
Implement new KNIME streamable API
Execute JChem Extensions on the DataRush
Increase in execution speed and scalability
© 2013 INFOCOM CORPORATION All right reserved. 6th KNIME Users Group Meeting and Workshop
Let’s try
JChem Extensions:
http://www.infocom.co.jp/bio/develop/jchemextension_en.html
http://www.infocom.co.jp/bio/develop/jchemextension_update_en.html
Download and Install via the update site
Update Site : https://www.infocom.co.jp/bio/knime/update/2.6
KNIME:
http://www.knime.org/
http://tech.knime.org/
E-MAIL: