Summary


From a discussion by the Editorial Board of the Journal of Cheminformatics, we decided a special issue of the Journal dedicated to education would be highly desirable. In particular, papers would (i) describe both the history and state of the art in different areas of cheminformatics, with the emphasis on being a practical guide, especially for people outside the field and (ii) show how freely available / open source / "libre" algorithms, tools, and resources can be used for cheminformatics


- chemical identity (descriptors) / Johnny, Christoph / CDK, Mold2 (http://www.fda.gov/ScienceResearch/BioinformaticsTools/Mold2/default.htm)
- chemical similarity; virtual screening / Peter, Jurgen / ChemAxon, OE, PubChem, Chemspider
- pharmacophores / Yvonnne / ChemAxon (?)
- Clustering; machine learning / Bob C, Curt, ?? / Weka, Orange
- cheminformatics toolkits (CDK, Bioclipse, KNIME, ...) / Egon Willighagen?
- QSAR / Alex / ChemBench, OCHEM
- Property prediction / Bobby, Jonathan/ ACDLabs, ChemAxon
- Cheminformatics, Networks and the Semantic Web / David, Rajarshi, Tony / Chemspider, Chem2Bio2RDF, ChemProt

"Raw" resources

Resources that could provide useful base material
ICEP (Indiana University)

Proposed Papers

all can feel free to add papers and contribute to the discussion for each paper

Best practises for chemical structure registration and searching in relational databases

Proposed by Chris Steinbeck, is ready for submission


Cheminformatics, Networks and the Semantic Web

Proposed by David Wild. Describing developments in data integration with the semantic web, and how the resulting networks of data can be used

Article(s) covering open source tools: (I (Michael Berthold) favor variant B, to be honest)

  • Variant A: Open Source Cheminformatics Tools and Toolkits

  • Proposed by Michael Berthold. This version would attempt to cover all software out there (and needs lots of co-authors, obviously!)

  • Variant B1: KNIME Integrating Cheminformatics Toolkits

  • Proposed by Michael Berthold. This version would focus on KNIME and the cheminformatics tools it integrates.
  • Variant Bx: ToolX Integrating Cheminformatics Toolkits

  • Written by others. Bioclipse, Taverna, Orange, ... come to mind?