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LICSS - A chemical spreadsheet in Microsoft Excel
Kevin R Lawson, Jonty Lawson Journal of Cheminformatics 2012, 4:3 (2 February 2012)
Abstract | Provisional PDF
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Editor’s summary
A lightweight open source chemical spreadsheet has been developed that runs within Microsoft Excel and can be used on sheets containing hundreds of thousands of compounds without compromising normal performance
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Predicting the mechanism of phospholipidosis
Robert Lowe, Hamse Y Mussa, Florian Nigsch, Robert C Glen, John BO Mitchell Journal of Cheminformatics 2012, 4:2 (26 January 2012)
Abstract | Provisional PDF
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Graphical abstract
An in silico approach was used to predict targets for phospholipidosis, a lysosomal disorder characterized by accumulation of phospholipids in tissues. By predicting targets for a database of compounds, they can be ranked by their potential to cause phospholipidosis
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Making SharePoint(R) Chemically Aware(TM)
Kartik Tallapragada, Joseph Chewning, David Kombo, Beverly Ludwick Journal of Cheminformatics 2012, 4:1 (12 January 2012)
Abstract | Provisional PDF
| PubMed | Cited on BioMed Central
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New developments on the cheminformatics open workflow environment CDK-Taverna
Andreas Truszkowski, Kalai Vanii Jayaseelan, Stefan Neumann, Egon L Willighagen, Achim Zielesny, Christoph Steinbeck Journal of Cheminformatics 2011, 3:54 (13 December 2011)
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Graphical abstract
The most up to date version of the CDK-Taverna project is described, which aims at building a free open-source cheminformatics pipelining solution through a combination of different open-source projects
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MyChemise: A 2D drawing program that uses morphing for visualisation purposes
Jörg-Hubertus Wilhelm Journal of Cheminformatics 2011, 3:53 (12 December 2011)
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Automated annotation of chemical names in the literature with tunable accuracy
Jun D. Zhang, Lewis Y. Geer, Evan E. Bolton, Stephen H. Bryant Journal of Cheminformatics 2011, 3:52 (22 November 2011)
Abstract | Provisional PDF
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An automated chemical name annotation system has been developed to annotate small molecule names in scientific abstracts with the aim of reproducing MeSH term annotations on biomedical and chemical literature
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An investigation into pharmaceutically relevant mutagenicity data and the influence on Ames predictive potential
Patrick McCarren, Clayton Springer, Lewis Whitehead Journal of Cheminformatics 2011, 3:51 (22 November 2011)
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2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope
Tsutomu Osoda, Satoru Miyano Journal of Cheminformatics 2011, 3:50 (2 November 2011)
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Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain
Abrar Hussain, Peter E Shaw, Jonathan D Hirst Journal of Cheminformatics 2011, 3:49 (1 November 2011)
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Semantic science and its communication - a personal view
Peter Murray-Rust Journal of Cheminformatics 2011, 3:48 (14 October 2011)
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Open Bibliography for Science, Technology, and Medicine
Richard Jones, Mark MacGillivray, Peter Murray-Rust, Jim Pitman, Peter Sefton, Ben O'Steen, William Waites Journal of Cheminformatics 2011, 3:47 (14 October 2011)
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Editor’s summary
BibJSON, a simple structured text data format suitable for serialisation and storage of large quantities of bibliographic data is presented and the concept of a distributed bibliography is explored
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The past, present and future of Scientific discourse
Henry S Rzepa Journal of Cheminformatics 2011, 3:46 (14 October 2011)
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The increased functionality offered by online publishing is explored by comparing a paper published in 1953 with one from 2010, illustrating how additional data sources can be implemented
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Ami - The chemist's amanuensis
Brian J Brooks, Adam L Thorn, Matthew Smith, Peter Matthews, Shaoming Chen, Ben O'Steen, Sam E Adams, Joe A Townsend, Peter Murray-Rust Journal of Cheminformatics 2011, 3:45 (14 October 2011)
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CML: Evolution and design
Peter Murray-Rust, Henry S Rzepa Journal of Cheminformatics 2011, 3:44 (14 October 2011)
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The semantics of Chemical Markup Language (CML): dictionaries and conventions
Peter Murray-Rust, Joe A Townsend, Sam E Adams, Weerapong Phadungsukanan, Jens Thomas Journal of Cheminformatics 2011, 3:43 (14 October 2011)
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The semantic architecture of the World-Wide Molecular Matrix (WWMM)
Peter Murray-Rust, Sam E Adams, Jim Downing, Joe A Townsend, Yong Zhang Journal of Cheminformatics 2011, 3:42 (14 October 2011)
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OSCAR4: a flexible architecture for chemical text-mining
David M Jessop, Sam E Adams, Egon L Willighagen, Lezan Hawizy, Peter Murray-Rust Journal of Cheminformatics 2011, 3:41 (14 October 2011)
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Mining chemical information from open patents
David M Jessop, Sam E Adams, Peter Murray-Rust Journal of Cheminformatics 2011, 3:40 (14 October 2011)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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CMLLite: a design philosophy for CML
Joe A Townsend, Peter Murray-Rust Journal of Cheminformatics 2011, 3:39 (14 October 2011)
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The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age
Sam Adams, Pablo de Castro, Pablo Echenique, Jorge Estrada, Marcus D Hanwell, Peter Murray-Rust, Paul Sherwood, Jens Thomas, Joe Townsend Journal of Cheminformatics 2011, 3:38 (14 October 2011)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
Noel M O'Boyle, Rajarshi Guha, Egon L Willighagen, Samuel E Adams, Jonathan Alvarsson, Jean-Claude Bradley, Igor V Filippov, Robert M Hanson, Marcus D Hanwell, Geoffrey R Hutchison, Craig A James, Nina Jeliazkova, Andrew SID Lang, Karol M Langner, David C Lonie, Daniel M Lowe, Jérôme Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L Tenderholt, Kevin J Theisen, Peter Murray-Rust Journal of Cheminformatics 2011, 3:37 (14 October 2011)
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The work carried out by the Blue Obelisk movement over the last five years is described, with a discussion of the current progress and future challenges in Open Data, Open Standards, and Open Source in chemistry
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Openness as infrastructure
John Wilbanks Journal of Cheminformatics 2011, 3:36 (14 October 2011)
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Three stories about the conduct of science: Past, future, and present
Cameron Neylon Journal of Cheminformatics 2011, 3:35 (14 October 2011)
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Adventures in public data
Dan W Zaharevitz Journal of Cheminformatics 2011, 3:34 (14 October 2011)
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Open Babel: An open chemical toolbox
Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, Geoffrey R Hutchison Journal of Cheminformatics 2011, 3:33 (7 October 2011)
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The first publication reporting the features, implementation and validation of the open source chemical toolbox - Open Babel - is described, which includes a summary of key advances in the 2.3 release
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