----- Forwarded message from Peter Murray-Rust <pm286@cam.ac.uk> ----- From: Peter Murray-Rust <pm286@cam.ac.uk> Date: Wed, 08 Dec 2004 09:50:16 +0000 To: JOELib devel <joelib-devel@lists.sourceforge.net>, JOELib help <joelib-help@lists.sourceforge.net>, cdk <cdk-devel@lists.sourceforge.net>, Octet Developer <octet-devel@lists.sourceforge.net>, QSAR Development <qsar-devel@lists.sourceforge.net>, OpenBabel-discuss@lists.sourceforge.net, Beda Kosata <beda@zirael.org> Subject: [QSAR-devel] Chemical Semantic Web and Thanks X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 [Crossposted to several OpenSource lists - please reply thoughtfully. I will collate significant replies] I presented an invited lecture at the Royal Soc Chem yesterday on "The Chemical Semantic Web" and highlighted the impressive contribution of the Open Source movement in chemistry. I hope I managed to acknowledge most people's contributions. It generated a lively discussion in which, I think, the Open Source approach came out very positively. Two common negative questions were presented: "Who pays for it" the implication was that if there was no commercial development the software was second-class and there was no future for it. My response was that the code would be eagerly adopted by the bioinformatics community (strongly confirmed by Mike Ashburner) and we are starting to set up strong links with the Bioinformatics community on small molecules. This question came from the pharma industry and so I challenged them to put something back into the communal process. It's noticeable that the pharma industry is a consumer of our efforts but has not contributed anything in return and continues to pay for overpriced software products that do not use modern methodology. (I spent 15 years in Glaxo so I feel I have a right to criticise the industry). I know that pharma industry reads this list and I would be delighted if there were some who wished to support communal activity. [I would suggest they mail me directly and I will summarise replies. All replies will be assumed to be Open unless specifically indicated]. One approach would be to support a physical workshop on chemical open source. Particular topics could be: - markup languages - communal chemical ontologies (e.g. descriptors) - Open datasets - use of InChI (we are very excited about this) - graphical components - common code libraries - web services (I'll mail later) The only contribution that I know of from the pharma industry to chemoinformatics is the JME editor which is free, but despite repeated requests is not Open and not likely to be. It could be withdrawn at any time. "Open source is unfair to commercial developers" I think this attitude is particularly strong in the US and perhaps Germany. The idea is that public funding should not be used to compete against commercial organisations. As Mike Ashburner replied, most Open software in bioinformatics is written by people on short term contracts often with no possibility of extension. I know that made contributors to these lists do not have jobs. I developed much of CML when I was unemployed after being made redundant from Glaxo. I would be more (slightly) more sympathetic to this view if the chemical software industry provided anything substantial to the community. I know of no support for Open efforts from the chemical software industry other than a very undersupported effort to get an Open Management Group spec for chemistry. I was invited to contribute CML as the core of this spec, but even then it was made clear that I would not even have my (foreign) travel expenses paid - even though I had no job. Note that "free" is not good enough and may even by counterproductive. Closed software often stifles development as there is no API and the software can be withdrawn at any time. That is why we are so keen to see a JChempaint component as a universal Open chemical editor for the web. In fact I think the tide is turning. The components that you are all developing are ideal for Web Services, which will have the potential to rapidly become a major player in the chemoinformatics market. Between the members of this community we have standards, data, transformers, algorithms, repositories, query languages, graphics and much more. I'll put forward a strategy in the next mail(s). Meanwhile - when you are hacking the latest set of bugs at 0200 in the morning, take heart - it really is appreciated - and yes - the day of Open Source for "chemistry" is dawning. In fact I think the centre of gravity of chemical software development is starting to shift towards bioscience [and materials] so that people will simply refer to the informatics of small molecules as "bioinformatics" Best P. Many thanks to those who have sponsored our Open Source development: Royal Soc. Chemistry, Nature Publishing Group, Cyprotex. More about this later. Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://productguide.itmanagersjournal.com/ _______________________________________________ Qsar-devel mailing list Qsar-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/qsar-devel ----- End forwarded message ----- -- Eugen* Leitl <a href="http://leitl.org">leitl</a> ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net