From: Peter Murray-R. <pm...@ca...> - 2004-12-08 09:49:21
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[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 It could be withdrawn at any time.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 |
From: E.L. W. <eg...@us...> - 2004-12-08 11:21:39
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=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Wednesday 08 December 2004 11:51, Eugen Leitl wrote: > 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.=20 Since CDK is licensed LGPL, it can be embedded in proprietary software. And because if this CDK is used in such software, and we did have=20 contributions from companies back into CDK. For example, the important=20 UniversalIsomorphismTest (isomorphism, mcss...) was contributed by Ixelis (http://www.ixelis.com/). > "Open source is unfair to commercial developers" > I think this attitude is particularly strong in the US and perhaps German= y. > 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. Same for me. Most my opensource work is not even part of my PhD, and all do= ne=20 in free hours! Totally unpaid work. Another argument I would like to put into this discussion: In the Netherlands big companies often have reduced taxes, or a special=20 agreement on the taxes they have to pay, while they make very much use of t= he=20 countries infrastructure. This is IMHO some form of public funding. The "Open source is unfair to commercial developers" argument is also rathe= r=20 unfair itself: most opensource licenses do *not* disallow embedding in=20 proprietary software! E.g. the LGPL (see earlier) and the BSD license. So=20 companies can directly benefit from many opensource projects without that=20 costing them anything. > 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. As said, some chemoinformatics companies break with this habit. > 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" Let's use molinformatics from now on... (short for molecular informatics). = I=20 used this term already in the CDK presentation at the CIC meeting, and will= =20 start using it as much as possible. Because what we do is deal with molecular information, small molecules=20 (chemoinformatics) and larger molecules (bioinformatics). Egon =2D --=20 e.w...@sc... PhD-student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFBtuO4d9R8I9Yza6YRAnvNAJsF3nzBc4nXgMXNBz+M56txJ58d3QCeIXBa 6J/p9hl79msQfRU2Z8GsvkQ=3D =3DViHR =2D----END PGP SIGNATURE----- |