bbgm was rethinking software access.\nThe blog observes:
\n\nActually, much of the work I have been doing in opensource chemoinformatics was done as ‘home’ science; I started as organic chemist\nstudent, and later data analyst, while the CDK/Jmol/JChemPaint was something I did at home because I liked, and needed it. I started\nin 1995 working on a website to aid my organic chemistry studies, the Woordenboek Organische Chemie (open data). And, I needed\nsemantic tools for 2D and 3D display of molecular structure. Commercial offerings were not an option, for me as student, so I got\ninvolved with the Chemical Markup Language, Jmol and\nJChemPaint in 1997-98.
\n\nNote, that in that time free academic licenses were rarer than now. I always had, and still have, the feeling that those clauses are\njust there to give academics a reason to support non-opensource tools. Also note that a lot of commercial offerings started as\nincorporation of the code base of some PhD work. Not uncommonly, the PhD would simply be hired by the company.
\n\nFact is, commercial chemoinformatics licenses are indeed unfriendly for scientists who maintain related hobbies at home. And,\ngiven my experience, I appreciate your worries: the high costs for those tools, which I certainly could not afford with my student\nfunding, drove me to the opensource ideas many, many years ago.
\n\nThe second issue brought up, regards the ability to make mash ups. Open source and open standards are indeed important to make\nmash ups, though the former only helps you work around lack of use of open standards. Using web services contributes to the\nsolution as it has a well-defined, open standard interface. Open source is particularly important for reproducibility of scientific\nresults (see my thesis ), and is the opposite of\nproprietary software, not commercial software. So, it seems bbgm is just looking for\nBlue Obelisk projects.
\n\nOn a practical note, I think that Bioclipse might just be what you are looking for, and integrates\nlocal services as well as services on the internet, just alike. Particularly, the upcoming\nBioclipse2 is strong at this, and supports\nSOAP, BioMart,\nBioMoby for online services (also\nsee this), as well as\nR, BioJava, CDK, Jmol as local services. You can even\nrun Taverna workflows from within Bioclipse, if you\nlike. Mash ups can be done in various ways. Hard code Java coders would go the RCP plugin way, for example\nthis nanotube example. Others will prefer\nscripting languages, such as JavaScript and Ruby (in addition to R and\nJmol scripting). Or, you might do record as script the tihngs you did graphically, using the\nrecording feature.
\n\nOf course, there are other solutions… Bioclipse is just one, one to which I contributed.
\n\nRunning webservices, is basically being hosting provider, and requires some commercial model. One conflicting problem is that,\nat least being said, that large groups withing the potential user base, aka pharma industry, does not even like sending over\ntheir highly secret data over an httpS:// line to the outside world.
Rajarshi and the rest of the Indiana group have been running chemoinformatics\nwebservices. They might be the provider you are looking for.
\n\nAll I can say to bbgm: “Yes, your two thoughts are indeed issues, and many from within the Blue Obelisk community have been\naddressing them.” Oh, and we will not stop either. Peter recently gave in\nNature a nice overview of what we, Blue Obelisk members, have been cooking on:\nChemistry for Everyone: and that includes the\nhobby scientist.
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