Comments on: Research and software testing http://www.simbiosys.com/blog/2008/06/03/research-and-software-testing/ Addressing the challenges of computational drug discovery Sun, 20 May 2012 03:37:02 +0000 http://wordpress.org/?v=2.0.11 by: Geoff Hutchison http://www.simbiosys.com/blog/2008/06/03/research-and-software-testing/#comment-1487 Wed, 04 Jun 2008 14:13:25 +0000 http://www.simbiosys.com/blog/2008/06/03/research-and-software-testing/#comment-1487 As someone who's part of the "Blue Obelisk," I'd suggest you take Peter's words with a large grain of salt. As ChemSpiderMan indicates, he has a clear agenda, which is not necessarily shared by others. One might argue he doesn't even reflect his own views -- if he's such a believer in open source software, why does he use a Windows laptop? In some very real sense, Peter has become the chemical software version of Richard Stallman. (I don't write those words lightly.) He's doing more talking than writing code. Indeed, when he contributed CML code to Open Babel, he wrote all of 6 unit tests. And he has since disappeared, except occasional complaints that CML support doesn't match his ever-changing standard. Personally, when Peter goes off on a rant, I tend to shrug my shoulders. I don't read his blog much anymore, and haven't commented in ages. As someone who’s part of the “Blue Obelisk,” I’d suggest you take Peter’s words with a large grain of salt. As ChemSpiderMan indicates, he has a clear agenda, which is not necessarily shared by others. One might argue he doesn’t even reflect his own views — if he’s such a believer in open source software, why does he use a Windows laptop?

In some very real sense, Peter has become the chemical software version of Richard Stallman. (I don’t write those words lightly.) He’s doing more talking than writing code. Indeed, when he contributed CML code to Open Babel, he wrote all of 6 unit tests. And he has since disappeared, except occasional complaints that CML support doesn’t match his ever-changing standard.

Personally, when Peter goes off on a rant, I tend to shrug my shoulders. I don’t read his blog much anymore, and haven’t commented in ages.

]]> by: ChemSpiderMan http://www.simbiosys.com/blog/2008/06/03/research-and-software-testing/#comment-1484 Wed, 04 Jun 2008 02:05:59 +0000 http://www.simbiosys.com/blog/2008/06/03/research-and-software-testing/#comment-1484 I've been reading PMR's posts and his views of "commercial cheminformatics" and, having been in the environment for over a decade, find his views truly insulting. The industry is full of hard-working, innovative and QUALITY-CONSCIOUS people who KNOW how to develop and care about delivering good software to their users. I don't doubt the value of Open Source so I suggest he focus on singing its praises rather than shooting non-Open Source. The ongoing bias towards "Openness is Superior" and everything else be damned is simply wrong. I understand his agenda...but it's his. Mind you, he hasn't stopped thrashing me for ChemSpider not being Open Source yet sings the praises of PubChem. PubChem is NOT Open Source so I guess it's their Open Data? They have policies about their data too..it is not declared Open Data. So, Pubchem is bad? No..I don't think so. As you say, PMR is now showing affection to Microsoft contrary to his Open SOurce position. Why? Because Microsoft's solution works (on, and he is getting eChemistry funding from Microsoft too as he willingly admits). I KNOW Microsoft tests their software. One of my closest friends HAS that role at Microsoft. So, what was the point of PMR's post...I think it's that Egon and Peter are doing what they should be doing in terms of testing? Oh. Ok. The rest of the industry does it anyway. I’ve been reading PMR’s posts and his views of “commercial cheminformatics” and, having been in the environment for over a decade, find his views truly insulting. The industry is full of hard-working, innovative and QUALITY-CONSCIOUS people who KNOW how to develop and care about delivering good software to their users. I don’t doubt the value of Open Source so I suggest he focus on singing its praises rather than shooting non-Open Source. The ongoing bias towards “Openness is Superior” and everything else be damned is simply wrong. I understand his agenda…but it’s his. Mind you, he hasn’t stopped thrashing me for ChemSpider not being Open Source yet sings the praises of PubChem. PubChem is NOT Open Source so I guess it’s their Open Data? They have policies about their data too..it is not declared Open Data. So, Pubchem is bad? No..I don’t think so.

As you say, PMR is now showing affection to Microsoft contrary to his Open SOurce position. Why? Because Microsoft’s solution works (on, and he is getting eChemistry funding from Microsoft too as he willingly admits). I KNOW Microsoft tests their software. One of my closest friends HAS that role at Microsoft.

So, what was the point of PMR’s post…I think it’s that Egon and Peter are doing what they should be doing in terms of testing? Oh. Ok. The rest of the industry does it anyway.

]]> by: Unilever Centre for Molecular Informatics, Cambridge - petermr’s blog » Blog Archive » Quality in chemical software - a debate http://www.simbiosys.com/blog/2008/06/03/research-and-software-testing/#comment-1482 Tue, 03 Jun 2008 19:50:12 +0000 http://www.simbiosys.com/blog/2008/06/03/research-and-software-testing/#comment-1482 [...] Research and software testing [...] […] Research and software testing […]

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