Comments for So much to do, so little time http://rguha.wordpress.com Trying to squeeze sense out of chemical data Mon, 23 Feb 2009 16:45:24 +0000 http://wordpress.com/ hourly 1 Comment on The ONS Challenge & Visualizing Chemical Space by Rajarshi Guha http://rguha.wordpress.com/2008/12/30/the-ons-challenge-visualizing-chemical-space/#comment-173 Rajarshi Guha Mon, 23 Feb 2009 16:45:24 +0000 http://rguha.wordpress.com/?p=217#comment-173 Hi Joe - there was an update to the service which required that Base64 encoded SMILES be provided. See the Update in http://blog.rguha.net/?p=53 Hi Joe – there was an update to the service which required that Base64 encoded SMILES be provided. See the Update in http://blog.rguha.net/?p=53

]]> Comment on The ONS Challenge & Visualizing Chemical Space by Joe Mulvaney http://rguha.wordpress.com/2008/12/30/the-ons-challenge-visualizing-chemical-space/#comment-172 Joe Mulvaney Mon, 23 Feb 2009 16:30:58 +0000 http://rguha.wordpress.com/?p=217#comment-172 FYI, the example link is currently broken. Clicking takes me to a mod_python exception page. Looks like something in the XML lib. If you can't reproduce, I can send the mod_python error report. FYI, the example link is currently broken. Clicking takes me to a mod_python exception page. Looks like something in the XML lib. If you can’t reproduce, I can send the mod_python error report.

]]> Comment on Papers About Systems You Can’t Use or Buy by Tobias Kind http://rguha.wordpress.com/2009/02/01/papers-about-systems-you-cant-use-or-buy/#comment-166 Tobias Kind Sat, 07 Feb 2009 07:37:33 +0000 http://rguha.wordpress.com/?p=291#comment-166 Hi Rajarshi, I think the cool thing is, that Thomas Sander actually replied here. After reading his post the whole message also got another taste. I would usually agree with your post from a comp chem point of view. If somebody reports of a system in a blurred manner only showing results instead of the methods its pretty useless. Its impossible to test if the system works really in that way or if its just wishful thinking. But that holds also true for all kind of conference talks or posters. The first problem I had was that from home I could not read about Advanced Biological and Chemical Discovery (ABCD) or OSIRIS an Entirely in-House Developed Drug Discovery Informatics System, because its ACS closed source. So if the authors dont want to pony up 1000 Dollars (or $3000) for ACS Open Access option its probably not worth (it). Or lets say its only important for a very small part of the scientific community or comp chem researchers and of no general interest. On the other hand I have to agree with Thomas that there is certainly pressure from outside and inside to report such a development. Its good for the reputation and also gives you scientific kudos. The OSIRIS system itself was built over 10 years according to the Actelion company report. http://www1.actelion.com/documents/AR_Actelion_1999.pdf If you look at actelion.com there are only three OSIRIS hits; so its of minor importance to the whole company or ... wait maybe it is, maybe its so good it must be held secretive and the the whole publications suddenly is an enlightenment?! (I could not read it because of closed access, so I just assume it is a satori) (google for OSIRIS site:actelion.com) I would say this is not about company bashing, allthough two of your links point to publications from companies, it is also not about open source or open data (the highest level of scientific reporting), but it is about proper scientific reporting with very detailed methods sections (many journals do not appreciate that). So here I agree again with you and would come to the conclusion: A non-opaque system or program should be 1) open source OR 2) commercially available OR 3) contain a very well description to fully reproduce the system. And we certainly should try to understand scientists in companies who are operating under the Sword of Damocles, hence their legal department, and are actually not allowed to disclose any valuable information. Kind regards Tobias Kind (FiehnLab) Hi Rajarshi,
I think the cool thing is, that Thomas Sander actually replied here.
After reading his post the whole message also got another taste.

I would usually agree with your post from a comp chem point of view.
If somebody reports of a system in a blurred manner only showing results
instead of the methods its pretty useless. Its impossible to test
if the system works really in that way or if its just wishful thinking.
But that holds also true for all kind of conference talks or posters.

The first problem I had was that from home I could not read about
Advanced Biological and Chemical Discovery (ABCD) or OSIRIS
an Entirely in-House Developed Drug Discovery Informatics System,
because its ACS closed source.

So if the authors dont want to pony up 1000 Dollars (or $3000) for
ACS Open Access option its probably not worth (it). Or lets say
its only important for a very small part of the scientific community
or comp chem researchers and of no general interest.

On the other hand I have to agree with Thomas that there is certainly
pressure from outside and inside to report such a development. Its good
for the reputation and also gives you scientific kudos. The OSIRIS system
itself was built over 10 years according to the Actelion company report.
http://www1.actelion.com/documents/AR_Actelion_1999.pdf

If you look at actelion.com there are only three OSIRIS hits; so its of
minor importance to the whole company or … wait maybe it is, maybe its
so good it must be held secretive and the the whole publications suddenly
is an enlightenment?! (I could not read it because of closed access,
so I just assume it is a satori) (google for OSIRIS site:actelion.com)

I would say this is not about company bashing, allthough two of your links
point to publications from companies, it is also not about open source
or open data (the highest level of scientific reporting), but it is about
proper scientific reporting with very detailed methods sections
(many journals do not appreciate that). So here I agree again with you and
would come to the conclusion: A non-opaque system or program should be

1) open source OR
2) commercially available OR
3) contain a very well description to fully reproduce the system.

And we certainly should try to understand scientists in companies who
are operating under the Sword of Damocles, hence their legal department,
and are actually not allowed to disclose any valuable information.

Kind regards
Tobias Kind (FiehnLab)

]]> Comment on Locality of References in a Paper by Vladimir Chupakhin http://rguha.wordpress.com/2008/09/30/locality-of-references-in-a-paper/#comment-165 Vladimir Chupakhin Fri, 06 Feb 2009 19:36:12 +0000 http://rguha.wordpress.com/?p=92#comment-165 The idea seems to be quite old - http://eigenfactor.org/map/maps.htm The idea seems to be quite old – http://eigenfactor.org/map/maps.htm

]]> Comment on Papers About Systems You Can’t Use or Buy by Rajarshi Guha http://rguha.wordpress.com/2009/02/01/papers-about-systems-you-cant-use-or-buy/#comment-163 Rajarshi Guha Wed, 04 Feb 2009 16:50:36 +0000 http://rguha.wordpress.com/?p=291#comment-163 Thomas, thanks a lot for the clarification. (I've copied your comment to the new blog at blog.rguha.net) Thomas, thanks a lot for the clarification. (I’ve copied your comment to the new blog at blog.rguha.net)

]]> Comment on Papers About Systems You Can’t Use or Buy by Thomas Sander http://rguha.wordpress.com/2009/02/01/papers-about-systems-you-cant-use-or-buy/#comment-162 Thomas Sander Wed, 04 Feb 2009 16:42:32 +0000 http://rguha.wordpress.com/?p=291#comment-162 The paper is a followup to a poster displayed on the ICCS2008, which caused great interest from cheminformaticians at larger corporations, who seek to convince upper management to support a higher degree of internal development. The main motivation for the paper was to prove by experience that this approach can work and to deliver an argument for those, who are willing to take the risk and go into a similar direction. Only if many drug companies develop their own software ideally on agreed open standards, the commercial software industry will be forced to improve their products and to support common standards. It is a shame that products from different vendors hardly interoperate. I agree that use of the paper is limited if your job is not related to developing chemistry related software. I also support the idea of open source and open tools. We are in a dialog with our management with the intend to release substantially more stuff (source code and/or tools). The J&J paper was actually cited. The paper is a followup to a poster displayed on the ICCS2008, which caused great interest from cheminformaticians at larger corporations, who seek to convince upper management to support a higher degree of internal development. The main motivation for the paper was to prove by experience that this approach can work and to deliver an argument for those, who are willing to take the risk and go into a similar direction. Only if many drug companies develop their own software ideally on agreed open standards, the commercial software industry will be forced to improve their products and to support common standards. It is a shame that products from different vendors hardly interoperate.

I agree that use of the paper is limited if your job is not related to developing chemistry related software. I also support the idea of open source and open tools. We are in a dialog with our management with the intend to release substantially more stuff (source code and/or tools).

The J&J paper was actually cited.

]]> Comment on Locality of References in a Paper by Rajarshi Guha http://rguha.wordpress.com/2008/09/30/locality-of-references-in-a-paper/#comment-159 Rajarshi Guha Mon, 02 Feb 2009 21:34:43 +0000 http://rguha.wordpress.com/?p=92#comment-159 Certainly an interesting view. It'd be interesting to look at if I could easily extract bibligraphies. PS. This blog has now moved to http://blog.rguha.net Certainly an interesting view. It’d be interesting to look at if I could easily extract bibligraphies.

PS. This blog has now moved to http://blog.rguha.net

]]> Comment on Locality of References in a Paper by Vladimir Chupakhin http://rguha.wordpress.com/2008/09/30/locality-of-references-in-a-paper/#comment-158 Vladimir Chupakhin Mon, 02 Feb 2009 21:31:17 +0000 http://rguha.wordpress.com/?p=92#comment-158 The web-like picture of the cited literature :) X (original) - X1 (cited in X) - X2 (cited in X1) - two levels would be enough I think. And for the molecular modeling and QSAR papers I think we will see some interesting intersections (would it?) The web-like picture of the cited literature :)

X (original) – X1 (cited in X) – X2 (cited in X1) – two levels would be enough I think. And for the molecular modeling and QSAR papers I think we will see some interesting intersections (would it?)

]]> Comment on Playing with REST Descriptor Services by Update to the REST Descriptor Services at So much to do, so little time http://rguha.wordpress.com/2009/01/07/playing-with-rest-descriptor-services/#comment-157 Update to the REST Descriptor Services at So much to do, so little time Mon, 02 Feb 2009 13:19:42 +0000 http://rguha.wordpress.com/?p=245#comment-157 [...] the example URL’s described in my previous post that involve SMILES strings, should be rewritten using base64 encoded SMILES. So to get a document [...] [...] the example URL’s described in my previous post that involve SMILES strings, should be rewritten using base64 encoded SMILES. So to get a document [...]

]]> Comment on Update to the REST Descriptor Services by Deploying Predictive Models at So much to do, so little time http://rguha.wordpress.com/2009/01/11/update-to-the-rest-descriptor-services/#comment-156 Deploying Predictive Models at So much to do, so little time Mon, 02 Feb 2009 06:29:36 +0000 http://rguha.wordpress.com/?p=250#comment-156 [...] the model. This leads to a limitation - the descriptor calculation step of the service uses the CDK descriptor service and so the models must employ the CDK descriptors. While restrictive it’s not too bad, since [...] [...] the model. This leads to a limitation – the descriptor calculation step of the service uses the CDK descriptor service and so the models must employ the CDK descriptors. While restrictive it’s not too bad, since [...]

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