Subject: Anybody agrees with me?

From: "Jan Dillen" <[email-masked]>
Date: Fri, 11 Feb 2000 17:23:07 +0200

> I just cannot help wondering why the guys who 
> develop these molecular modeling softwares
> have not met together and defined a "standard".

I remember a time when some programs required
a stack of 70 punch cards whereas others required
120 of them.  Is is a pity people did not agree 
about a standard in those days. 

IMHO, "the guys who develop these molecular 
modeling softwares", are very hard working scientists
whose prime concern is to get something useful out
of the codes there develop, educate students,
promote the science they embrace, and give their 
work away for free in the form of "simpler programs"
to colleagues, co-workers, and yes, scientific
competitors.

We do have a standard in molecular modeling.
Actually we have several. Three of them are 
"reading the manual", "cursing to the manual", 
and "re-writing the manual".

Me, "tired of learning" ? No way!.

Jan Dillen
(A guy who develops molecular modeling software)

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From: Jan Labanowski <[email-masked]>
Date: Fri, 11 Feb 2000 12:16:25 -0500 (EST)

Dear,

Since we have an explosive discussion on the CCL, I need to say a word.
Cool down... It is not the first time...

1) Some tell me that I should stop some voices from appearing on the list.
   Sorry to say, but I do not moderate the list, i.e., I am not reviewing
   messages which come to the list. If my software finds something which
   is suspicious, it stops it. I do not... As long as it is remotely about
   chemistry it CAN go to the list. AT THE SAME TIME, PLEASE!!! PLEASE!!!
   read the rules: 
               http://www.ccl.net/chemistry/aboutccl/rules/
   Why I do not censor the list? Because I would be liable, and would loose
   my "internet operator" status (a printing shop), and became an editor
   or a publisher, i.e., a person responsible for what is printed.
   Needless to say, at this moment I cannot afford to hire a few lawyers
   specializing in patent, defamation, copyright, etc., law which will
   review the stuff which is being posted. Sorry to say, but the battle
   for freedom of speech in the media is lost, at least in the US. It
   the lawyers den, and it is for big guys only. Small guys like me
   (or the "Village Inquirer" and likes) cannot stay in publishing business.

2) As to the standardization issue, I think that it would be much
   better for the discussion itself if it was less heated and had more
   practical suggestions. I do not think we will be able to standardize
   interfaces and GUIs easily. The problem is that the mouse on a Mac
   has one button, and on the SGI, it has 3 (with PC in the middle...).
   But of course, we can go a long way in having standard convention in
   visualization. And in fact we have, but you have to admit that this
   is the area of active development and research. In my opinion we could
   do a much faster progress in representing data uniformly, rather than on the
   GUI side. The issue of passing data between different packages from
   different vendors/authors/groups is really a pain, since more and
   more, we have to use methods in tandem.  I am a great proponent of XML.
   PLEASE VISIT the:
                    http://www.xml-cml.org/
   PLEASE DO NOT FLAME ME FOR THIS. I am not talking about
   junking legacy formats!!! There is so much investment in them that it
   would be a tragedy if this happened overnight.  I am asking 
   developers to consider producing the both XML output and traditional output.
   It is only additional write statements. No big deal. The big deal is
   to agree what tags to use and what is the DTD. But even well formed XML
   will do. 

   I believe that in the past, market forces were making managers believe
   that proprietary format is good for business and helps to have
   "loyal customers" (read: trapped customers). But it seems that at least
   some chemistry software developers realized quickly (and painfully)
   that:
      a) customers want interoperability,
      b) customers ain't stupid, and even managers who hold the purse
         do not believe the stories about solving science
         problems by clicking buttons.
      c) if you do not publish the input/output file formats, the
         people will tell you to go elsewhere.
   Yet still we develop thousands of filters, converters, and 
   edit files so something else "can eat it". What a waste...
   Again... with the new XML paradigm, there is a chance.
   Everything is ASCII, free format, easily parsable, with ton
   of free and commercial parsers which can be plugged in (and BTW, 
   everybody in this business wrote his 10 line long fast & dirty perl XML
   parser, including me). 
   Please visit http://www.xml-cml.org/ (Yes, I have nothing to do with them).
   Chemists were first in this business, and we should continue to be there.
   I would strongly encourage software vendors and commercial users to
   support this initiative. 
   Do you really want those physicists to do it again to us {:-)}...
   (do not ask me what... I am just teasing you guys...).

Jan

Jan K. Labanowski            |    phone: 614-292-9279,  FAX: 614-292-7168
Ohio Supercomputer Center    |    Internet: [email-masked] 
1224 Kinnear Rd,             |    http://www.ccl.net/chemistry.html
Columbus, OH 43212-1163      |    http://www.ccl.net/

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From: "Rzepa, Henry" <[email-masked]>
Date: Fri, 11 Feb 2000 18:44:33 +0000

>   PLEASE VISIT the:
>                    http://www.xml-cml.org/
>...   Please visit http://www.xml-cml.org/ (Yes, I have nothing to do with them).

Since Jan has been kind enough to note the above site, I should also note 
the excellent series of tutorials on XML, and related aspects, by
Miloslav Nic (an organic chemist!)

http://zvon.vscht.cz/ZvonHTML/Zvon/zvonTutorials_en.html

In another (this time shameless) plug, might I note that  Chemint2000
(http://www.chemint.org/ ) in September of this year in Washington DC, will have
a session on the  application of XML and its relevance to chemistry.
We anticipate that Peter Murray-Rust, Miloslav and myself, amongst others,
will lead the discussions!  Book now for a place!!! (sorry Jan). 

Finally, on the aspect of  interconverting marked up chemical information 
components, and legacy program outputs, we are in the process of building
a library of  what we call XSL template fragments. These are used to 
build formal stylesheet transforms for interconverting XML/CML
and such legacy outputs. We would expect the library to be modular
and interchangeable. If you don't like the  GUI, change the stylesheet!
Please contact me for further details. 

Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0)20 7594 5804 (Fax)
Dept. Chemistry, Imperial College, London, SW7  2AY, UK. 
http://www.ch.ic.ac.uk/rzepa/