Subject: Re: CCL:[QSAR-devel] Chemical Semantic Web and Thanks (fwd from pm286.-at-.cam.ac.uk)

From: Joe Leonard <jle.-at-.theworld.com>
Date: Wed, 8 Dec 2004 20:28:49 -0500

On Dec 8, 2004, at 5:51 AM, Eugen Leitl wrote:

> ----- Forwarded message from Peter Murray-Rust <pm286.-at-.cam.ac.uk> -----
> [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.

Open source tools, in terms of O/S and languages are big wins - Linux 
has
made cheap hardware possible.  The GCC language suite, Perl/Python, 
etc.,
have been huge benefits as well.  I think we'll see work in the 
scripting languages
become the basis for inter-group collaborations, given that developer 
time's
back to being a critical resource.

>
> 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.

Not true for those areas which have a broad/deep interest amongst the
general development community.  However, as one gets more and more
specialized, the number of people capable of and interested in working
on something gets small - particularly those in a position to do in a la
Open Source.  Outside of Academia, we've got to work for a living, and
it's usually not on Open Source projects.

>  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.

How many pharma/biotech's are actively developing more than "glue 
routines"?
Places like Merck and Vertex have published a bit of what they've 
developed
over the years, but aside from Vertex feeding OpenEye, I'm unfamiliar 
with
any contributed code that is generally available.

There's real sensitivity towards IP in this industry, which might 
extend to the
"competitive advantage" of in-house code.  It's probably difficult to 
justify
development people on the payroll, and "they'll give it away" isn't 
want management
wants to hear.

Chemists, on the whole, aren't all that good when it comes to 
professional
development.  They've got OLD tools, which (unfortunately) tend to be 
in old
languages.  They also tend to be monolithic solutions, which isn't the 
easiest
to use in other applications.

> 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).

Yeah, but paying 2-20 FTE's worth of money for software rental probably 
fits
their management/budget structure.  It seems easier to get cash than 
headcount,
and "having somebody to call for support" satisfies a lot of people.  
 From what
I've seen over the years, modelers are paid to know medicinal 
chemistry, some
organic synthesis and then their own tools.  Real development skills, 
on the whole,
just aren't as available or as valuable - it doesn't directly help 
projects.

There's also no effort on the part of the customer base to realize 
where things
are and maybe where they should be.  Probably too difficult to work 
with those
of competitor companies - better to use the software companies as 
neutral agencies?

>  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

This is going to be difficult - people like John Dearden and others 
have been asking
for this for years and years.  Who's going to get this data in a form 
which is consistent
across labs (assuming such can be done)?

> - use of InChI (we are very excited about this)
> - graphical components

This, aside from things like PyMol, seems to be the hardest.  One can 
get QM codes,
and even some classical codes on the web, but graphics is rare.  Maybe 
it's because
Chemists can't or won't write this (and CS people aren't interested 
enough to try -
"chemistry, yuck!")?

> - common code libraries

Hell, our community can't even agree on common data formats...!  This 
would be a
HUGE win, coupled with common data representations in languages such as 
Python.
There are several efforts which have shown scripting languages to be a 
real win
as they are easily extended for discipline-specific knowledge and 
they're pretty
much platform independent.  This kind of work allows for both serious 
development
and user scripting - thus only one environment must be 
maintained/documented, etc.

> - 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.

Programming is hard.  Groups with 1-2 people, unless they're willing to 
"go in the
hole" for several years, just can't create all that's necessary to use 
modern
environments well.  It's hard for some sites to justify applications 
modelers - asking
for some of them who'll only develop code (and probably cost more due 
to rarity)
isn't a game group leaders want to play unless there's LOTS of money 
and head
count available?

>
> "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.

Commercial developers should be able to compete on IP and implementation
quality.  Modelers seem to be a community who really do seek out the 
better
mousetrap.  Therefore, for commercial vendors to keep their customers, 
they'll
need to offer what can't easily be created otherwise, or offer tools 
which are
really new/state of art.  Given that the major vendors are public 
companies and
the modeler community is a mature market, I'm not entirely optimistic 
when
I think of where new stuff's going to come from.  It's tough for them 
to compete
with people like Microsoft or other software companies...

Perhaps some kind of industry/non-profit consortium might be created to 
do
this work, which would semi-commercialize it?  Can't see it being truly 
Open
Source until there's more of a desire to share and fund...

> 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.

Again, Linux and things like Perl/Python are critical to modern 
development.
The collapse of hardware prices has made it a little more difficult for 
the
commercial vendors, but it's a WONDERFUL time to be a user right now!
I'm less interested in web development as methods and server 
development,
but that's me - there's work on GUI tools in Python, for example, 
although it's
nowhere near as advanced as Java.

Is our academic brethren training people who actually know how to 
develop
code, or are they concentrating on science and what can be published?  
If
they're Chemistry faculty, I think the science is the better choice, at 
least for
the student's employability.  Would industry hire developers, or do 
they want
those with applications experience?  Are we all just a little too 
conservative,
or merely being careful in what we back with lots of money?

> 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.

To me, for things to be really open, they should be done in a scripting 
language.
Compiled languages aren't accessible by 50-75% of our community - having
the source is meaningless as they'll never look at it.  We've all got 
supercomputers
for $500, so lets make better use of developer time than CPU time.

>
> 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).

Common data structures.  Common file formats.  Perhaps if each 
commercial,
semi-commercial and Open Source vendor could contribute a reader and a
writer for their "personal" file formats towards something like 
OpenBabel?
Maybe we could agree on some commonality which would (hopefully)
reduce the number of wheels which get reinvented each year?

>
> 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"

Will pharma pay the cash needed to give the (putative) Open Source
developers a lifestyle like their modeler cousins?  Is this something
Academia can/should jump on (what with their extra bodies and lower
costs)?  Is this a role for Government labs?  Multi-Government efforts?

Joe