Subject: Re: CCL:Sequence Classes and CORBA Servers

From: Konrad Hinsen <[email-masked]>
Date: Tue, 11 Nov 1997 12:08:19 +0100

> The demand for 50 copies is imposed by the OMG. They lack the infrastructure
> and logistics to run off the responses themselves for the distribution among
> attendants at meetings, and therefore ask the submitters to do this. I think
> this is not unreasonable, given the amount of work that is going on in the
> OMG.

But it does raise the question whether an OMG acitivity is the right
way to arrive at useful standards for scientific computing.

The OMG was founded by and for large companies; participation of
small companies and academic groups, although not ruled out in
principle, was not one of the design goals. Few small groups
and companies can even afford to participate in OMG activities
with their heavy administrative overhead. A look at the member
list of the life sciences group confirms this - there are hardly
any academics in it.

On the other hand, much innovative work happens in academic groups and
small companies. Given that there is still very little practical
experience with OO techniques in scientific applications, it doesn't
seem useful to me to start a standards committee at all at this time,
much less one which excludes an important part of the people working
in the field.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                          | E-Mail: [email-masked]
Laboratoire de Dynamique Moleculaire   | Tel.: +33-4.76.88.99.28
Institut de Biologie Structurale       | Fax:  +33-4.76.88.54.94
41, av. des Martyrs                    | Deutsch/Esperanto/English/
38027 Grenoble Cedex 1, France         | Nederlands/Francais
-------------------------------------------------------------------------------

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From: Jeroen Coppieters <[email-masked]>
Date: Tue, 11 Nov 1997 12:05:02 +0000 (GMT)

I had a typo in my address list of the previous mail. I resent it
seperately to [email-masked] (instead of [email-masked])
Above is the full list of adresses the message went to.
If you reply, make sure you  got the correct address: [email-masked]
Jeroen

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From: Jeroen Coppieters <[email-masked]>
Date: Tue, 11 Nov 1997 11:57:16 +0000 (GMT)

On Tue, 11 Nov 1997, Konrad Hinsen wrote:
[ I added Mark Lowenstein from OMG and the lifesciences mailing list to
the recipients. If the readers of any of the other lists above feel that
this topic should not be discussed on their list, then please let us know
Jeroen]

> and companies can even afford to participate in OMG activities

OMG was founded by and for large companies, but they have been (and are)
trying
hard to make it open to all, including academia. A look at the membership
list of OMG shows that many universities are members. I do not see that
academics from lifesciences departments would be poorer than their
counterparts from other departments. You do not have to attend each
meeting to be involved. Most decisions can be reached by email
discussions.

> list of the life sciences group confirms this - there are hardly

There is no 'membership' to the life sciences research group. It is open
to anyone who wants to contribute (by attending or by submitting
information). I guess you have been looking at the attendace list for last
meeting. This was the first meeting of the LSR group, so I do not think
you can call it representative. I would like to repeat that this is an
open forum, so anyone who feels he/she has something to share, please come
forward.

> experience with OO techniques in scientific applications, it doesn't

OO has been around for a long time (and has been thought to undergrads for
ages). Many developers of scientific software (both academic and
commercial) are well educated in OO. On the other hand many life science
researchers have been thinking about objects, long before OO became
fashionable.

> much less one which excludes an important part of the people working
The whole point of the OMG approach is that it is possible to start
modeling subdomains, without the need for an allencompassing model of the
world. I agree that innovative work happens in academic groups and small
companies. But that does not mean that a standard interface for common
objects would restrain that research. There is a core of entities, that
many researchers use and would like to be able to exchange without
constant reformating overhead.
Large companies are backing this proposal, which you seem to interprete
negative. I think that it's this backing which gives us hope of achieving
something. Previous (mostly academic) standarisation attempts failed,
because of the lack of worldwide support.
Large pharms do innovative work as well, and also rely on academic groups
and small companies (via funding, contracting etc). So it's in their
interest to see them involved.

Jeroen

EMBL Outstation EBI                             Jeroen Coppieters
(European Bioinformatics Institute)      Research and Development 
Wellcome Trust Genome Campus     [email-masked]
Hinxton                                      (or [email-masked])
Cambridge CB10 1SD UK                            ++44 1223 494422
http://www.ebi.ac.uk                         fax ++44 1223 494468

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From: Philip Lijnzaad <[email-masked]>
Date: Tue, 11 Nov 1997 12:37:34 GMT

Konrad, 

thanks for your response.

> way to arrive at useful standards for scientific computing.

Well, that depends, I suppose. A sizeable amount of scientific computing
(even if it's not cutting edge) is being done in the corporate world. Why not
join efforts here, and arrive at a standard that will benefit both corporate
and academic users ? Once there are reasonable standards, people will
probably use them, and I think this is much preferable to the ad hoc
solutions that keep popping up.

> Few small groups
> with their heavy administrative overhead. 

I cannot agree on this.  Academics will go a very long way to make things
easier for themselves and especially to make their work more widely known to
others. E.g. the amount of work that goes into polishing an article, getting
your web server up and running, tricking your java applet to display just
what you want, getting your demo ANSI C compliant, etc.  etc.  are not
neglible. Scientist are prepared to do all this because it makes their work
more useful for others.  Along similar lines, I think spending a bit of time
standardizing some of the entities you work with, is time very well
spent. Or, along a different line, look at the work that goes into
standardization of nomenclature in medicin, taxonomy, chemistry, physics. It
is very much an academic effort, a lot of work, and it is very much needed. I
think compared to this, the OMG process is not all that heavy.

> small companies. 

Yes, I agree, and I think that it makes little sense to spend effort
standardizing the cutting edge. But a lot of work has been in long use, and
could benefit from standardization.

> Given that there is still very little practical experience with OO
> techniques in scientific applications,

I don't agree on this: there is a lot of OO analysis going on, especially in
bioinformatics. The main reason is that the data is so complex that it
becomes too difficult to manage without OO. Take a look at rhdb, gdb, acedb,
anubis, srs, micado, and many others. 

> much less one which excludes an important part of the people working

'Excluding' is not true.  If you refer to the 50 copies: it is not uncommon
for scientists in academia to copy 100-page chapters from a textbook, or 20
copies of a 10-page article for the journal club.  If you refer to the
membership fee, there are academic discounts, and you don't need to be an OMG
member to respond to the RFI. Moreover, a large number of academic institutes
is actually meber of the OMG. If you refer to the administrative overhead,
see my point about other scientific standards.

So, even if the process may seem a bit cumbersome, I think it is very well
worth it. Yours,

                                                                      Philip

-- 
Philip Lijnzaad, [email-masked] | European Bioinformatics Institute
+44 (0)1223 49 4639                 | Wellcome Trust Genome Campus, Hinxton
+44 (0)1223 49 4468 (fax)           | Cambridge CB10 1SD,  GREAT BRITAIN
PGP fingerprint: E1 03 BF 80 94 61 B6 FC  50 3D 1F 64 40 75 FB 53

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From: Konrad Hinsen <[email-masked]>
Date: Tue, 11 Nov 1997 14:34:25 +0100

> researchers have been thinking about objects, long before OO became

Maybe other branches of life sciences are more up to date, but in the
field I am familiar with (protein modelling), I couldn't name any
widely used tool based on OO technology, much less any published
OO interface used by more than one software supplier. Yes, there
are OO libraries etc. for certain applications, but they are used
only by a handful of people.

> objects would restrain that research. There is a core of entities, that

It might prove insufficient and would then not be used at all.

> negative. I think that it's this backing which gives us hope of achieving

Not at all. I just wish there were an additional less formal channel
to encourage participation of people who can't dedicate significant
resources (most of all time) to this.

> and academic users ? Once there are reasonable standards, people will

No objections. But it is very well conceivable that a better standard
(for everyone) could be reached by encouraging participation from
academic scientists.

> others. E.g. the amount of work that goes into polishing an article, getting

Only to the extent that helps in getting jobs and funding.

> spent. Or, along a different line, look at the work that goes into

I agree, but unless people who decide about jobs and funding agree as well,
such efforts are still difficult to justify for most of us.

> copies of a 10-page article for the journal club.  If you refer to the

That's not the point; it is not the cost of copying that is the problem.
But most scientists I know hate bureaucracy and would not be willing
to deal with an organization that imposes such rules, certainly not
unless it provides clear and immediate benefits to them.

My expectation is that most academic scientist will completely ignore
the OMG effort and continue work as before. And that would be a lost
opportunity for everyone in my opinion.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                          | E-Mail: [email-masked]
Laboratoire de Dynamique Moleculaire   | Tel.: +33-4.76.88.99.28
Institut de Biologie Structurale       | Fax:  +33-4.76.88.54.94
41, av. des Martyrs                    | Deutsch/Esperanto/English/
38027 Grenoble Cedex 1, France         | Nederlands/Francais
-------------------------------------------------------------------------------

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From: "Peter Shenkin" <[email-masked]>
Date: Tue, 11 Nov 1997 11:40:35 -0500

We have been thinking about CORBA.

I know the big players in molecular modeling are serious about CORBA
as well.

Here, however, is a major problem that I see (aside from specification
of classes, which I realize was the original topic).

Most applications of CORBA are written in-house by large firms who
have purchased CORBA technology, which is expensive.  Even the
run-time ORB is expensive to put on all platforms.

We, on the other hand, as a (small) third-party vendor, cannot
with impunity build our distributed applications around CORBA,
because there's no guarantee that our customers will have the
technology up and running in-house.  They would have to license
it, possibly from us -- but that would be a significant extra
expense for them and bookkeeping of pass-through expenses for us.

CORBA technology is now being integrated into WWW browsers, but
not all jobs will be run from (or tied to) browsers; some will 
just be large distributed number-crunching applications launched
from a shell or from some front end.

How do those who are enthusiastic about the technology feel this
issue can be addressed?

	-P.

-- 
****************** Sir Isaiah Berlin, 1909 - 1997, RIP ********************
* Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 *
** NY, NY  10027;  [email-masked];  (212)854-5143;  FAX: 678-9039 ***
*MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html *

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From: Gerald Loeffler <[email-masked]>
Date: Tue, 11 Nov 1997 19:03:49 +0100

Two things:

1) Just a remark - without becoming political, which is honestly not what I want:

What is striking to me is the apparent absence of any representative of the NCBI in
the OMG Life Sciences Group (am I wrong?). Without judging the scientific influence of
any of the organizations involved in the OMG effort, I wonder how a standard in
bioinformatics can be developed without support and contribution from the NCBI?!

2) I started this thread by a question mainly about class libraries for sequences and
homology searches. When can we expect an early specification or even implementation
from the OMG Life Sciences Group?

    cheers,
    gerald

--
Gerald Loeffler
PostDoc in Theoretical Biophysics

EMail: [email-masked]
WWW:   http://www.imp.univie.ac.at/Loeffler/
Phone: +43 1 79730 554
Fax:   +43 1 7987153
SMail: I.M.P. - Research Institute of Molecular Pathology
       Dr. Bohr-Gasse 7
       A-1030 Vienna
       AUSTRIA

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From: Jon Siegel <[email-masked]>
Date: Tue, 11 Nov 1997 16:00:51 -0500

Hello, Gerald and all --

Good questions both, but properly addressed to the group since it is they 
(perhaps including you, Gerald?) who determine the direction and speed of 
your work. Could someone please help Gerald with these queries? 

Thanks and see you in New Brunswick --

Jon Siegel
OMG DTC Chair

>from the OMG Life Sciences Group?

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