Subject: BioCoRE - a structural biology portal

From: Gila Budescu <[email-masked]>
Date: Wed, 15 Mar 2000 14:56:33 -0600

Please look at  http://www.ks.uiuc.edu/Research/collaboratory/
for an instant fulfillment of your wishes. The project started on 2/99 and
first official release was announced on 2/2000. We are looking forward to
supporting your work.
Gila Budescu

regarding Liew Fui fah's message:
>From [email-masked] Tue Mar 14 23:12 CST 2000
Date: Wed, 15 Mar 2000 11:28:44 +0800
From: "Liew Fui fah" <[email-masked]>
To: <[email-masked]>
Subject: CCL:Molecular Modeling - expert opinion needed
WAA24980
Sender: "Computational Chemistry List" <[email-masked]>
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Dear CCLers,

Nowadays, Internet has become a tool for scientists in order to perform
their work efficiently. Almost every one of us relies on the Internet to
have discussion, looking for information and communicating with others.
Indeed, through Internet we are effectively engaged with research,
publications and information sharing that need collaboration with
geographically dispersed colleagues.

With a thought of fully utilizing the strength of Internet, I foresee there
is a possibility to develop a web based molecular modeling station/portal,
that would allow chemists to carry out experiment work, share information
and modeling results with just a simple login to the server through an
Internet browser. The molecular modeling engine, computing facilities and
the working space are provided by the station.
 
In order to carry out an analysis on this idea, I need expert opinion from
fellow CCLers as to inspect the need and how should such a web based
molecular modeling station perform. Please kindly give your opinions from a
user or developer*s perspective with respect to the following aspects.
(These are some basic guidelines for the survey, you are most welcome to add
additional comments)

A. Interface
- What are the interface features that you would like to see and use when
manipulating your structure? Beside the common editing and browsing tools,
you are welcome to suggest new feature the meet your requirements.
- Would you like to have an interface setting that match the way you want to
work?   
- How do you like the information of transition states, molecular
properties, orbitals, vibration, electronic spectrum, etc to be displayed?
- Which molecular modeling package(s) that has the user interface that you
like most. 
 
B. Modeling Methods
- What are the general features / methods that are a *must* for a molecular
modeling package? 
- What modeling methods are you using?
- What are the advance characteristics of a molecular modeling package that
will meet you requirements?
- Please suggest the molecular modeling package(s) that you like to use most
in terms of it accuracy and ease to use.

C. Platform
- Since it will be a web based molecular modeling station, it is ideal to
have access from multi-platform machine. As a reference, please suggest the
platforms that most of the chemists engage with while they carry out their
work.
- Would you like to have a direct access to the web based station at your
current working platform?
- What platform do you think that is most capable to operate as a server
which can handle large amount of job load and provide enough storage?

D. Technologies
- Do you think that Java will meet most of the web based application
requirements while incorporating various plug-ins and formats (e.g. XML,
SVG). What is your comment on this particular technology?
- Please suggest other technologies that you think is powerful in developing
a web based chemical application. (if any)

E. Database
- What are the existing databases that you would like to use in your
searches? Please provide references.

F. General
- What do you think about a web based molecular modeling station/portal?
- Will it be convenient to do molecular modeling job in a remote machine
through Internet?

Your opinions and comments are very useful to my research, please kindly
reply to [email-masked]

Thanks.

Regards,

Liew Fui Fah, 
University Malaya, Malaysia.
[email-masked] 

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-- 
Barry Isralewitz     Theoretical Biophysics Group    Beckman 3121
Office Phone: (217) 244-1612     Home Phone: (217) 337-6364
email: [email-masked]     http://www.ks.uiuc.edu/~barryi

---

From: Eugene Leitl <[email-masked]>
Date: Wed, 15 Mar 2000 22:43:34 -0800 (PST)

So, how many truckloads of DEC (Compaq) Alphas have been shipped to
UIUC recently? ;)

Seriously, for system sizes and user numbers beyond the trivial we're
talking serious amounts of tightly coupled iron here (you do mention
"Interactive MD" in "Description"). Also, (with the possible exception
of server-side Java), Java VM implementations are known to be so buggy
and slow to be unusable in practice.

I haven't missed the frequent occurance of "distributed" in your
overview article, but does it really work in practice? (I know
VMD/NAMD does, but your approach seems to be different, both because
of use of nonlocal networking with necessarily poor latency and
throughput, and trivial portability at the price of very poor
performance due to Java).

Could you perhaps elaborate further on your interesting approach?

Gila Budescu writes:
 > [...]