Transcript CICCMarlon_Jan27_06

Community Grids Lab Work
Marlon Pierce
CICC Quarterly Meeting
Jan 27, 2006
Some Notes on Our Approach

Everything is based around Web
Services.


We build some.
We inherit some






Web
Service
NIH’s COMPARE and
Cambridge’s WWMM suite.
Services are fundamental units of
action
Clients to services can come in
different varieties.

Web
Service
We take some


UDDI, WS-Context
Web
Service
Taverna workflow clients
Portlet-based portal clients
Other client environments and
tools (like BPEL workflow
engines) are compatible.
All work with our same services.
Portal
Taverna
Why Taverna?

Taverna is an open-source workflow and annotation
tool developed by the UK e-Science program.


Taverna works with generic Web Services




A nice client-side workbench tool for collecting services into
a meta-application.
WSIF helps you build client interfaces from WSDL.
Designed to support bio-informatics applications.
Also used extensively by our Cambridge
collaborators.
We anticipate extensive, ongoing support for it
through the OMII.

For example, maybe better Globus and OGSA-DAI client
support.
Summary of Services

Execution and File Web Services (J. Kim)



Makebits, dvikm
Supporting Wild Use Cases
VOTable Services (S. Patel)

Generic XML tabular data model from Virtual Observatory
community.


Potentially useful as intermediate data format for application
(BCI, CDK codes) output and for screening center results.
Sima will discuss a use case.

Comes with parsers and a Java API.

Wrapped now as a Web Service



VOTables serve as data model.
Table instances on remote servers can thus be manipulated.
Inherited tools (VOPlot) can plot VOTable data.
Upcoming Work: Globus and TeraGrid



Globus services will greatly simplify running codes on high
performance computing environments.
 Secure job submission, support for PBS, secure remote file
management.
 Available on TeraGrid.
 Dvikmeans and some CDK codes should benefit.
It has been a little problematic to develop Taverna clients.
 Not currently well documented
We are working on intermediate Globus services for this.
 Wrapping the Java CoG Kit for protection from Globus version
changes.
 And the CoG’s nice API.
 But expect UK efforts in long term to replace.
Cambridge Tools

Downloads put together by Nick Day:


A bundled Tomcat server that includes all services
and also portlets (i.e. service clients for browsers).





http://wwmm.ch.cam.ac.uk/download/
Services listed on next slide.
Portlets are compatible with OGCE, LEAD, and other work
that IU has done.
A version of Taverna that includes CDK and
Jumbo51 tools.
Some workflow examples (Jake will demo)
We really would like to explore some applications
using these but need help from chemists,
cheminformatics folks.
Jumbo and Open Babel

Jumbo is Peter Murray-Rust’s suite of Java
tools for manipulating the Chemistry Markup
Language.


Can also form the basis for CML Web Services
Open Babel is a “cross-platform program and
library designed to interconvert between
many file formats used in molecular
modeling, computational chemistry, and
many related areas.”

Wrap with Web Services
CDK: the Chemistry Development Kit

CDK is a Java-based, object-oriented set of chemistry libraries
and packages.
 Model-view-controller design to separate structure from
representation (i.e. 2d, 3d, text for same data model).
 Data classes: element, isotope, atom, bond, etc.


Lots of tools



Allows you to programmatically build your molecules, etc.
Format converters, rotators, translators, surface area calculators.
CDK forms the basis for several other applications:
 Jchempaint: Java editor for 2D chemical structures.
 Seneca: distributed/parallel application for computer-assisted
structure elucidation (CASE)
 Nmrshiftdb: open, online database for organic structures and their
nuclear magnetic resonance (nmr) spectra.
Can form basis of yet more services....
WWMM Web Services















XindiceServer
OBServer (i.e. OpenBabel)
Mopac
JumboToolServer
JumboConverter
INChiServer
INChiGoogle
Gamess
Exist
CMLRSSServer
CML2SVG
CML2Jmol
CML2Gamess
CDX2CML
Build3d
Some notes from Peter Murray Rust




InChI Generator - this will generate a unique identifier for a
molecule. This will increasingly be the unique handle for
retrieving molecules
Openbabel: will convert from any format to any other format
InChIGoogle: searches for any molecules on the web that have
InChIs
“The value of any particular service will increase proportionally to
the total number. A chemoinformatics app consists of tens of
different functionalities. Other things in our pipeline are 2D
layout, 2D image generation, etc. By the time all these add up
then there is quite a lot!” --PMR
Web Site, Blog, and Mailing List


The web site, www.chembiogrid.org, is plain old HTML (for simplicity
and long-term maintainability) backed by a WebDAV server.
You can use DAV clients (built into Windows, for example) to log into
the server and upload web material.





We also set up a Wiki....
We are blogging related stuff (on VOTables, Taverna Life Lessons, etc)
at http://communitygrids.blogspot.com.



Our DAV server runs inside of Tomcat, so it can serve up HTML, JSP, and
similar stuff.
But not Perl, PHP, CGI or similar.
It’s virtually hosted through Apache, so if you really want PHP, we can work
something out.
I think this is a useful way to post notes.
We can create a specific blog for this project if you want.
Mailing list: [email protected].

Contact me if you want to subscribe.