David Wild wins $120k Grant from Lilly for Web Service Devlelopment

Informatics Faculty Member Receives $120K Grant from Eli Lilly & Company for Research Project

Eli Lilly and Company has awarded a one-year, $120,000 grant to Professor David Wild of the Indiana University School of Informatics to research ways to data mine the ever-increasing amount of publicly available information about chemical compounds and their biological activities.

David Wild Wild, Assistant Professor and Associate Director of the Chemical Informatics Program for the School, is developing a software tool that will aggregate data from a multitude of online databases and computation tools using a web service infrastructure that was previously developed through funding from the NIH. The tool will be a "one-stop-shop" for understanding the properties and behavior of chemical compounds, in particular existing and potential drug molecules.

"The creation of this software is significant because it will enable a comprehensive picture of a potential drug's behavior to be assessed, not just using static information from databases, but also using active on-the-fly predictions and calculations from state-of-the-art tools," said Professor Wild. "Drug researchers will have a single tool that can give them needed information from the public arena, and we hope it will help to speed up the drug discovery pipeline."

More information at http://djwild.info

Two students awarded Symyx PhD Fellowships in Informatics

Dazhi (David) Jiao and Jae Hong Shin at the IU School of Informatics will be continuing their studies in a doctoral program thanks to a partnership between the School and Symyx Technologies, Inc.

For full story, see http://www.informatics.indiana.edu/headline.asp.

Cheminformatics student Dazhi Jiao is accepted into the Google Summer of Code

From http://code.google.com/soc/2008/genmapp/appinfo.html?csaid=4236C0DBB86F4A10

Title	Integration of Cheminformatics Tools in Cytoscape
Student	Dazhi Jiao
Mentor	John "Scooter" Morris
Abstract
Biological networks that contain small molecules are of special interests in biological and chemical informatics researches. For example, there are some recent research on the relationships of protein networks and ligands networks, based on the facts that proteins with similar binding sites bind similar ligands. This project proposes an addition of cheminformatics tools to Cytoscape to facilitate such research. 1.2D depiction is a basic requirement for chemistry research. I will integrate the 2D depiction functionality of the Chemistry Development Kit (CDK) (http://cdk.sourceforge.net) into Cytoscape, so that users can view the 2D structure of any molecule that has annotation of either SMILES string or other commonly used structure annotations. CDK is an open source Java library for structural cheminformatics and bioinformatics. 2.Linkout to chemical resources that focuses on biological activities of small molecules, sush as PubChem, MACiE, and ChEBI. PubChem (http://pubchem.ncbi.nlm.nih.gov/) is one of the largest chemical databases that provide information on the biological activities of small molecules. MACiE (Machanism, Annotation and Classification in Enzymes) (http://www.ebi.ac.uk/thornton-srv/databases/MACiE/) contains fully annotated enzyme reaction mechanisms, including information on substrates. Chemical Entities of Biological Interest (ChEBI) (http://www.ebi.ac.uk/chebi/) is a dictionary of molecular entities focusing on small molecules. 3.Implementation of a plugin to calculate the Tanimoto similarity between molecules in a network. This will use the implementation of Tanimoto similarity implementation in CDK, which calculates the Tanimoto coefficients based on fingerprints of compounds.(http://www.daylight.com/dayhtml/doc/theory/theory.finger.html) 4.Extend the plugin mentioned in 3 to clustering nodes in a network based on the Tanimoto similarity of molecules that associated with each node. For example, nodes in a protein network can be used to generate a new network based on the Tanimoto similarities between the ligands that bind to the proteins. The mapping of this generated network to the original network might be of interests to researchers.

NSF Cyber Enabled Discovery and Innovation

This could be an opportunity worth pursuing at the NSF

Taken from http://www.nsf.gov/news/news_summ.jsp?cntn_id=108366

-- David Wild

February 5, 2007

America's preeminence in information technology is widely recognized as essential to our economic competitiveness. The infusion of computation into science and engineering has revolutionized how research is carried out and applied. Once used by only a handful of elite researchers on select problems, advanced computing has now become essential to future progress and exploration. Coupled with continuing improvements in microprocessor speeds, converging advances in networking, software, visualization, data systems and collaboration platforms are changing the way research and education are accomplished.

Still, the broad and complex questions posed by 21st Century inquiry require access to new information technology capabilities, such as distributed wired and wireless observing network complexes, and sophisticated simulation tools that permit exploration of phenomena that can never be observed or replicated by experiment. New concepts and tools are needed to address the challenges posed by a world of petascale computers grinding away at 1 quadrillion operations per second, massive data flows and databases, and an economy dependent on digitally enabled activity.

In fiscal year (FY) 2008, the National Science Foundation (NSF) will begin the Cyber-enabled Discovery and Innovation (CDI) initiative to explore radically new concepts, approaches and tools at the intersection of computational and physical or biological worlds. For four decades, NSF has provided leadership in the scientific revolution made possible by information technology. Through investments ranging from supercomputing centers and the Internet to software and algorithm development, NSF-supported information technology has stimulated scientific breakthroughs across all science and engineering fields.

CDI includes five themes:

• Knowledge extraction. Knowledge extraction encompasses a variety of techniques-such as data mining, visualization and using basic concepts from computation, geometry and topology that help investigators find what is most important in the nearly infinite amounts of data from sensors, telescopes, satellites, the Internet and surveys. Combining underlying concepts with different types of data from multiple sources, high-bandwidth communications, and tera- to petascale computation power, scientists and engineers can make sense of today's massive volumes of data.
• Interacting elements. Analyzing the flow of electricity or information across the power grid or Internet, describing protein folding and unfolding, and finding principles for scaling from the quantum to the nano to the macro scales, require scientists and engineers to understand interacting systems. Such systems--ranging from atomic particles to galaxies and from computer networks to societies--are at the heart of many science and engineering challenges, and their understanding and control are major sources of innovation. A large number of interacting elements, random interactions and aggregate or emergent phenomena are key factors in such systems. CDI will improve our ability to predict and deduce interactions in complex systems to better understand, design and control them.
• Computational experimentation. Computational experimentation allows insight into complex, real-world systems such as hurricanes, nerve synapse activity, or the Big Bang, by enabling the creation of a virtual description. Simulation and other dynamic modeling techniques allow us to experiment with complex systems in ways that would be unimaginable in the real world. It also lets us guide real-world operations and experimentation in cases that have potential for unforeseen or extreme events. CDI will provide new modeling techniques ranging from mathematical formulations to multiscale simulation techniques.
• Virtual environments. Virtual environments are important mechanisms to enhance discovery, learning and innovation. They permit collaboration among diverse populations spread across geographic distances and at different times. Scheduling and operation of distributed facilities and sensor arrays, data extraction and analysis, international, real-time comparisons of global climate models, and injecting discovery and innovative environments into learning and training all use virtual environments. CDI will develop new techniques for building and utilizing virtual environments, especially in the context of cyberinfrastructure.
• Educating researchers and students in computational discovery. The promise of these new technologies, as well as their diffusion into other segments of the economy, will not be realized without education. CDI will integrate computational discovery techniques into the basic education of all scientists and engineers as well as development of new techniques for using computational discovery in all areas. Special focus will be placed on using virtual environments and cyberinfrastructure at all education levels. By enhancing human cognition and perception addressing complexity, computational tools provide an essential component to workforce development.

In FY 2008, NSF will begin CDI as a 5-year initiative with first-year funding of $52 million and a suggested growth of $50 million per year for 5 years.

-NSF-

Daylight Web Services Demo

From: "Daylight CIS, Inc." <daylight-announce@daylight.com>

Date: September 17, 2007 10:35:13 AM EDT

To: daylight-announce@daylight.com

Subject: Daylight Web Services Demo

*********************************

Daylight Web Services Demo

http://demo.daylight.com

*********************************

NETWORK ACCESS TO CHEMISTRY-ORIENTED PROCESSES

Daylight Web Services provide a valuable mechanism for delivering cheminformatics functionality within an organization. Web services use standard, open protocols to pass parameter data along with a particular service request over a network, thus triggering an action and the return of a defined response. Daylight Web Services use standard protocols with SOAP messaging to provide easy access to Daylight functions and are ready to use in user-designed workflows, web-based applications, or command line applications.

CHECK OUT THE DEMO

A demo of the web services is available at http://demo.daylight.com.  We encourage you to take a look.

The demo is a simple application that utilizes the following Daylight Web Services:

     * getDepiction - converts a single SMILES string or TDT into a structural diagram in GIF format

     * canonicalizeSmiles - parses a list of molecules or reactions and generates the corresponding canonical SMILES

     * getProperties - calculates values for a specified list of different physical properties for one or more input SMILES

     * convert Structure - inter-converts data and structures between MDL chemical table-based file formats and Daylight SMILES-base formats

     * derive Scaffold - generates a single SMARTS scaffold that captures all common substructure elements including ring topology from a list of SMILES

     * derived SDClusters - partitions moderately-sized sets of input SMILES into clusters with significant scaffolds

The first four web services are located on the Core Services page. The later two can be accessed from the Scaffolds and Clustering pages, respectively. See the application Help page for demo instructions.

LET US KNOW WHAT YOU THINK

How do they look?   Would they be useful to you?  What other web services could you use?  We'd like to hear your thoughts -- please send feedback to peter@daylight.com.

Thanks!

Peter

__________________________________________

Peter Nielsen

Director, Marketing & Business Development

DAYLIGHT CHEMICAL INFORMATION SYSTEMS, Inc.

http://www.daylight.com

office: 802-223-9831

cell: 802-598-4819

_______________________________________________

If you prefer not to receive these occasional notices of Daylight news and upcoming events, please send mail to: daylight-announce-unsubscribe@daylight.com.

This email constitutes an advertisement or solicitation under (S. 877).

Daylight Chemical Information Systems, Inc.

120 Vantis, Suite 550

Aliso Viejo, CA 92656

Fwd: Call for Papers and Invited Sessions Proposals

This might be worth considering -- David

Begin forwarded message:

From: "Chair" <wm-sci08@sciiis.org>

Date: September 8, 2007 1:49:44 AM EDT

To: <DJWILD@INDIANA.EDU>

Subject: Call for Papers and Invited Sessions Proposals

Dear David J. Wild:

We invite you to submit a paper/abstract to the 12th World Multi-Conference on Systemics, Cybernetics and Informatics: WM-SCI '08 (http://sciiis.org/WM-SCI08). It will take place in Orlando, Florida, USA, on June 29th to July 2nd, 2008.

The deadlines are the following:

Submissions: October 24th, 2007

Acceptance: November 28th, 2007

Camera-ready: February 14th, 2008

We are emphasizing the area of Application of Informatics and Cybernetics in Chemistry  which, we think, is related to your specific academic or professional area.

Submitted papers or extended abstracts will have three kinds of reviews: double-blind (by at least three reviewers), non-blind, and participative peer-to-peer reviews.

Authors of accepted papers who registered in the conference can have access to the reviews made to their submission so they can accordingly improve the final version of their papers. Non-registered authors may not have access to the reviews of their respective submissions.

Awards will be granted to the best paper of those presented at each session. From these session's best papers, the best 10%-20% of the papers presented at the conference will be selected for their publication in Volume 6 of JSCI Journal (www.iiisci.org/Journal/SCI) and sent free to over 220 research libraries. Libraries of journal author's organizations will receive complimentary subscriptions of at least one volume (6 issues).

Also, we would like to invite you to organize an invited session related to a topic of your research interest. If you are interested in organizing an invited session, please, fill out the respective form provided in the conference web page. We will send you a password, so you can include and modify papers in your invited session.

More details about the reviewing process, the acceptance policy, organizing invited sessions, and submission deadlines can be found at our web site.

If the deadlines are tight and you need more time, let us know about a suitable time for you and I will inform you if it is feasible for us.

Best regards,

Professor Nagib C. Callaos

WM-SCI '08 General Chair

www.sciiis.org/Nagib-Callaos

If you wish to be removed from this mailing list, please send an email to wmsci.remove@sciiis.org with REMOVE MLWM-SCI in the subject line Address: Torre Profesional La California, Av. Francisco de Miranda, Caracas, Venezuela.

[Fwd: FW: Jean-Claude Bradley's talk at ACS Chicago]

Jean-Claude's talk is really worth viewing.

Gary

------------------------------------------------------------------------

*From:* Jean-Claude Bradley [mailto:jeanclaude.bradley@gmail.com]
*Sent:* Tuesday, April 03, 2007 1:57 PM
*To:* Wiggins, Gary D.
*Subject:* Jean-Claude Bradley's talk at ACS Chicago

No problem - talking with you was more interesting than the first
presentation :)
It is always nice to meet the person behind the mailing list.
Thanks for mentioning by blog at your talk!

By the way my talks were recorded and available here in case someone
wants more info:
http://drexel-coas-talks-mp3-podcast.blogspot.com/

On 4/3/07, *Wiggins, Gary D.* < wiggins@indiana.edu
<mailto:wiggins@indiana.edu>> wrote:

I' m sorry that I didn' t realize there was a CHED session on
communication that paralleled the CINF session. I hope that I didn 't
make you late by directing you to our session.

Incidentally, I' ve had a chance to look at your very interesting Useful
Chemistry blog. I plan to talk about it as part of a lectu re I 'll be
giving in Columbus, Ohio on May 8.

Gary

Gary Wiggins

Director, Program in Chemical Informatics

Adjunct Professor of Informatics

School of Informatics

Eigenmann Hall Room 1126

1900 East Tenth Street

Bloomington, Indiana 47406

Phone: 812-856-1086

Fax: 812-856-4764

E-mail: wiggins@indiana.edu <mailto:wiggins@indiana.edu>

--
Jean-Claude Bradley, Ph. D.
E-Learning Coordinator for the College of Arts and Sciences
Associate Professor of Chemistry
Drexel University

http://drexel-coas-elearning.blogspot.com
http://drexel-coas-talks-mp3-podcast.blogspot.com/
http://usefulchem.blogspot.com <http://usefulchem.blogspot.com>