VCU Biological Complexity

"Signal Stabilization and Sensitivity Enhancement in Liquid Chromatography/Mass Spectrometry Through Formation of Derivatives, Adducts and Ion Pairs"
Tuesday, March 1, 2005 * 2:00 pm
Room 2122, Oliver Hall
Monroe Park Campus

"Signal Stabilization and Sensitivity Enhancement in Liquid Chromatography/Mass Spectrometry Through Formation of Derivatives, Adducts and Ion Pairs"
H. Thomas Karnes, Ph.D.
Professor and Director of Analytical Laboratories
VCU School of Pharmacy

All Fellows and members are invited to attend.

|| Thursday, March 3, 2005||

Analysis of Microbial Metabolism Using Genome-Wide Metabolic Reconstructions and Large-Scale Mechanistic Models
Thursday, March 3, 2005 * 11:30-12:30
*Oliver Hall
Room 2125

Analysis of Microbial Metabolism Using Genome-Wide Metabolic Reconstructions and Large-Scale Mechanistic Models
Dr. Evgeni Nikolaev, Department of Biomedical Engineering
Cornell University, Ithaca NY

Our second candidate for the faculty position in Mathematical Biology, Dr. Evgeni Nikolaev, has developed some very interesting approaches to dealing with modeling and comparing metabolomes in cellular and subcellular systems. Please mark your calendars and try to join us for his upcoming seminar!

The ability to rapidly annotate complete genomes, produce genome-wide metabolic reconstructions, and carry out high-throughput experiments has dramatically reshaped biological research and its applications in biotechnology and medicine. However, even in the post-genomic era, understanding the relationship between molecular function and cellular physiology still presents a fundamental challenge. In this endeavor, accurate mathematical models have become indispensable tools in formulating plausible hypotheses and improving decision-making abilities. Due to intrinsic complexity of cellular systems, various modeling frameworks are needed to address specific problems of cellular organization and function. Specifically, in this talk the following three distinct frameworks and their limitations will be discussed, (1) genome-scale stoichiometric analysis, (2) large-scale kinetic modeling, and (3) ‘single-cell’ models. First, we discuss how certain coupling relationships between steady-state reaction fluxes and metabolite concentrations can be extracted from stoichiometry alone. The analysis is demonstrated on genome-scale metabolic reconstructions of Helicobacter pylori, Escherichia coli, and Saccharomyces cerevisiae. Some of results include enzyme subsets, alternative knockouts, and subsets of metabolites present in common conserved pools. While successful in many instances, stoichiometric analysis does not capture dynamic effects mediated by metabolite concentrations, enzyme activities, and genetic control. To address these and similar important issues, in the second part of the talk, we discuss a general hybrid stochastic/deterministic optimization framework to directly validate the interconnections between distributed control of flux, cellular economy of supply and demand, and negative feedback stabilization. The approach is demonstrated on a large-scale mechanistic model of central metabolism of Escherichia coli with the objective to identify minimal enzyme sets leading to significant many-fold improvements of the serine production. Real cells, though, grow, their geometry changes, DNAs replicate, etc. To account for such important processes, the Cornell Escherichia coli chemically structural and physiological accurate model will be very briefly discussed.

Contact Dr. Greg Buck for more information or if you would like to speak with Dr. Nikolaev during his visit.

* Reminder: reciprocal parking for MCV campus parkers is available in the new deck at the corner of Harrison and Cary (right across the street from the Trani Center and Oliver Hall).

Mass Spectrometry in the Ambient Environment
Wedensday, March 9, 2005 * 3:30
Business Building
Room 2114

Mass Spectrometry in the Ambient Environment
Dr. R. Graham Cooks
Purdue University

|| Tuesday, March 15, 2005||

NCBI Bioinformatics Field Guide - Lecture/General Session
Tuesday, March 15, 2005 * 9:00am - Noon
Trani Center for Life Sciences
Room 155 and BCCL, Monroe Park Campus

Sponsored by the VCU Libraries

The NCBI (National Center for Biotechnology Information) Field Guide to GenBank and NCBI Molecular Biology Resources trains researchers to effectively search freely available resources to find molecular biology and genetics information. The popular lecture and hands-on computer workshop on GenBank and related data domains covers the effective use of the NCBI Entrez databases and search engine, BLAST, genome data, and related resources. The updated class now features the NCBI assembly and annotation of human, mouse and rat genomes, the updated map viewer genome displays, the new genome-specific BLAST pages, the new NCBI curated conserved domains, and Cn3D 4.1.

Class instructors are biologists on the User Services staff of the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health. The lecture will be held on the MCV campus and broadcast to the Monroe Park campus. Locations and information about hands-on sessions and consultations TBA.

Registration is required, and registration for the Lecture/General Session is expected by those registering for hands-on training sessions. Depending on the anticipated level of attendees, the schedule may be adjusted for some of the sessions and/or add sites on each campus.

Contact Cate Canevari for more information.

NIH BCIG Seminar: "User Interfaces for Bio-Informatics Visualization"
Thursday, March 17, 2005 * 3:00-4:30pm
NIH Clinical Center (Building 10) Medical Board Room (Room 2C116)

NIH BCIG Seminar: "User Interfaces for Bio-Informatics Visualization"
Ben Shneiderman, Ph.D., University of Maryland

Note: This tutorial is open to anyone interested in the subject matter. Registration is not required; however, it is a good idea to arrive early, as seating is limited.

Human perceptual skills are remarkable, but largely underutilized by current graphical user interfaces. The next generation of animated GUIs and visual data mining tools can provide bio-informatics researchers with remarkable capabilities if designers follow the Visual Information-Seeking Mantra: Overview first, zoom and filter, then details-on-demand. Then dynamic queries allow user control of widgets, such as sliders and buttons that update the result set within 100msec. Seven types of information visualizations (1-, 2-, 3-, multi-dimensional data, temporal, tree and network data) will be shown with examples. Success stories with pharmaceutical drug discovery and microarray data using tools based on our work (www.spotfire.com) will be the starting point. Then recent work will be shown using three new research tools for gene expression analysis that are free for downloading:

Ben Shneiderman,Ph.D. is a professor in the Department of Computer Science, Founding Director (1983-2000) of the Human-Computer Interaction Laboratory, and Member of the Institute for Advanced Computer Studies and the Institute for Systems Research, all at the University of Maryland at College Park (full resume). He has taught previously at the State University of New York and at Indiana University. He was made a Fellow of the ACM in 1997, elected a Fellow of the American Association for the Advancement of Science in 2001, and received the ACM CHI (Computer Human Interaction) Lifetime Achievement Award in 2001. He was the Co-Chair of the ACM Policy 98 Conference, May 1998 and is the Founding Chair of the ACM Conference on Universal Usability, November 16-17, 2000. Dr. Shneiderman is the author of Software Psychology: Human Factors in Computer and Information Systems (1980). His comprehensive text Designing the User Interface: Strategies for Effective Human-Computer Interaction (1st edition 1987, 2nd edition 1992, 3rd edition 1998, book site Addison-Wesley Publishers, Reading, MA), came out in its 4th edition in April 2004 with Catherine Plaisant as co-author. His 1989 book, co-authored with Greg Kearsley, Hypertext Hands-On!, contains a hypertext version on two disks. He is the originator of the Hyperties hypermedia system, which was produced by Cognetics Corp., Princeton Junction, NJ. He was a member of the Board of Directors (1996-2001) of Spotfire whose products are based on his dynamic queries and starfield display research in information visualization. Dr. Shneiderman was a Computer Science Advisor (1999-2002) to Smartmoney which implemented marketmap, a variant of his treemap concept. He is an advisor for treemap supplier HiveGroup and for ClockWise3D, as well as a member of the Technical Advisory Board for ILOG. In addition, he has co-authored two textbooks, edited three technical books, published more than 200 technical papers and book chapters. His 1993-edited book Sparks of Innovation in Human-Computer Interaction collects 25 papers from the past 10 years of research at the University of Maryland. In 1999 he co-authored Readings in Information Visualization: Using Vision to Think with Stu Card and Jock Mackinlay, then in 2003 continued in this direction by co-authoring The Craft of Information Visualization: Readings and Reflections with Ben Bederson. Ben Shneiderman's vision of the future is presented in his October 2002 book Leonardo's Laptop: Human Needs and the New Computing Technologies, won the IEEE 2003 award for Distinguished Literary Contribution. Ben Shneiderman has been on the Editorial Advisory Boards of nine journals including the ACM Transactions on Computer- Human Interaction and the ACM Interactions. He edited the Ablex Publishing Co. book series on "Human-Computer Interaction." He has consulted and lectured for many organizations including Apple, AT&T, Citicorp, GE, Honeywell, IBM, Intel, Library of Congress, Microsoft, NASA, NCR, and university research groups. Dr. Shneiderman's early work included database research including performance and index optimization. He is also known in software engineering, especially for his widely used innovation of structured flowcharts, commonly known as Nassi-Shneiderman Diagrams. He teaches popular short courses on information visualization and has organized an annual satellite television presentation on User Interface Strategies seen by thousands of professionals from 1987 to 1997.

Ben Shneiderman's homepage

References Relevant To This Tutorial:

Molecular/personalized medicine:

Standardizing genotype variation nomenclature:

More information, visit the BCIG web site www.nih-bcig.org, check the on-line NIH Record http://calendar.nih.gov/cgi-bin/calendar or call or write Jim DeLeo, BCIG Chairman jdeleo@nih.gov, (301)-496-3848. For NIH visitor information go to http://www.nih.gov/about/visitor/. To have your name added to the BCIG list server, send Jim an e-mail note with your name, e-mail address and telephone number.

BCIG is always looking for good brainstorming facilitators, tutorial instructors and speakers. If you would like to serve BCIG in one of these roles, and/or if you can suggest someone who could, please let Jim DeLeo know.

|| Thursday, March 17, 2005||

"Regulation of G-protein and MAPK Activity Revealed by Mathematical Modeling and Experimental Analysis"
Thursday, March 17, 2005 * 12:00 - 1:00p.m.
Oliver Hall-Education Wing, Rm. 2122

Regulation of G-protein and MAPK Activity Revealed by Mathematical Modeling and Experimental Analysis
Dr. Necmettin Yildirim
Postdoctoral Fellow, Department of Mathematics
University of North Carolina at Chapel Hill

Dr. Yildirim will be visiting VCU on Thursday and Friday. He is a candidate for a tenure track faculty position in Mathematical Biology in the Center, Math, Biology, /other departments. Please contact Dr. Gregory Buck if you would like to speak with him.

Reminder: Reciprocal parking for MCV Campus people is available at the Cary Street Deck (Cary and Harrison).