Call for Papers and Posters

Proposal for Computational and Symbolic Systems Biology Session

at the Pacific Symposium on Biocomputing 2004

 

It has become increasingly evident that the use of large-scale experimental data and the invocation of systems biology principles are gaining widespread acceptance in mainstream biology. The approaches to date have typically involved a mixture of computational integration of the data and pathway inference. The amount of research in this area has exploded in recent years, as witnessed by the number of research presentations at meetings by the Biopathways Consortium and the International Conference on Systems Biology. This is the first Systems Biology session within PSB, and will include a broad range of topics from computational systems biology, to the use of logical inference engines in pathways and related disease mechanisms.

 

Large-scale data analysis has become more common with the advent of microarray technologies and mass spectrometry. The amount of quantitative data these yield is on the order of thousands of individual molecular channels, and has been used to successfully identify patterns indicative of biological responses or disease states. However, it has become apparent that single genes or their products do not cause most of the biological phenomena observed. The findings have drawn researchers to the conclusion that the most interesting phenomena in biology result from the inter-related actions of many components within the system.

 

Systems Biology is a nascent field of research that continues to evolve, and in its current form relies on a variety of novel computational approaches, including, dynamics modeling, multivariate analysis, and Bayesian networks. Yet it is also highly dependent on experimental design, such as how one perturbs a particular system under investigation. Therefore, a key aspect of this field is that the computational side is very closely tied to the experimental wet-lab side, and focus on one without regard for the other will be inadequate. What will differentiate this session from other computational biology programs is that it will rely on the inclusion of experimental design models to show its full potential.

 

Pathways informatics has been a growing area of interest, as evidenced by the previous three sessions of pathways and genomics. Research in this area is typically divided into sub-groups that refer to metabolic, cell signaling, gene regulatory, and protein interaction pathways. It is also clear that to some extent these different areas are artificially defined, and that from a systems perspective will often need to be consolidated. Therefore, research into the interlinking of these areas will be of great interest to the general community. Analysis of gene expression data will for the most part make sense within the context of a system, taking into account the roles of cell signaling and transcription factor machinery. Studies that combine different pathway information will eventually be more successful in correctly interpreting microarray data, than methods that simply try to “cluster” microarray patterns.

 

Modeling in Systems Biology is often thought of as systems simulation, but in reality it can involve other forms of models and therefore requires a broader definition. Models may be numerically computable, but they also may be symbolical and accessible to inferential logic. Logical formalisms that describe complex phenomena are just as important as modeling molecular dynamics, and may lead to faster insight where the computational complexities are too great for a full-scale simulation. Work in the areas of concurrent process calculi, such as Pi-Calculus and Ambient Calculus show some exciting new potential in life science applications. These research topics need to be presented in parallel to the more numerically driven approaches, since they may offer a way to merge much of the symbolic knowledge derived already from genome research.

 

Although much of Systems Biology is about thinking beyond the genome, it is obvious that the proper utilization of genomic information when contemplating about the “system” is critical in a comprehensive analysis. It is therefore key to demonstrate how researchers can combine genomics information and place it in the “context” of a systems biology framework. Since the relevance of Systems Biology to Drug Discovery is rapidly gaining acceptance, and we are interested in presentations from researchers members of the pharmaceutics community who are applying Systems Biology as part of a high-throughput strategy.

 

This is to be an open perspective of the field, and will include papers that illustrate the many facets of this growing field. Topics we feel are relevant to this session include:

 

Papers addressing any of the mentioned topics (or other related topics) using multiple types of data are welcome. The session is especially interested in combining methods for analyzing and simulating multiple types of experimental data and will give a strong preference towards papers that combine more than one of the following types of data: gene expression profiles, protein expression profiles, protein-protein interaction data, regulatory networks, disease models, and pathway databases. Descriptions into the computational complexity and performance of the methods are strongly encouraged, as well as demonstrating the statistical significance of findings based on experimental data.

Individuals who cannot submit to this session but are willing to help referee submissions are kindly requested to contact either of the session co-chairs.

General Information on PSB 2004:

The Pacific Symposium on Biocomputing (PSB 2004) is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. PSB 2004 will be held January 6-10, 2004 at the Fairmont Orchid on the Big Island of Hawaii. Tutorials will be offered prior to the start of the conference.

PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are targeted to provide a forum for publication and discussion of research in biocomputing's "hot topics." In this way, PSB provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field. More information on the conference can be obtained from the conference web page: http://psb.stanford.edu/.

General Information on Papers, Abstracts, and Demonstrations:

The scientific core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. Accepted papers will be published in a hard-bound archival proceedings volume (which is fully indexed in Medline), and the best of these will be presented orally to the entire conference. Researchers wishing to present their research without official publication are encouraged to submit a one page abstract, and present their work in discussion, poster, and demonstration sessions. Workstations and Internet connections will be available for demonstrations; please submit detailed requests for demonstration facilities along with your paper or abstract if you require them.

Paper Formatting and Submission:

All papers must be submitted to russ.altman@stanford.edu in electronic format. The only acceptable file formats are Adobe Acrobat (*.pdf) and Microsoft Word (*.doc). Attached files should be named with the last name of the first author (e.g. altman.pdf or altman.doc). Hardcopy submissions or unprocessed TeX or LaTeX files will be rejected without review.

Each paper must be accompanied by a cover letter. The cover letter must state the following:

Submitted papers are limited to twelve (12) pages in the official PSB publication format. Please format your paper according to these instructions, which can be found at ftp://ftp-smi.stanford.edu/pub/altman/psb/. If figures cannot be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit.

Important Dates:

Session Co-chairs: