Scope:
Colorful analogies to catastrophic events, including floods, avalanches, tidal waves, and even explosions, have often been used to describe the overwhelming nature of high-throughput, biological data. The deluge of data shows no sign of abating, particularly as new technologies appear (protein chips) and established technologies are improved (mass spectrometers, DNA micro-arrays) or re-implemented on industrial scales. Finding new ways to integrate, manage, visualize, and interpret data from diverse sources is one of the grand challenges for modern bioinformatics, which merges information technology, computer science, statistics, applied mathematics, and biology. Topics of interest to this workshop include, but are not limited to:

• Protein-protein interactions
• mRNA and protein expression
• Functional annotation of genes and proteins
• Ontological classifications
• Signaling and regulatory pathways
• Biology-specific knowledge representation
• Biological data preparation and cleansing
• High-throughput experimental data monitoring and tracking
• Sequence- or structure-based data analysis
• Knowledge curation, annotation, and reporting
• Use of natural language processing techniques and/or artificial intelligence techniques to automatically extract multiple biological objects such as gene names, protein names, drugs, organisms, disease, etc., from free-text.
• Information and knowledge extraction such as object-object interactions (ex: protein interactions, functions, etc.).
• Software systems to support biological research that integrates multi-format and multi-type data from heterogeneous databases.
• Information visualization techniques for biological networks and integrated biological systems.
• Application of machine learning in the mining of very large dimensional data such as microarray and mass-spectrometry data.
• Computational methods that model cellular mechanisms, the protein machine, pathways, and regulatory networks.
• Algorithms for processing and interpreting large-scale mass-spectrometry data
• Comparative genomics and genome dynamics (i.e., evolution of whole genomes, e.g., by translocations, reversals, duplications, etc.)
• Modeling of small molecule ligand binding to proteins.
• An informatics technique, strategy, and tool that combine multiple types of data.
• Investigation of genome, transcriptome, proteome, or metabolome data, using multiple computational techniques, strategies, and tools.
• High-performance systems engineering ideas and strategies using concepts learned from bioinformatics.
• Significant biological discoveries using a consistent suite of investigative tools.

Other novel bioinformatics topics in life sciences may also be considered, as long as the topics contribute to the expansion of a system-scale understanding of biological processes and/or the creation of practical informatics solutions for real-world life science problems.

Important Dates:

Instructions for Paper Submission:
All papers should represent original and previously unpublished works that are currently not under review in any conference or journal. Both basic and applied research papers are welcome.

Submissions should include an abstract, key words, the e-mail address of the corresponding author, and must not exceed 15 pages, including tables and figures, in PDF format. Please send your submission to: bioin@cs.iupui.edu .

All enquiries and questions should be directed to the Workshop Chairs. Additional details are available at the Workshop home page at http://www.cs.iupui.edu/~bioin/bioinformatics05/and at the conference home page at http://keysoftlab.nju.edu.cn/ispa2005/

Workshop Chairs:
Mathew Palakal
Department of Computer & Information Science
Indiana University Purdue University Indianapolis , USA
mpalakal@cs.iupui.edu

Jake Chen
School of Informatics/Computer Science
Indiana University Purdue University Indianapolis , USA
jakechen@iupui.edu

Zongben Xu
Xian Jiaotong University, China
zbxu@mail.xjtu.edu.cn