18th International Conference on Systems Engineering (ICSEng '05)

Special Session on Computer Infrastructure for Systems Biology
August 16-18 2005 * Las Vegas, NV USA

Special Session Call for Papers

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ICSEng-BIO '05
  Important Dates
  Contact Chairs
  Accepted Papers

The session final program (date/place/time) has been posted on this site (html or pdf). It is to be held on 08/17/2005 at the University of Nevada Las Vegas Campus (UNLV), in Classroom Building Complex A (CBC #A, UNLV map label #55) close to the library.


The special session's goal is to bring forth ideas and collaborations among industrial and academic bioinformaticians, biocomputing professionals, data analysts, and system biologists to facilitate systems biology research and findings. Both research papers (6 pages, IEEE Proceedings format) and poster papers (2 pages) are solicited to explore case histories of building and maintaining IT infrastructures that support advanced biological research. Both industrial and academic contributions are welcome.

Topics of Interests

Systems Biology is an emerging field that seeks to analyze disparate forms of biological data with an aim of uncovering the function and interaction of the underlying biological systems. It is characterized by voluminous and heterogeneous data, incomplete data sets, low data signal/noise ratios, and extreme difficulties in precisely reproducing experimental conditions. These drawbacks are offset by the profound interest in the field by the Pharmaceutical and Biotechnology industries and by the illumination of biological research in general.

We welcome papers/presentations that examine fresh perspectives and profound experiences in the research and development of computer systems enabling systems biology. Topics of interests include (but are not limited to):

* Microarray Data Analysis
* Functional Imaging and Pattern Recognition
* Biological database integration and knowledge representation
* Ontologies and semantic web systems for biology
* Biomedical literature text mining
* Micro-surgery and micro-manipulation
* Application of nanotechnology to biological systems
* Protein-protein interactions
* Proteomics
* Protein-small molecule interactions
* Metabolic and Genetic Pathways
* Visualization of complex data relationships
* Biological data tracking and labelling
* Clinical Informatics
* Laboratory Information Management Systems
* Measuring cellular metabolism and cellular signalling


* Computer and IT professionals from the biotechnology and pharmaceutical industries.
* Bioinformatics researchers with an interest in real-world applications.
* Researchers and developers interested in application of computational systems to biological problems.

Important Dates

Abstracts Due: March 28, 2005
Notification of Acceptance: April 25, 2005
Final paper Due: May 25, 2005


Abstracts in English reporting original and unpublished research results and experience are solicited. All abstracts are to be submitted in PDF or MS word version electronically.

Abstracts for refereeing should be double-spaced and must include the special session keyword "Computer Infrastructure for Systems Biology" to reach us correctly. For detailed submission instruction and submission site, go to: http://bio.informatics.iupui.edu/bio-05/submission.stm. Note that submission implies the willingness of at least one of the authors to register and present the paper.

All abstracts will be peer reviewed by two independent members from the scientific committee, and may be accepted into the program as one of the format on a competitive basis:

  • Full papers not to exceed 6 Proceedings-formatted pages, and will be invited for podium presentations;
  • Poster papers not to exceed 2 Proceedings-formatted pages, and will be given a poster board to display work.


Accepted and registered papers will be included in the ICSEng'05 conference proceedings published by IEEE Computer Science Press. Selected high-quality full papers will also be published in the International Journal on Computational Intelligence and Applications by World Scientific Publishing Company Press.

Contact the Chairs

Jake Y. Chen
Assistant Professor
Indiana University School of Informatics
Indianapolis, IN 46202
Email: jakechen@iupui.edu
Web site: http://bio.informatics.iupui.edu/CV/

Bradley K. Sherman
Director of Bioinformatics
Mendel Biotechnology, Inc.
21375 Cabot Boulevard
Hayward, CA 94545
Email: icse@mendelbio.com

Scientific Committee

Charlie Berger, Senior Director of Life Sciences/Data Mining Products, Oracle Corporation, USA
John Carlis, Ph.D., Professor of Computer Science, University of Minneosta, USA
Fan Hsu, Ph.D., Director of Proteomics, University of California Santa Cruz, USA
David Hart, Ph.D., Manager of High-Performance Computing Group, Indiana University, USA
Daisuke Kihara, Ph.D., Assistant Professor of Biology and Computer Science, Purdue University, USA
Andrey Sivachenko, Ph.D., Senior Scientist, Ariadne Genomics, USA
Susie Stephens, Ph.D., Principle Product Manager of Life Sciences, Oracle Corporation, USA
Chen Su, Ph.D., Principle Research Scientist, Integrative Biology, Eli Lilly Companies, USA
Geert Wenes, Ph.D., Manager, Emerging Market and Technologies, Cray, Inc., USA
Hisayoshi Zaima, Ph.D., Manager, Hitachi Life Sciences Group, Japan

Accepted Papers

Accepted Full Papers with Podium Presentations

A High-Throughput Adaptive Computing Infrastructure for Bioinformatics Research
Stuart Pineo
Permeable Observations of Multifactor Database for Transcription Network
Miho Sera
Selecting Maximally Informative Genes: the Interplay Between Accuracy and Complexity
Yannis P. Androulakis
Integrated Workflows for Systems Biology in an Object-Relational DBMS
Andrew MacBride
Data integration and Knowledge Aggregation in the Life Sciences*
Susie Stephens
Abstracting Genes to Gene Ontology Terms Allows Comparison Across Multiple Species
Ernst R. Dow
Identifying Candidate Genes Using The BioWarehouse: A Case Study
Peter Karp
Experiments in Text-base Mining and Analysis of Biological Information from Medline on Functional-Related Genes
Rahul Singh
Classification of Pathology Data using a probablistic model
John Eberhardt
Novel DBMS Extensions for Functional Brain Image Analysis
Kristin R. Munch
Consistency, Feasibility and Multiplicity of Fluxes in Metabolic Pathways
R. Nigan

* presentation only


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