Projects

Agent-Based Systems

	Towards Adaptive Supply Networks (2003-) - We explore adaptive control of supply networks methods, with the aim to improve delivery precision, robustness and costs. Activities include simulation modeling of supply chains and benchmarking through the Trading Agent Competition. (Stiftelsen SISU)
	Autonomic Networked Systems (2003-) - IBM's Autonomic Computing initiative proposes self-managing systems, with self-configuring, self-optimizing, self-healing, and self-protecting capabilities. We explore self-management concepts for networked systems, such as ERP systems, telecom systems and C&C systems. (VINNOVA)
	Trading Agent Competition (2001-) - TAC is an international forum designed to promote and encourage high quality research into trading agent problems, initiated by Prof. Michael Wellman at U Mich. Since 2002, we provide the TAC software platforms and run the competitions. In 2003, SICS and CMU created the new TAC Supply Chain Management game format.

Networked Embedded Systems

Combinatorial Problem Solving and Prolog Technology

• SICStus Prolog
• Quintus Prolog
• Global Constraints
• NET-WMS

• Dispensation Order Generator for DNA Sequencing
• GENFUNK
• Trading Agent Competition
• A case study on airport crew rostering
• A study on using the case global constraint for configuration problems
• A study on optimization methods for configuration problems (SICS Technical Report T99-04)
• Frequency planning for cellular telephone networks
• Optimization of print mask design for inkjet printers
• TACIT
• Verification and optimization using constraints and logic

Biotechnology

• DispGen (2003) - a project to develop a dispensation order generator for Pyrosequencing's sequence analysis instruments, using constraint programming technology. The generator computes an instruction sequence based on an input specification. Funding provided by Pyrosequencing AB, an Uppsala company offering complete solutions for applications including genetics, drug discovery, microbiology, SNP and mutation analysis, forensic identification, pharmacogenomics, and bacterial and viral typing.

• GENKOMB (2003) - The aim of the GENKOMB project was to find and analyse transcription factor binding sites in the human genome, by correlating expression data for a set of genes with the nucleotide sequences in their upstream regions. Apart from detecting transcription factor binding sites, this project has resulted in programs for matching weight matrices to DNA sequences and multiple alignment of short nucleotide sequences. In collaboration with AstraZeneca AB.

  Main funding provided by VINNOVA.

• GENFUNK (2001-2002) - This project, carried out in collaboration with Global Genomics AB, studied a novel approach of measuring the global gene expression in a tissue sample. In the method, mRNA is extracted from the sample and transformed into cDNA captured on magnetic beads. This is then acted on by type IIS restriction endonucleases, which recognize certain short DNA sequences and cut the DNA close to those sequences. The resulting fragments are amplified in PCR with selected ligation fragments, and displayed in capillary electrophoresis. Determining the gene expression levels from the peak data is combinatorial optimization problem, which can in principle be solved, to give expression levels of most genes active in sampled cells, with good accuracy.

  Main funding provided by VINNOVA.

Adaptive Robust Computing

• Multiparty Computation Protocols
• SAITS