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Toolkit: BioInform s Surfing Report: Web-Based Tools from ICSB 2004


BioNetGen, from Los Alamos National Laboratory, generates computational models of cellular signaling networks:

Copasi (Complex Pathway Simulator), from the Virginia Bioinformatics Institute, provides stochastic and deterministic simulation and steady-state analysis of biochemical pathways:

IdentiCS (Identification of Coding Sequences from Raw Genome Sequences), from the German Research Center for Biotechnology, reconstructs metabolic networks from unfinished genome sequences:

Kegg2SBML, from Keio University, converts the KEGG database to SBML format:

LifeDB (Database for Localization, Interaction, Functional Assays and Expression of Proteins), from the German Cancer Research Center, was designed to collect, view, and mine data from a number of sources, including expression data, localization information, proteomics data, and information from functional assays:

Pathway Hunter Tool, from the University of Cologne, finds the shortest path between given metabolites in a biological network:

PaVESy (Pathway Visualization Editing System), from the Max Planck Institute of Molecular Plant Physiology, is an SQL-based relational system for editing and visualizing biological pathways:

PySCeS (Python Simulator for Cellular Systems), from the University of Stellenbosch, performs a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis for a network of coupled reactions:

ScrumPy, from Oxford Brookes University, is a Python-based molecular modeling package:

Filed under

The Scan

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.

US Survey Data Suggests Ancestry Testing Leads Way in Awareness, Use of Genetic Testing Awareness

Although roughly three-quarters of surveyed individuals in a Genetics in Medicine study reported awareness of genetic testing, use of such tests was lower and varied with income, ancestry, and disease history.

Coral Genome Leads to Alternative Amino Acid Pathway Found in Other Non-Model Animals

An alternative cysteine biosynthesis pathway unearthed in the Acropora loripes genome subsequently turned up in sequences from non-mammalian, -nematode, or -arthropod animals, researchers report in Science Advances.

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.