Skip to main content
Premium Trial:

Request an Annual Quote

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

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.