Nervous Molecular Systems Biology Laboratory

Introduction to System Biology

Systems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses a new perspective (holism instead of reduction). Particularly from year 2000 onwards, the term is used widely in the biosciences, and in a variety of contexts. An often stated ambition of systems biology is the modeling and discovery of emergent properties, properties of a system whose theoretical description is only possible using techniques which fall under the remit of systems biology.

Microarry Data Analysis

• Gene Expression Omnibus: A public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted.
• Affymetrix Power Tools (APT): Affymetrix Power Tools (APT) are a set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChip® arrays.
• ArrayExpress The ArrayExpress Archive is a database of functional genomics experiments including gene expression.
• Microarray Expression Data Analysis References
• Microarray Data Analysis: An (Opinionated) Guide to Microarray Data Analysis.
• Genomic Annotation Resources: Genomic Annotation Resources.

Software & Database Manuals

• CASCADE_SCAN: mining signal transduction network from high-throughput data.
• Stem Cells: The National Institutes of Health resource for stem cell research.
• CGI Programming in C: An introduction to writing CGI programs in the C language.
• Gnuplot Short Course: Gnuplot is a powerful freeware program for plotting both 2D and 3D data.
• Statistical Softwares: A guide to statistical softwares such as SPSS, MATLAB, BioPerl, GNU Scientific Library and R.
• Databases: Databases applied in transcriptional regulatory network and signaling network construction.
• Regulatory Networks in Stem Cells: Integrated Stem Cell Molecular Interaction Database (iScMiD) is an initial database for disseminating and displaying gene regulatory networks in stem cells.

Community Links

• Institute of Systems Biology: Links to sites providing mouse clones, mice and ES cell lines, colony management software, and to databases of other mammals and model organisms.
• Institute of Systems Biology, Shanghai University: An (Opinionated) Guide to Microarray Data Analysis.