User:Jarle Pahr/Systems biology

Notes on Systems Biology topics and software

Organizations and websites

ISSB - International Society for Systems Biology: http://www.issb.org/

International Conference on Systems Biology: http://www.icsb2013.dk/

Persons/research labs

Bernhard Ø Palsson: http://gcrg.ucsd.edu/Researchers/Palsson

Publications - Systems Biology Research Group at UCSD: http://systemsbiology.ucsd.edu/publications

Adam Feist: http://systemsbiology.ucsd.edu/Researchers/Feist

Eberhard Voit: http://www.bme.gatech.edu/facultystaff/faculty_record.php?id=81

Hiroaki Kitano: http://en.wikipedia.org/wiki/Hiroaki_Kitano

Uri Alon: http://www.weizmann.ac.il/mcb/UriAlon/

Systems Biology Institute: http://www.sbi.jp/

Databases

TF checkpoint: http://norstore-trd-bio0.hpc.ntnu.no/

Software

Gene2Pathway: http://www.bioconductor.org/packages/2.11/bioc/html/gene2pathway.html

OpenCOBRA: http://opencobra.sourceforge.net/openCOBRA/Welcome.html

http://sourceforge.net/projects/opencobra/

PyCobra developer forum: http://sourceforge.net/projects/opencobra/forums/forum/1841961

OpenCOBRA forums: http://sourceforge.net/projects/opencobra/forums

GeneCircuits: http://ccsb.fudan.edu.cn/genecircuits/

Petri nets

http://www.scholarpedia.org/article/Petri_net

Gene regulation

Simulation of E. coli Gene Regulation including Overlapping Cell Cycles, Growth, Division, Time Delays and Noise : http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0062380

Metabolic modelling

Models

RECON 2: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2488.html

Bibliography

In silico method for modelling metabolism and gene product expression at genome scale: http://www.nature.com/ncomms/journal/v3/n7/full/ncomms1928.html