User:Jarle Pahr/Systems biology

Notes on Systems Biology topics and software

Blogs

http://nlenov.wordpress.com/

Youtube

http://www.youtube.com/watch?v=fHzQYtrZmDw

Uri Alon Systems Biology lecture 1: http://www.youtube.com/watch?v=Z__BHVFP0Lk

Courses and lectures

https://www.coursera.org/course/sysbio?from_restricted_preview=1&course_id=970222&r=https%3A%2F%2Fclass.coursera.org%2Fsysbio-001%2Fauth%2Fauth_redirector%3Ftype%3Dlogin%26subtype%3Dnormal%26visiting%3D

https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=334

Projects and initiatives

http://www.the-dream-project.org/

Formats and standards

SBML:

SBGN: http://en.wikipedia.org/wiki/Systems_Biology_Graphical_Notation

SBOL: http://www.sbolstandard.org/

Organizations and websites

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

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

Institute for systems biology: https://www.systemsbiology.org/

SBML.org: http://sbml.org/Main_Page

Semantic Systems Biology: http://www.semantic-systems-biology.org/

Systems Biology @Nature.com: http://www.nature.com/sysbio/index.html

BMC Systems Biology Gateway: http://www.biomedcentral.com/gateways/systemsbiology

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/

Ina Koch: http://owww.molgen.mpg.de/~koch_i/publications_pr/index.html

• Petri nets

Voigt lab: http://web.mit.edu/voigtlab/papers.html

Databases

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

http://www.ebi.ac.uk/metabolights/

http://genemania.org/

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/

Generic Model Organism Database (GMOD) project: http://www.gmod.org/wiki/Main_Page

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

Executable biology

http://www.slideshare.net/nxk/executable-biology-tutorial

http://www.nature.com/nbt/journal/v25/n11/abs/nbt1356.html

http://mtc.epfl.ch/~tah/Publications/executable_biology.pdf

http://www.cs.nott.ac.uk/~jpt/papers/pmcb-08.pdf

Bibliography

Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0023126

Dissecting specific and global transcriptional regulation of bacterial gene expression: http://www.nature.com/msb/journal/v9/n1/full/msb201314.html?WT.mc_id=%20TOC_MSB_13

Computational meta’omics for microbial community studies: http://www.nature.com/msb/journal/v9/n1/full/msb201322.html?WT.mc_id=%20TOC_MSB_13

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia: http://www.nature.com/nbt/journal/v31/n6/full/nbt.2594.html

Systems biology beyond degree, hubs and scale-free networks: the case for multiple metrics in complex networks: http://link.springer.com/article/10.1007%2Fs11693-009-9050-7