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Notes on Systems Biology topics and software | 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/ | TF checkpoint: http://norstore-trd-bio0.hpc.ntnu.no/ | ||
Software | http://www.ebi.ac.uk/metabolights/ | ||
http://genemania.org/ | |||
=Software= | |||
Gene2Pathway: http://www.bioconductor.org/packages/2.11/bioc/html/gene2pathway.html | Gene2Pathway: http://www.bioconductor.org/packages/2.11/bioc/html/gene2pathway.html | ||
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http://sourceforge.net/projects/opencobra/ | 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= | =Metabolic modelling= | ||
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==Models== | ==Models== | ||
RECON 2: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2488.html | 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 |
Latest revision as of 15:31, 16 February 2014
Notes on Systems Biology topics and software
Blogs
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://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/
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