Difference between revisions of "Computational Biology"

From Jtkwiki
Jump to navigationJump to search
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
 +
Computational Biology is an interdisciplinary field of science which, on the one hand, uses computing to analyse biological systems and, on the other hand, investigates biological systems as computing systems.
 +
 +
== Information Theory in Computational Biology ==
 +
 +
* [http://www.ccrnp.ncifcrf.gov/~toms/ Tom Schneider]: [http://www.ccrnp.ncifcrf.gov/~toms/papers/emmgeo/ 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence]
 +
 +
 
== Computational Biology Software ==
 
== Computational Biology Software ==
 +
 
* [http://www.transsys.net/ transsys] is a system for modelling gene regulatory networks
 
* [http://www.transsys.net/ transsys] is a system for modelling gene regulatory networks
* [http://www.bioclipse.net/ Biocliopse]
+
* [http://ibis.inrialpes.fr/article122.html gna]
 +
* [http://www.cytoscape.org/ cytoscape]
 +
* [http://www.bioclipse.net/ Bioclipse]
 +
* [http://exon.niaid.nih.gov/cas/ dCAS cDNA Annotation System]
 +
* [http://www.gridqtl.org.uk/ gridqtl]
 +
* [https://sourmash.readthedocs.io/en/latest/ Sourmash] tools for MinHash based sketches of genomic sequences
 +
 
 +
 
 +
=== [http://www.r-project.org/ R] Packages / Collections ===
 +
 
 +
* [http://www.bioconductor.org/ BioConductor]
 +
* [http://adegenet.r-forge.r-project.org/ adegenet] is a package for exploratory analysis of genetic data, such as genome wide SNPs etc.
 +
 
 +
== Standards ==
 +
 
 +
* [http://biomodels.net/miriam/ MIRIAM] is a standard for annotating models
  
  
Line 7: Line 30:
  
 
* [http://www.bioconductor.org/ Bioconductor]
 
* [http://www.bioconductor.org/ Bioconductor]
* [http://www.mas.ncl.ac.uk/~ncsg3/microarray/ Analysing yeast time course microarray data]
+
* [http://www.mas.ncl.ac.uk/~ncsg3/microarray/ Analysing yeast time course microarray data] by [http://www.mas.ncl.ac.uk/~ncsg3/ Colin Gillespie]
 +
 
 +
 
 +
== Genome Assembly etc ==
 +
 
 +
* [http://sourceforge.net/apps/mediawiki/wgs-assembler/ wgs] (aka Celera Assembler / CABOG)
 +
* [http://sourceforge.net/apps/mediawiki/mira-assembler/ mira]
 +
* [http://cortexassembler.sourceforge.net/ cortex]
 +
* [http://www.ebi.ac.uk/~zerbino/velvet/ velvet]
 +
* [http://genome.sph.umich.edu/wiki/BamUtil BamUtil]
 +
* [http://www.ncbi.nlm.nih.gov/tools/gbench/releasenotes/ NCBI Genome Workbench]
 +
* [http://code.google.com/p/pysam/ pysam]
 +
* [http://bamview.sourceforge.net/ BamView]
 +
 
 +
 
 +
== Databases etc ==
 +
 
 +
* [http://www.modencode.org/ model organism encyclopedia of DNA elements (modENCODE)]
 +
 
 +
 
 +
== Related Stuff ==
 +
 
 +
* [https://ccrma.stanford.edu/~dattorro/mybook.html Convex Optimization and Euclidean Distance Geometry]

Latest revision as of 10:18, 6 September 2018

Computational Biology is an interdisciplinary field of science which, on the one hand, uses computing to analyse biological systems and, on the other hand, investigates biological systems as computing systems.

Information Theory in Computational Biology


Computational Biology Software


R Packages / Collections

  • BioConductor
  • adegenet is a package for exploratory analysis of genetic data, such as genome wide SNPs etc.

Standards

  • MIRIAM is a standard for annotating models


Gene Expression Analysis


Genome Assembly etc


Databases etc


Related Stuff