Difference between revisions of "Computational Biology"
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| + | 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. | ||
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| + | == Information Theory in Computational Biology == | ||
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| + | * [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] | ||
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== Computational Biology Software == | == Computational Biology Software == | ||
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* [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/ | + | * [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 | ||
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| + | === [http://www.r-project.org/ R] Packages / Collections === | ||
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| + | * [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. | ||
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| + | == Standards == | ||
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| + | * [http://biomodels.net/miriam/ MIRIAM] is a standard for annotating models | ||
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* [http://www.bioconductor.org/ Bioconductor] | * [http://www.bioconductor.org/ Bioconductor] | ||
* [http://www.mas.ncl.ac.uk/~ncsg3/microarray/ Analysing yeast time course microarray data] by [http://www.mas.ncl.ac.uk/~ncsg3/ Colin Gillespie] | * [http://www.mas.ncl.ac.uk/~ncsg3/microarray/ Analysing yeast time course microarray data] by [http://www.mas.ncl.ac.uk/~ncsg3/ Colin Gillespie] | ||
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| + | == Genome Assembly etc == | ||
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| + | * [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] | ||
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| + | == Databases etc == | ||
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| + | * [http://www.modencode.org/ model organism encyclopedia of DNA elements (modENCODE)] | ||
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| + | == Related Stuff == | ||
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| + | * [https://ccrma.stanford.edu/~dattorro/mybook.html Convex Optimization and Euclidean Distance Geometry] | ||
Latest revision as of 09:18, 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.
Contents
Information Theory in Computational Biology
- Tom Schneider: 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence
Computational Biology Software
- transsys is a system for modelling gene regulatory networks
- gna
- cytoscape
- Bioclipse
- dCAS cDNA Annotation System
- gridqtl
- Sourmash tools for MinHash based sketches of genomic sequences
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
