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en:tools_for_bio [2013/06/09 10:10] (current)
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 +=====Tools for bio=====
 +Useful softwares and web pages for your research. Please add software in this page !
 +====Restriction enzymes====
 +  *[[http://​www.neb.com/​nebecomm/​default.asp|New England BioLabs]]
 +    *[[http://​tools.neb.com/​NEBcutter2/​index.php|NEBcutter v2.0]]
 +    *[[http://​www.neb.com/​nebecomm/​DoubleDigestCalculator.asp|Double Digest Finder]]
 +
 +
 +====Plasmid map====
 +===PlasMapper===
 +  *[[http://​wishart.biology.ualberta.ca/​PlasMapper/​|PlasMapper]] ​
 +
 + From web site --- //The PlasMapper server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid sequences up to 20,000 bp may be annotated and displayed. Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format. PlasMapper supports an extensive array of display options. //
 +
 +{{ bio:​plasmap25_1197849057936.png?​200}}
 +This tool enables researchers to draw plasmid map quickly. For example, a map on the right hand was drawn by just inputing a sequence of pUC19 and clicking '​Graphic Map' button.
 +
 +
 +Reference -> PubMed:​[[pubmed>​15415271]]
 +
 +
 +===Others===
 +  *[[http://​www.matsubarase.com/​draw_plasmid/​index.php|Plasmid drawing software beta (Japanese site)]]
 +Draw plasmid maps on your web-browser. Quality of drawing lines and curves are substantially smooth by SVG.
 +
 +  *[[http://​www.acaclone.com/​|pDRAW32 DNA analysis software (English site)]]
 +Freeware for drawing plasmid maps.
 +
 +
 +
 +
 +====Nucleic acid structure====
 +===mfold===
 +The **[[mfold]]** is the well-known program that predicts the secondary structure of RNA and DNA.
 +  *[[http://​www.bioinfo.rpi.edu/​~zukerm/​|Michael Zuker'​s Home Page]]
 +    *[[http://​www.bioinfo.rpi.edu/​applications/​mfold/​|RNA & DNA Folding ​ Applications]]
 +===SimTK RNA Folding===
 +  *[[https://​simtk.org/​xml/​rna-folding.xml|SimTK RNA Folding]]
 +
 +The **ToRNADo** is a one of the SimTK projects that can display the structure of RNA molecule.
 +  *[[http://​simbios.stanford.edu/​index.html|National NIH Center for Physics-based Simulation of Biological Structures]]
 +
 +
 +====Modeling softwares====
 +<jmol ala.pdb.gz 100 100></​jmol>​
 +  *[[http://​jmol.sourceforge.net/​|Jmol(英語サイト)]]\\ Open-source 3D molecular viewer. You can use Jmol plugin in this Wiki.\\ See the [[pdb:​start_en|PDB page]].
 +  *[[http://​cuemol.sourceforge.jp/​ja/​index.php?​FrontPage|CueMol (Japanese site)]]
 +Freeware for windows.
 +  *[[http://​www.mdl.com/​products/​framework/​chime/​index.jsp|Chime]]
 +  *[[http://​www.umass.edu/​microbio/​rasmol/​index2.htm|Rasmol]]
 +  *[[http://​www.ks.uiuc.edu/​Research/​vmd/​|Visual Molecular Dynamics]]
 +
 +
 +
 +====Desktop dictionary====
 +  *[[http://​www.answers.com/​main/​product_info.jsp|Answers.com]]
 +Point or select the word or phrase and 'Alt + click' to show the meaning.
 +
 +====Image manipulating====
 +===GIMP===
 +
 +[[computer:​en:​GIMP|{{computer:​en:​gimp_2.13_ubuntu.png?​150|}}]]
 +\\ {{icon>​commons}}
 +
 +  *[[computer:​en:​GIMP]]
 +
 +This is a freeware have been developing by open-source community. Almost platforms (Win/​Mac/​Linux) are supported.
 +  *[[http://​www.gimp.org/​|GIMP Home]]
 +
 +===Cytoscape(Freeware)===
 +[[http://​www.cytoscape.org/​|{{bio:​cytoscape_ss1s.png?​150|}}]]
 +  *[[http://​www.cytoscape.org/​|Cytoscape]]
 +//Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. //
 +
 +
 +=====Podcast=====
 +Audio news from the following journals are available.
 +You can import audio file to play PC or other audio players.
 +  *[[http://​www.sciencemag.org/​about/​podcast.dtl|Science podcast]]
 +  *[[http://​www.nature.com/​nature/​podcast/​index.html|Nature podcast]]