Biosoftware for Mac

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Biosoftware for Mac is a resource to recommend pieces of software that you found helpful in your life science research, be it in data organisation, analysis, publishing/presenting, or any other biology-related task. Help it grow by contributing content.
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Text processing

 * general into to LaTeX
 * Getting started with LaTeX on a Mac
 * Word vs. LaTeX side by side comparison
 * LaTeX template for PhD thesis
 * TeXShop (LaTeX editor, free)


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Reference management

 * BibDesk (BibTex reference database w PubMed download, free)
 * Skim - PDF reader and annotation software (free)
 * Papers (bibliography software by MekenTosj, shareware )
 * JabRef (Open source reference manager = free)


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DNA/RNA

 * EnzymeX (restriction enzyme analysis + info)
 * 4peaks (simple sequence viewer)
 * ApE - A Plasmid Editor (software review)




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Graph/Diagram software

 * Grace (runs on Mac's XWindow) - WYSIWYG 2D plotting tool
 * GraphPad Prism (Mac/Win) - basic biostatistics, curve fitting and graphing
 * IGOR (Mac/Win) - 2D/3D graphs and stats
 * KaleidaGraph (Mac/Win) graphing and data analysis
 * for more see here


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Unix (and OS/X!) Bio Developer Tools

 * Eclipse - Programming environment, editor, etc for Java, Perl, C, ...
 * BioPerl - File conversion, sequence analysis, database searches, graphics, ..
 * BioPython - File conversion, sequence analysis, database searches, graphics, ..
 * BioLib - File conversion, sequence analysis
 * Graphviz - Text command language for vector graphics. Very good OS/X version too.


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Quotes
Make software that you want to use and that you would want to use often. As long as you are making something that you want to use, then your heart will be in it.
 * Cabel Sasser, 2006

All programmers are playwrights and all computers are lousy actors.
 * Unknown

Where a calculator on the ENIAC is equipped with 18,000 vacuum tubes and weighs 30 tons, computers in the future may have only 1,000 vaccuum tubes and perhaps weigh 1.5 tons.
 * unknown, 1949

To err is human--and to blame it on a computer is even more so.
 * Robert Orben

I think computer viruses should count as life. I think it says something about human nature that the only form of life we have created so far is purely destructive. We've created life in our own image.
 * Stephen Hawking


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Recommended Links
Mac biosoftware lists
 * Apple's list of life science software
 * mac encryption powerful multifunctional system utility for Mac OS

General software databases:
 * i use this, especially scientific software
 * super useful is the freeware AppFresh that works with the i use this website
 * versiontracker, esp. Math/Science category
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Tips and tricks

 * PPT to PDF on a Mac - It is possible to save PDF from any Mac application by printing and then saving the output as a PDF. This page explains how you can save PDFs beyond the typical office printer format.
 * Using OpenOffice you can save any file to wikitext.


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