Biosoftware for Mac

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<b>Biosoftware for Mac</b> 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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[[Image:Biomac.jpg|100px|center]]
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<font face="tahoma" size="2" color="#000099">'''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 ===
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* general into to [[LaTeX]]
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* [[Getting started with LaTeX on a Mac]]
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* [[Word vs. LaTeX]] side by side comparison
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<font size="3" color="#000000"><b>Text processing</b></font>
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* background: [[LaTeX]], [[Word vs. LaTeX]]
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* [[LaTeX template for PhD thesis]]
* [[LaTeX template for PhD thesis]]
* [http://www.uoregon.edu/~koch/texshop/obtaining.html TeXShop] (LaTeX editor, free)
* [http://www.uoregon.edu/~koch/texshop/obtaining.html TeXShop] (LaTeX editor, free)
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<font size="3" color="#000000"><b>Reference management</b></font>
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=== Reference management ===
* [http://bibdesk.sourceforge.net/ BibDesk] (BibTex reference database w PubMed download, free)
* [http://bibdesk.sourceforge.net/ BibDesk] (BibTex reference database w PubMed download, free)
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* [https://sourceforge.net/projects/skim-app Skim] (PDF reader and annotation programme, free)
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* [[Skim - PDF reader and annotation software]] (free)
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* [[Papers (bibliography software)|Papers]] (bibliography software by MekenTosj, shareware )
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* [http://jabref.sourceforge.net/ JabRef] (Open source reference manager = free)
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<font size="3" color="#000000"><b>DNA/RNA</b></font>
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=== DNA/RNA ===
* [http://mekentosj.com/enzymex/ EnzymeX] (restriction enzyme analysis + info)
* [http://mekentosj.com/enzymex/ EnzymeX] (restriction enzyme analysis + info)
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* [http://mekentosj.com/4peaks/ 4peaks] (simple sequence viewer)
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* [[ApE - A Plasmid Editor (software review)|ApE - A Plasmid Editor (free, multi-platform)]]
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* [[Gene Construction Kit software review|GCK - Gene Construction Kit ($€¥ Mac)]]
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* [http://www.clcbio.com/products/clc-sequence-viewer/ CLC Sequence Viewer (free, multi-platform)]
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<font size="3" color="#000000"><b>Quotes</b></font>
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:name (1999-2000)
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=== Graph/Diagram software ===
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* Grace (runs on Mac's XWindow) - WYSIWYG 2D plotting tool [http://plasma-gate.weizmann.ac.il/Grace/]
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* GraphPad Prism (Mac/Win) - basic biostatistics, curve fitting and graphing [http://www.graphpad.com/prism/Prism.htm]
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* IGOR (Mac/Win) - 2D/3D graphs and stats [http://www.wavemetrics.com/]
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* KaleidaGraph (Mac/Win) graphing and data analysis [http://www.synergy.com/]
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* for more see here [http://www.dmoz.org/Science/Math/Software/Graphing/]
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=== Unix (and OS/X!) Bio Developer Tools ===
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* [http://eclipse.org Eclipse] - Programming environment, editor, etc for Java, Perl, C, ...
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* [http://bioperl.org BioPerl] - File conversion, sequence analysis, database searches, graphics, ..
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* [http://biopython.org BioPython] - File conversion, sequence analysis, database searches, graphics, ..
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* [http://biolib.open-bio.org BioLib] - File conversion, sequence analysis
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* [http://www.graphviz.org/ Graphviz] - Text command language for vector graphics.  Very good OS/X version too.
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<font size="3" color="#000000"><b>Recommended Links</b></font><br>
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Topic
 
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Topic:
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=== Quotes ===
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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.
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:Cabel Sasser, 2006
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All programmers are playwrights and all computers are lousy actors.
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:Unknown
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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.
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:unknown, 1949
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To err is human--and to blame it on a computer is even more so.
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:Robert Orben
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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.
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:Stephen Hawking
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=== Recommended Links ===
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Mac biosoftware lists
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* [http://www.apple.com/science/software/lifescience.html Apple's list of life science software]
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* [http://mackeeper.zeobit.com/mac-encryption mac encryption] powerful multifunctional system utility for Mac OS
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General software databases:
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* [http://osx.iusethis.com/ i use this], especially [http://osx.iusethis.com/tag/scientific scientific software]
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** super useful is the freeware [http://metaquark.de/appfresh/ AppFresh] that works with the [http://osx.iusethis.com/ i use this] website
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* [http://www.versiontracker.com/macosx/ versiontracker], esp. [http://www.versiontracker.com/macosx/home-edu/math-scientific Math/Science category]
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=== Tips and tricks ===
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* [[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.
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* Using [http://openoffice.org OpenOffice] you can save any file to wikitext.
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Current revision


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.

Text processing


Reference management


DNA/RNA


Graph/Diagram software

  • Grace (runs on Mac's XWindow) - WYSIWYG 2D plotting tool [1]
  • GraphPad Prism (Mac/Win) - basic biostatistics, curve fitting and graphing [2]
  • IGOR (Mac/Win) - 2D/3D graphs and stats [3]
  • KaleidaGraph (Mac/Win) graphing and data analysis [4]
  • for more see here [5]


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.

Add a section

  • add an item

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


Recommended Links

Mac biosoftware lists

General software databases:

Topic:

  • add link


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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