Biosoftware for Mac: Difference between revisions

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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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<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]]
<font size="3" color="#000000"><b>Text processing</b></font>
* [[Getting started with LaTeX on a Mac]]
* background: [[LaTeX]], [[Word vs. LaTeX]]
* [[Word vs. LaTeX]] side by side comparison
* [[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)




<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)
* [https://sourceforge.net/projects/skim-app Skim] (PDF reader and annotation programme, free)
* [[Skim - PDF reader and annotation software]] (free)
* add here
* [[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>
=== DNA/RNA ===
* [http://openwetware.org/wiki/Genome_compiler Genome Compiler (free, multi-platform)]
* [http://mekentosj.com/enzymex/ EnzymeX] (restriction enzyme analysis + info)
* [http://mekentosj.com/enzymex/ EnzymeX] (restriction enzyme analysis + info)
* add here
* [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)]]
* [[Gene Construction Kit software review|GCK - Gene Construction Kit ($€¥ Mac)]]
* [http://www.clcbio.com/products/clc-sequence-viewer/ CLC Sequence Viewer (free, multi-platform)]
 
 
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=== Graph/Diagram software ===
* Grace (runs on Mac's XWindow) - WYSIWYG 2D plotting tool [http://plasma-gate.weizmann.ac.il/Grace/]
* GraphPad Prism (Mac/Win) - basic biostatistics, curve fitting and graphing [http://www.graphpad.com/prism/Prism.htm]
* IGOR (Mac/Win) - 2D/3D graphs and stats [http://www.wavemetrics.com/]
* KaleidaGraph (Mac/Win) graphing and data analysis [http://www.synergy.com/]
* for more see here [http://www.dmoz.org/Science/Math/Software/Graphing/]
 
 
 
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=== Unix (and OS/X!) Bio Developer Tools ===
* [http://eclipse.org Eclipse] - Programming environment, editor, etc for Java, Perl, C, ...
* [http://bioperl.org BioPerl] - File conversion, sequence analysis, database searches, graphics, ..
* [http://biopython.org BioPython] - File conversion, sequence analysis, database searches, graphics, ..
* [http://biolib.open-bio.org BioLib] - File conversion, sequence analysis
* [http://www.graphviz.org/ Graphviz] - Text command language for vector graphics.  Very good OS/X version too.
 
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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.
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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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.
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
:Stephen Hawking
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=== Recommended Links ===
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<font size="3" color="#000000"><b>Recommended Links</b></font><br>


Mac biosoftware lists
Mac biosoftware lists
* [http://www.pure-mac.com/science.html Pure Mac's list of software for natural sciences]
* [http://www.apple.com/science/software/lifescience.html Apple's list of life science software]
* [http://www.apple.com/science/software/lifescience.html Apple's list of life science software]
* [http://www.macinchem.fsnet.co.uk/macosx.htm Macs in chemistry software listing]
* [http://mackeeper.zeobit.com/mac-encryption mac encryption] powerful multifunctional system utility for Mac OS
* add a link


General software databases:
General software databases:
* [http://osx.iusethis.com/ i use this], especially [http://osx.iusethis.com/tag/scientific scientific software]
** super useful is the freeware [http://metaquark.de/appfresh/ AppFresh] that works with the [http://osx.iusethis.com/ i use this] website
* [http://www.versiontracker.com/macosx/ versiontracker], esp. [http://www.versiontracker.com/macosx/home-edu/math-scientific Math/Science category]
* [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 ===
* [[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 [http://openoffice.org OpenOffice] you can save any file to wikitext.
 
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Latest revision as of 05:24, 5 November 2015


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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