Arcadia
It says: Arcadia is a light-weight, cross-platform, C++ desktop application designed for visualizing biological networks such as metabolic pathways.
License: Freeware, Source code available
http://sourceforge.net/projects/arcadiapathways/
BD CellQuest Pro
Software for displaying and analyzing flow cytometry (FACS) data
License: Commercial
BD FACStation
Software for displaying and analyzing flow cytometry (FACS) data. Software CD contains BD CellQuest Pro, BD FACSComp, BD Worklist Manager, BD Loader Manager, and BD Plate Manager applications.
License: Commercial
http://www.biocompare.com/12104-Equipment/854415-BD-FACStation-v60x-for-Mac-OS-X/
CellDesigner
It says: CellDesigner is a modeling tool of biochemical networks with graphical user interface. It is designed to be SBW (Systems Biology Workbench) compliant, and support SBML (Systems Biology Markup Language) format.
License: Freeware
http://systems-biology.org/software/celldesigner/
ChemSpotlight
It says: ChemSpotlight is a Spotlight metadata importer plugin for Mac OS X, which reads common chemical file formats using the Open Babel chemistry library.
License: Freeware
http://chemspotlight.openmolecules.net
Cytostream
It says: A graphical user interface for the automated analysis of flow cytometry (FACS) data.
License: Commercial
https://code.google.com/p/cytostream/
EasyChem
It says: EasyChem is designed to draw chemical molecules in an intuitive way, with a very high quality. Exporting is done to various formats.
License: Freeware, Source code available
http://sourceforge.net/projects/easychem/
Edinburgh Pathway Editor
It says: Edinburgh Pathway Editor is a visual editor for Systems Biology. It allows you to draw Graphical Notations commonly used in Systems Biology.
License: Freeware, Source code available
http://epe.sourceforge.net/SourceForge/EPE.html
Escape Medical Viewer
EMV 4 is an elegant, robust and lightweight DICOM viewer, anonymizer and converter for MacOS. Can also be used for basic analysis of echocardiographic data.
License: Commercial, Trial available
http://www.escape.gr/dicom/emvmac.html
Heart Pro
imedicalapps.com: Heart Pro III app is a cardiac anatomy masterclass with uses for physicians and students alike. Heart Pro III allows a detailed look at the anatomy of the heart from a range of perspectives while including detailed anatomical information and a range of animations among other features.
License: Commercial
http://applications.3d4medical.com/heart_pro
iNMR
It says: iNMR can do all the things you expect from a traditional NMR program (and ten times more).
License: Commercial, Trial available
Lab Assistant
Digital Lab book. It says: Lab Assistant helps you organize your experiments. No scientist should be without this.
License: Freeware
http://nucleobytes.com/index.php/labassistant
MarvinBeans
It says: Powerful and fast sketching of molecules, queries and reactions. Characterizing molecules directly on the canvas. Visualizing attractive 2D & 3D structures accurately.
License: Freeware, but you need to register
http://www.chemaxon.com/download/marvin-suite/
mMass
Open Source Mass Spectrometry Tool
License: Freeware, Source code available
MZmine 2
It says: A framework for differential analysis of mass spectrometry data.
License: Freeware, Source code available. Needs Java to run.
http://sourceforge.net/projects/mzmine/
OpenChrom
It says: OpenChrom is a tool for gas chromatography and mass spectrometry. The focus is to handle data files from different GC/MS and GC/FID systems and vendors. Its functionality and algorithms can be extended using a flexible plugin approach, based on Eclipse RCP.
License: Freeware, Source code available.
http://sourceforge.net/projects/openchrom/
OpenMS
It says: An open source framework for LC-MS based proteomics. OpenMS offers datastructures and algorithms for the processing of mass spectrometry data. The library is written in C++.
License: Freeware, Source code available.
http://sourceforge.net/projects/open-ms/
Papers
Is a reference management software for organizing scientific papers and citations. For a comparison of reference management software see this list.
License: Commercial, Trial available
PhysioDesigner
It says: PhysioDesigner is an open platform that supports multilevel modeling of physiological systems in the field of integrated life sciences and systems biology, including physiology and neuroscience. Users can combine and build mathematical models of biological and physiological functions on PhysioDesigner.
License: Freeware
ProteinGlimpse
It is powered by Jmol, a free, open source Dashboard molecule viewer.
License: Freeware
http://www.apple.com/downloads/dashboard/reference/proteinglimpse.html
Protein-ms
It says: Tools for mass spectrometry, especially for protein mass spectrometry and proteomics.
License: Freeware, Source code available.
http://sourceforge.net/projects/protms/
Sparky
It says: Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.
License: Freeware, Source code available
http://www.cgl.ucsf.edu/home/sparky/
Structural
It says: This handy little application calculates the molecular weight of a molecule from it’s empirical formula. It has over a hundred preset compounds, which can be added to.
License: Freeware
http://totlandweb.info/Applications/Structural/
Virtual Cell (VCell)
It says: The Virtual Cell is a software modeling environment for quantitative cell biological research. Users can create simple or complex multi-layered models with a Java web-based interface. Distinct biological and mathematical frameworks exist within a single graphical interface designed for experimental cell biologists or theoretical biophysicists..
License: Freeware, but you need to register
http://www.nrcam.uchc.edu/vcell_software/login.html?current=two
VisANT
It says: Integrative Visual Analysis Tool for Biological Networks and Pathways.
License: Freeware, but based on Java