(For those new to the column, Forward Migration is our term for companies moving from Wintel machines to Macs — or at least adding or increasing the number of Macs they use. A forward migration kit is an overview of Mac OS products for a particular occupation, such as dentistry, accounting, etc.)
This is the second part of our three-part series on biogtechnical software for the Mac platform. The products mentioned were found at Apple’s Macintosh Products Guide (an invaluable resource that you should check out) or sent to us by MacCentral readers.
Ambicode for Mac OS X
is an editor for selecting subsets of genetic code and choosing wobble amino acids with reduced degeneracy. It’s useful to design random oligos with particular amino acid representation — or so I’m told (I don’t do much of that sort of thing myself).
Advanced Biosystems (ABI), formerly known as Perkin-Elmer, use Macs to control many of their systems, such as automated DNA sequencers and quantitative PCR machines. The software they provide (such as Primer Xpress for oligonucleotide primer design and GeneScan Analysis analyzes data to size and quantitate DNA fragments) is
worth a look.
makes several products for the Mac, including GeneJockey, a user-friendly sequence editor/analyzer. MacCentral readers praised it as being quick and requiring little RAM (less than 4MB).
is the well-known software devoted to the control of Fluorescence Associated Cell Sorter (FACS) apparatus. It was developed on a Mac by Becton Dickinson.
is software suite that includes such components as ChemDraw, Chem3D, ChemFinder, ChemInfo and E-Lab Notebook, all designed to transform your Mac “into a chemical publishing, modeling, and database workstation.”
is a chemical structure visualization plug-in for Internet Explorer and Netscape Communicator. Users can draw structures with ISIS/Draw and visualize them in 2D or 3D.
is a helper application for your Web browser that allows you to view 3-dimensional structures from NCBI’s Entrez retrieval service.
is sequence analysis software. It’s a comprehensive software suite with integrated BLAST and Entrez searching. DNAStar’s analysis tools include Contig Assembly, Gene Discovery, Primer Design, Alignment, Restriction Mapping, and Protein Structure.
lets you view and edit trace files (electropherogram data).
FCS Assistant and FCSPress are both from
FCSPress.com. FCS Assistant is a utility program that lets you edit Flow Cytometry Standard (FCS) files and export data from them. FCSPress lets you produce presentation quality graphics and generate statistics from your flow-cytometric data.
is an analytical workbench that enables scientists to visualize and manipulate gene expression data. Experimental data from microarrays, Affymetrix chips, SAGE, or any technique that associates numbers with genes can be imported for analysis.
The Genetics Computer Group makes a GCG analyzing system that was developed originally for UNIX, then implemented to be used by any platform via a Web browser under a UNIX server. Supposedly, it will be soon available for Mac OS X.
Genotyper Analysis Software and Genotyper Software
are tools for genotyping with Human Identification (HID) casework, databasing, and linkage mapping applications.
Intelligent Imaging Innovations
offers two products worth checking out. SlideBook is a powerful and user-friendly image processing software package, specifically designed for multi-dimensional digital microscopy, according to Daniel Dvorkin of Intelligent Imaging Innovations. SlideBook includes an image database as well as tools for processing, analysis and visualization, he told MacCentral. It’s a modular package that allows the user to purchase specific functionality as required.
The company also makes Purple De-Haze for Adobe Photoshop, an under-$500 plug-in for no-neighbors deconvolution of microscopic images, Dvorkin said. Purple De-Haze offers highly customizable configurations to conform to almost any combination of lenses, microscopes, cameras, and media. Owners of Purple De-Haze are also entitled to substantial discounts on other Intelligent Imaging Innovations products.
has agarose/acrylamide gel analysis software for both the Mac and Windows platforms, said Andy Fleisher of the University of California at Davis. “My lab uses the PC version of the Kodak software,” he said. “The lab I used to work in only used Macs, and we used the Applied Biosystems Sequence Analysis software and software from Biorad (http://www.biorad.com) for an ELISA plate reader machine.”
is a 2D/3D motion analysis system that includes software, MacReflex CCD camera and MacReflex video processor. The software collects data from the video cameras and performs automatic sorting and tracking of the video data for use in both human engineering and industry. The data is further processed in an application program of your choice. The video processor connects to the modem port.
is a software package for standard DNA sequence analysis for the molecular biology laboratory. MacVector is a native Mac application that integrates Internet database searches.
is often used for genetic linkage analysis.
is a free, Mac-only package for image analysis and graphing. “I work at a biotech start-up, and I have biologists constantly using my G4 for NIH-image work,” Aaron Rafael said.
Molecular Biology Insights
is a multi-functional program that searches for, analyzes, and selects oligonucleotides for PCR, sequencing, site-directed mutagenesis, gene synthesis, and various hybridization applications. It calculates melting temperature, secondary structure of oligonucleotides, PCR optimal annealing temperature, and priming efficiency based on nearest-neighbor thermodynamic values and other algorithms developed experimentally.
from Okanagan University College lets you view molecular models from chemistry. There are over 1,400 molecular models in PDB format.
Next week: part III.