(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 third and final part of our 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.
BioDiscovery is an image analysis software for the DNA chip market. It analyzes images from the scannned DNA arrays, which are printed either on nylon membranes or glass slides.
Gene Codes Corp. is a DNA sequencing and analysis software package. It has been on the Mac for 10 years.
SeqPup is a biological sequence editor and analysis program. It includes links to network services and external analysis programs.
Signals and Systems for Mathematica by
Wolfram Research Inc. analyzes signals, designs filters, and performs routine signal processing operations. Built-in tools simplify tasks that involve linear transforms, standard signal representations, and visualization. It performs algebraic manipulations on signals and systems to derive, analyze, improve, and implement new algorithms.
SoftPump Syringe Pump Control Software by
World Precision Instruments provides a graphical user interface for defining protocols for introducing fluids to, and extracting fluids from, laboratory animals.
Spike2 for Macintosh by
Cambridge Electronic Design captures event and waveform data to hard disk with simultaneous output of control pulses, steps, ramps and sinewaves. A flexible analysis environment allows multiple windows for both raw and processed data, with simultaneous data acquisition and analysis. Spike processing options includes INTH, PSTH and RATE histograms and correlations.
Caesar Software LLC helps provide a well-organized and comprehensive description of each strain’s characteristics, easy retrieval of strain information, and the ability to publish the strain database on the Worldwide Web.
Swiss-PdbViewer is an application that provides a user-friendly interface allowing you to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts.
Vector NTi is an integrated database and analysis program for biotech and molecular biology, including DNA, protein, 3D structure database searching, and more. It’s distributed by
InforMax, who also develop a free DNA vector display utility called Vector NTi Viewer.
Visible Human CD Collection by
Research Systems is a digital photographic reference for exploring human anatomy, equipping medical researchers, practitioners and educators. More than 20,000 image slices from a human male and female are compressed for convenient access onto two CD-ROMs.
We’ll conclude our series with comments and product announcements from MacCentral readers.
PE ABI makes a peptide synthesizer that runs on the Mac. However, it’s a “funny machine,” according to Daniel Harrington.
“From what we can tell, it runs through a modem-type connection (they’ve used the same software and interface for a very long time),” he said. “So it’s funny to see a recent PMac come with the system — it’s really overkill. Regardless, this machine is the absolute standard for peptide synthesis, and is enormously useful to people who study these molecules. It saves a huge amount of synthesis time.”
Several folks are also excited about the new UNIX abilities of Mac OS X and what these will make possible in respect to scientific software for the Mac.
“Some months ago I tried to purchase a commercial molecular sequence analysis program, but the purchase luckily failed as the company could not provide a local distributor in Thailand,” Rudi Grams told MacCentral. “Now Mac OS X gives me the chance to run UNIX-based software that can do the same task as the commercial package, but for free.”
He urges interested parties to have a look at the
EMBOSS program suite. No Mac OS X compatibility is mentioned, but Grams said he has it up and running on his Cube, though it took some time to get it correctly installed.
In fact, now that Mac OS X is out, various other packages — traditionally the preserve of high-end UNIX servers — have been ported/compiled, we’re told. Of these BLAST is probably the best known. Wu-blast and NCBI-blast have both been ported and/or compiled cleanly from the source code. Bill van Etten has also ported hmmer (which looks for domains within a sequence) and the NCBI toolkit (which also contains NCBI-blast). Other packages can be found in the
Softrak software repository of Stepwise, under the OS X science section.
Jan Morren of the Labo Moleculaire en Vasculaire Biologie said their spreadsheet software of choice is DeltaGraph rather than Excel because the former is better at plotting for publications.
“Some of us still use SigmaPlot, but this has no support for newer Mac OS versions,” she said.
Ted Sobel, chief software architect of
Electrical Geodesics said they use Macs as the base for their dense array EEG system.
Don Briggs said he’s developing a data analysis application suitable for flow cytometry. It’s a Cocoa/Objective-C application.
Alas, some readers also reported a bit of discouraging news. Applied Biosystems (formerly known as Perkin-Elmer) supplied Mac-based DNA sequencers and other high-end molecular biology hardware with Macs to run them and Mac software for data analysis (including DNA sequencing, DNA fragment analysis, quantitative PCR, and primer design). While they still support this hardware and software, all their new equipment is using Windows NT software, according to Daniel E. Sabath, M.D., Ph.D., University of Washington Department of Laboratory Medicine.
This transition has been the “single biggest loss over the past several years,” according to Robin Colgrove, medical researcher and long time Mac and UNIX user. He told MacCentral that the move was a “major headache” for his Mac/UNIX lab.
“I have been on their case about this, but am making no headway,” he said. “I have been trying to make the case to them that the open nature of Darwin in Mac OS X would be a much better base for their software, but the suits do not want to listen. Given the importance of biotech, this is a big big loss if it cannot be reversed, and pressure from potential buyers may help keep their software cross-platform.
The software in question is Sequence Analysis (which comes in several versions) and the hardware is Applied Biosystems’ new capillary electrophoresis sequencing machines, which so far only run NT. The client version of Sequence Analysis still run on Macs (so far, anyway), but there are major file translation problems, said Colgrove.
Some Web sites worth checking out are the
Macs in Chemistry page, the
National Center for Biotechnology Information,
Prot3D, and the
MGC-Department Cell Biology and Genetics Center for Biomedical Genetics Erasmus University.
Finally, some folks mentioned products for which I could find no ULR, including DNA Inspector, Phyllip (for phylogenetic analysis), AutoAssembler, CAD Gene, and DNASIS-Mac.
If you don’t see your favorite product here, please check
part 1 and