Missing Mac OS 9 functionality in Mac OS X? Check out Adam’s roundup of Mac OS X utilities that replace that Mac OS 9 look-and-feel. Mark Anbinder covers Apple’s Macworld Tokyo announcements of a 23" LCD display, a 10 GB iPod, Bluetooth support, and iMac price increases. Then Gideon Greenspan joins us with an overview of how computers are used in biology. Finally, two important Mac OS X releases fill out the issue: Retrospect 5.0 and Mailsmith 1.5.
Retrospect 5.0 Backs Up Mac OS X — Dantz Development is shipping Retrospect 5.0, which runs on either Mac OS 9 or Mac OS X and can back up and restore both operating systems. Although the Herculean task of supporting full backup and restore of Mac OS X-based Macs prevented Dantz from adding significant new features in Retrospect 5.0, it does include other welcome changes. File backup sets are no longer constrained by resource fork size limitations, so you can realistically use hard drives as backup media; files larger than 2 GB can now be backed up; and more backup devices are supported (including all currently shipping Apple optical drives). Retrospect ships in four different versions, each with different capabilities and prices. All versions are available immediately from Dantz; resellers should have them soon. French, German, and Japanese localized versions are scheduled for release in the second quarter of 2002, and international users can upgrade an English version purchased now to the corresponding localized product for free when it becomes available. [ACE]
Mailsmith Joins Native Email Clients — Mac OS X users looking for a powerful email application to replace Apple’s bundled Mail program can now add Bare Bones Software’s Mailsmith 1.5 to the list of choices. New features in Mailsmith 1.5 include one-step filter creation, support for draft messages, approximate text translation of HTML messages, random signature support, the capability to display image and movie attachments within Mailsmith, a Glossary feature for inserting frequently used bits of boilerplate text, improved scripting and grep functionality, keyboard assignments for scripts and stationery, and more. Upgrades from previous versions of Mailsmith cost $40 (free for copies purchased in 2002); the program retails for $100, with a limited-time discount price of $70 until 31-May-02, after which it will be replaced with an $80 price for owners of BBEdit, Emailer, or Eudora. A free demo is available as an 8.2 MB download. [ACE]
Palm Desktop 4.0 Released — Palm, Inc. today made Palm Desktop 4.0 for Macintosh available as a free download. The new version adds Mac OS X compatibility, support for records marked private, and the capability to import and export vCard and vCal files. (As a quick example of vCard use, you can drag a contact’s title bar icon directly to the Contacts folder of a mounted iPod to add it to the rudimentary address book feature added in last week’s iPod 1.1 software update.) Palm Desktop 4.0 is a 10 MB download.
TidBITS Moves Up in Best of Mac Web Survey — In the Low End Mac Web site’s third Best of the Mac Web survey, TidBITS moved up from 5th to 3rd in user ratings. As with the last time, we came in behind VersionTracker and As the Apple Turns, but in this installment of the survey, we managed to move past MacSurfer’s Headline News and MacFixIt, which fell to 10th place (Low End Mac speculated the drop may be due to MacFixIt’s new subscription model). Other notable changes include the rise of the Mac Minute news site from 11th to 6th place, and the drop of The Mac Show from 15th to 50th after the loss of Shawn King, whose new Your Mac Life radio show ranked 18th. Although the Best of the Mac Web survey is an unabashed popularity contest, the more times it occurs, the more the changes from one survey to another prove interesting. Thanks to all of you who voted in this installment of the survey! [ACE]
Apple CEO Steve Jobs last week unveiled two new products in his keynote address at Macworld Expo in Tokyo. A new 23-inch Apple Cinema HD Display with 1920 x 1200 resolution joins the company’s existing LCD flat-panel displays and will sell for $3,500 when it becomes available next month. (In contast, the 22-inch Apple Cinema Display, still available for $2,500, offers a mere 1600 by 1024 resolution.) The company says the new display’s resolution will allow editing of HDTV (high definition television) digital video "with room to spare." At the same time, Apple introduced a more capacious iPod, a $500 version of the portable MP3 player with a 10 GB internal hard drive, available immediately. The existing 5 GB model remains available for $400. For an extra $50, either model can be personalized at the Apple Store with laser engraving of two lines of text containing up to 27 characters each.
Jobs also previewed Apple’s upcoming support for Bluetooth. The short-range wireless communication technology is intended to link personal electronic devices such as computers, cell phones, and personal digital assistants when they’re in close proximity. Promising "a Bluetooth solution that actually works and is easy to use," Jobs said that, in early April 2002, Mac OS X users will be able to download free preview software from Apple’s Web site for use with the D-Link USB Bluetooth adapter, itself to be offered at the Apple Store for $50. Apple’s Bluetooth software will automatically recognize other Bluetooth devices that come into range and offer to connect to them.
At the same event, Jobs made the surprise announcement that, effective 21-Mar-02, current flat-panel iMac configurations have increased in price by $100; orders placed prior to that date retain the price at the time of order. Citing rising component costs for memory and flat-panel screens, Jobs defended the price hikes as a better alternative to keeping the original pricing but reducing features. Given the demand for the new iMac, we don’t see the price increase as a deal-killer: Apple says it has shipped 125,000 new iMacs since the model’s introduction in January and is now shipping 5,000 iMacs per day.
Everyone knows that the group that’s by far the most important to Apple is composed of small utility developers. Several years back, Apple saw that the Mac market was stagnating because almost every conceivable utility had already been developed. Realizing drastic resuscitation measures were necessary, Apple moved quickly to replace the Mac OS with the NeXTstep-based Mac OS X, hoping to give Mac developers the opportunity to restore Mac OS 9 functionality to Mac OS X and further extend Mac OS X’s limited interface, to draw Unix hackers into the Mac camp, and to provide a market for all seven NeXT utility developers.
Sarcasm aside, the number of utilities available for Mac OS X has indeed mushroomed of late. In preparing for this article, we turned to TidBITS Talk for recommendations, and the response was overwhelming – so much so that we’ve decided to publish a group of articles on the topic; this one will focus on utilities that restore Mac OS 9 functionality to Mac OS X. Read through the TidBITS Talk discussion for an unfiltered view of what’s coming up.
Without further ado, here are the top utilities for restoring Mac OS 9 functionality to Mac OS X, though please note that these are not intended to be full-fledged reviews – we simply don’t have enough experience with each utility. If we’ve missed your favorite utility, bring it up on TidBITS Talk.
WindowShade X — The windowshade functionality that’s been in the Mac OS since System 7.5 actually dates back to an independent control panel for System 6 from Robert Johnson. Double-click a window’s title bar or click the collapse box and the window "rolls up" into the title bar. You can still position the title bar anywhere on screen; it’s an efficient way to reduce the space taken up by windows. Mac OS X eliminated this approach in favor of minimizing windows to Dock icons. Unfortunately, Mac OS X’s approach fills up the Dock quickly, and it can often be difficult to distinguish between different minimized windows. But with Unsanity’s WindowShade X, you get everything Mac OS 9 could do and more. There are four methods of invoking WindowShade X (the minimize button, double-clicking the title bar, Control-double-clicking the title bar, and pressing Command-M), and each method can cause a window to minimize to the Dock, roll up into the title bar, make the window transparent, or hide the application. Although you can control the opacity of windows made transparent, I find that option, like almost all other transparent interface features in Mac OS X, utterly annoying. WindowShade X is $7 shareware, and it’s a 374K download.
ASM & X-Assist — In Mac OS X, Apple tried to do too much with the Dock, making it serve as an application launcher, list of running applications, and more. Mac OS 9 broke those features out, and in particular, the list of running applications was always tucked away in the menu bar’s application menu. In Mac OS X, the clock and other menu bar icons take over that space until you install ASM or X-Assist, both of which return the application menu to the upper right corner. In ASM’s preferences panel, you choose whether it should show as an icon or a menu title, or both, and how much space the menu should take up. Other settings control how the contents of the ASM menu appear, what special commands (such as for hiding and showing applications) appear, and so on. Most important, it offers a return to Mac OS 9’s window layering, which ties all of an application’s windows together, so clicking one brings them all to the front (that happens in Mac OS X only if you click the application’s Dock icon or switch applications using Command-Tab). ASM also offers a Single Application Mode that hides all applications other than the current one. X-Assist replicates most of ASM’s feature set and offers two additional features: the capability to display a user-defined hierarchical menu of files, folders, and disks (much as you can do in Mac OS 9’s Apple menu), and support for special plug-ins (the included samples can set the Mac’s volume and play MP3 files). Though both appear to work, several people have said that they found ASM more stable. ASM author Frank Vercruesse asks for donations if you like ASM, which is a 354K download for version 2.0.2; X-Assist is free and is a 291K download.
FruitMenu & Classic Menu — The Apple menu has been a fixture of the Mac OS for years, and although Apple wisely kept it in Mac OS X, it’s a shadow of its former customizable self. Two utilities, Sig Software’s Classic Menu and Unsanity’s FruitMenu, recall the old days. Classic Menu is the simpler of the two; it merely displays the contents of the Classic Menu Items folder located in your Library folder’s Preferences folder. Populate it with aliases to files, folders, and disks, and you’ll have something that works much like the old Apple menu when you click on the Apple menu icon itself. Other helpful menu items add aliases of selected items to the Classic Menu Items folder, open that folder in the Finder, and let you select a different folder to use. Access the default Mac OS X Apple menu (which has useful commands like Log Out and Restart) by clicking right next to the Apple menu icon. Although FruitMenu provides the same functionality as Classic Menu, it more closely resembles Power On Software’s Action Menus in providing a preference panel for arranging your Apple menu and offering custom items not normally available, such as one that displays your current IP address. Overall, FruitMenu feels a bit more powerful, and it’s only $7 shareware, compared to Classic Menu’s $10, but both will do the job. FruitMenu 1.5.2 is a 481K download; Classic Menu is a mere 43K download.
SharePoints — In Mac OS 9, you could share any particular folder you wanted, and you could create users and groups that would have access to different folders. That functionality, though present under the hood in Mac OS X, wasn’t easily accessible until the release of SharePoints. Operating either as a stand-alone application or as a preferences panel, SharePoints lets you share any given folder and create users who can access specific shared folders but who cannot login via Telnet or SSH and who lack home directories. As a small bonus, SharePoints lets you specify a custom message to be displayed to users on connection. The author asks that for donations if you like SharePoints; SharePoints 2.0.4 is an 824K download.
Xounds — Although Apple has only dabbled in interface sounds, the sound effects for interface actions available from the Appearance control panel were effective at providing an additional dimension to using the Mac OS. Those disappeared in Mac OS X, but Unsanity’s Xounds can bring many of them back again. Xounds offers to import existing sound sets (though importing a third-party set and switching between it and the sounds from Mac OS 9 caused Xounds to stop working until I reinstalled Xounds), and provides roughly the same level of control as you had in Mac OS 9. You can choose to play sound effects associated with menus, windows, controls, and the Finder, although dragging sounds aren’t yet supported. Xounds 1.1.2 is a 384K download; it’s $7 shareware and works for only an hour per login if left unregistered.
Next Up — Keep in mind that I chose these utilities based purely on the fact that they returned features to Mac OS X that existed in a stock installation of Mac OS 9. In future installments in this series, I’ll look at utilities that extend Mac OS X’s new features in useful and interesting ways, utilities that bring to Mac OS X features that independent developers had added to Mac OS 9, and utilities that bring Mac OS X’s Unix underpinnings into the light of Aqua.
Those of us with even a passing interest in science are used to the idea that computers play a central role in understanding physics and chemistry, especially high-powered computation used in areas such as weather prediction and molecular visualization. However, over the past few years, a new target for that computation has emerged and begun to attract media attention. It’s called computational biology (or more catchy, bioinformatics) and it refers to the digital storage, categorization, and analysis of biological data.
If your most recent encounter with biology took place in high school, you may be surprised by any such crossover with computing. Although I always found it fascinating, I remember biology never quite having the rigor of its counterparts in the science curriculum. Some cells did this, other cells had that, and different organisms did all sorts of strange things, especially when dissected by over-enthusiastic schoolchildren. But there seemed to be few universal principles equivalent in scope to Newton’s equations or the periodic table of elements.
Digitizing Life — Thanks to the wonders of molecular biology, many such fundamentals are now known to exist. An overview of some of the basics should give an impression of what is involved – bear in mind that we’re dealing with the natural world in all its complexity, so everything that follows has been vastly simplified.
Life as we know it is encoded in a set of long molecules called DNA, identical copies of which are found in every cell in a living organism such as a human being. Everything that happens within an organism can be traced back to its DNA – just like the hard disk in a computer. In humans, each cell contains 46 separate DNA molecules called chromosomes, analogous perhaps to hard disk partitions. Your chromosomes contain a mixture of information duplicated from those of your parents, which is one reason why you inherited so many of their characteristics.
Any one DNA molecule consists of a series of connected nucleotides forming a chain that can run to lengths of many millions. There are only four possible nucleotides, so any DNA molecule can be represented as a sequence using only four letters. This is where the digitization begins – the entire set of chromosomes for a human being can be stored in a few gigabytes of space (even less after compression) and you can even download a recent draft to your own computer.
According to present-day understanding, only a fraction of your DNA has a purpose – the other 98 percent or so is affectionately named "junk." The meaningful bits, known as genes, are short stretches scattered unevenly throughout the chromosomes (think of them as fragmented program files, if you like). They can be pretty hard to find – we currently have confirmed the existence of about 15,000 human genes, but scientists are still bickering over the total number – most estimates lie around 30,000. There’s even a sweepstakes where you can add your own guess.
Genes are interesting because machinery in the cell translates them into another type of molecule called proteins. These proteins perform the organism’s real metabolic work and can be thought of as currently running programs. A protein molecule contains a series of connected amino acids forming a chain, similar to how nucleotides make up DNA. However, in contrast to DNA, proteins are made from 20 different amino acids and are rarely more than a few thousand such elements in length. Sequences of proteins are another type of digital data that bioinformatics regularly deals with.
How are these proteins able to do all the work set out for them: building cells, transporting materials, sending signals and carefully managing each cell’s energy factory? When released into a cell’s watery innards, proteins fold up upon themselves, forming a huge variety of shapes that make them connect to other proteins and molecules in specific ways, catalyzing any number of chemical reactions. Trying to work out which shape a particular protein sequence will fold into is an extremely difficult problem. A biannual contest called CASP (a shortened acronym for Critical Assessment of Techniques for Protein Structure Prediction) is held between different research groups around the world, and IBM is building its fastest ever supercomputer to work on it, at a hoped-for rate of no more than one protein per year.
Again, this is just a basic overview. If you’re thirsting for more information on molecular genetics, the U.S. Human Genome Project has published a good online primer.
Open-Sourcing the Human Being — With the basic biology lesson out of the way, let’s talk about how bioinformatics applies to the real world. One bioinformatics application you’ve probably heard of is the Human Genome Project. Its seemingly simple goal is to read the roughly three billion nucleotides that make up the human set of chromosomes. This is made possible by the fact that, even though there are millions of points at which healthy human DNA sequences can differ from one another, every one of us is identical in the other 99.9 percent of points. If you find that scary (or perhaps inspiring), remember that your DNA is also about 99 percent identical to the chimp at your local zoo.
Discussions on the genome project began in 1984, but it was not until 1995 that the work began in earnest via an international collaboration of publicly funded laboratories in the United States, United Kingdom, France, Japan, Germany, and China. The public project moved along slowly until 1999 when Celera Genomics, a private venture, joined the fray. Armed with an improved experimental method and gobs of computing power, Celera promised to complete a first draft of the genome within a year. After much politicized mud slinging, a deal was made and the two groups’ results were published simultaneously in February 2001.
What does all this have to do with bioinformatics? For a start, computers were required to store and index the resulting sequences and make them available to researchers around the world over the Internet. But the real algorithmic problem stemmed from the way in which DNA molecules have to be read. In the biological world, there is no such thing as a debugger which lets you freeze a cell and poke around inside, observing and manipulating at will. Instead, a series of steps must be cleverly combined for a scientist to gain access to a desired item of information.
For any DNA molecule, only about the first 1,000 nucleotides can be ascertained using available laboratory techniques. Longer sequences are scanned by making several copies of the molecule and breaking these up randomly into short fragments, each of which is read separately. The original order of these fragments is lost, so, after reading them, there remains the task of reconstructing the original sequence. It’s not unlike trying to rebuild an encyclopedia using a few photocopies which have been run through an office shredder – the number of possibilities to be tried is vast. Forget about trying to do it by hand – Celera’s draft build required about a week of running time on a 56-processor array with over 100 GB of memory.
The Human Genome Project is a classic example of a bioinformatics problem, and scientists are hopeful that the results will have many practical effects. An immediate consequence is increased speed in the development of new medicines by enabling scientists to hone in quickly on potential drug target genes. It can also be expected to lead the way to personalized health care, as relationships are discovered between the genetic variations that exist between human beings and our susceptibility to certain diseases or treatment responses.
In the distant future, it opens up the possibility of curing disease and even tweaking ourselves through direct manipulation of our DNA. Naturally, the ethical issues raised are daunting and could wreak havoc with our basic notion of what it is to be a human being. However, this is also an area where the field of bioinformatics will shine: the storage, categorization, and analysis of the data promises to better inform the people who will be dealing with these ethical issues.
Apples are Growing — As interesting as all the above may be, you may be wondering what bioinformatics has to do with the Macintosh. Macs are already playing a large role in the bioinformatics domain and will probably continue to do so. Firstly, as with any other sector filled with independently thinking individuals, the scientific community has a high proportion of Mac users. This has been particularly true in biology, where until recently versatile graphics capabilities have been more important than raw computing power.
Nonetheless, until recently the Macintosh had one critical limitation regarding its long-term suitability in the field: the natural preference of bioinformaticians for Unix-based platforms. This is firstly a result of the availability of free, reliable Unix tools such as perl and grep, which make it highly suitable for processing large quantities of text-oriented data. Furthermore, since the explosion of activity in computational biology began around 1995, exactly when the Internet was establishing itself as a mainstream platform for scientific collaboration, the vast majority of bioinformatics applications run over the Internet. Unix’s stable and efficient implementation of TCP/IP, in conjunction with the free Apache Web server, make it ideal for providing these Web-based services. For some idea of what’s available, take a look at the site of the American National Center for Biotechnology Information.
It should be fairly obvious where this takes us: Mac OS X, soon to be the mainstream Macintosh operating system, is not only based on Unix but provides full support for all of its tools – perl, grep, and Apache included. On its own, this does not necessarily place it ahead of other Unix platforms. But if we add the fact that it contains a modern user interface and runs desktop applications such as Microsoft Office and modern Web browsers, it’s not hard to see why Mac OS X is a natural choice for bioinformatics servers and desktops. This has been noted in several places, including an O’Reilly Network article and an Apple viewpoint article. It’s also proven to be more than wishful thinking: Genentech, the company that ordered 1,000 new iMacs (and whose Chairman and CEO is one of Apple’s board members), is one of the founders of the biotechnology industry.
A further bonus for Macs is that the PowerPC G4 processor, with its Velocity Engine processing unit, is ideal for many types of biological computations. BLAST (short for Basic Local Alignment Search Tool) is probably the most popular bioinformatics tool available today. It takes the sequence of a DNA or protein molecule as input and searches for other known molecules which are likely to be connected in evolutionary origin or biological function. Apple’s Advanced Computation Group, in collaboration with others, developed a high-throughput version of BLAST, which they claim makes a dual 1 GHz Power Mac G4 up to five times faster than a PC with a 2 GHz Pentium 4 processor. Fast BLAST searches are crucial to today’s biologists.
Try This at Home — There is at least one way in which all Mac users can get involved in computational biology. A project named Folding@Home, developed in the same style as U.C. Berkeley’s alien-searching SETI@home, lets you contribute to a distributed effort to calculate the physical structure of protein sequences. Folding@Home’s Mac OS X client, a screensaver and application, is now available and provides a real-time graphical view of the structures being tested.
That aside, unless you happen to be involved in the academic or commercial computational biology world, the bioinformatics revolution will remain, for now, a distant blip on your daily horizon. But don’t expect it to stay there forever – if the promise of the field is even partially fulfilled, you will start seeing its effects seeping into your daily life.
[In one life, Gideon Greenspan is the persona behind Sig Software, a Macintosh shareware company which develops products such as Drop Drawers, Classic Menu, Email Effects, and NameCleaner. In the other, he is a Ph.D. student of bioinformatics in the Computer Science department of Israel’s Technion. He hopes one day to overcome this dichotomy!]