MacResearch

Although it may seem like this website has a slight bias towards the biological sciences, we've not forgotten the large community of Mac-loving astronomers. There are a wealth of astronomy applications available for OS X, but some of these applications come as ports from other platforms and need a bit of tweaking to run properly. IRAF is one such application. IRAF is the Image Reduction and Analysis Facility, a general purpose software system for the reduction and analysis of scientific data. IRAF includes a good selection of programs for general image processing and graphics applications, plus a large number of programs for the reduction and analysis of optical astronomy data within the NOAO package. External or layered packages are also available for the analysis of HST, XRAY and EUV data. If you'd like to get started with IRAF on OS X then head over to the instructions at the MacIRAF Web Page. More information on IRAF can be found at the official IRAF project page.

These aren't the newest articles on the web, but they are the only "OS X centric" introductory bioinformatics articles I've found to date. The best part is that they are published by the MacDevCenter at O'Reilly which has always had a very high quality of information. The first article is titled very plainly "Introduction to Bioinformatics" and it surveys several of the major subdomains within bioinformatics. The second article is titled "Bioinformatics and Comparative Genomics" providing a more in depth explanation of the comparative genomics subdomain of bioinformatics. All of the software mentioned in the articles is available for OS X unless stated otherwise. I'd like to make a large directory of such "OS X Centric" primers and tutorials for various disciplines once I've collected enough links.

I always tell people that my favorite aspect of UNIX is the fact that you can quickly and easily string together a few command-line utilities and do things that would require days worth of custom programming to pull off on Windows. There are plenty of UNIX geeks using OS X these days, but I'd wager that the majority of scientific Mac users are still a bit shy when it comes to the terminal and are perhaps a bit glad that it is safely tucked away in the /Applications/Utilities folder. I thought I'd write up a practical example of how you can use the Terminal application and a few handy command-line utilities to make your life easier. In this example I'm going to illustrate how you can automate the retrieval of protein sequence data from NCBI's genbank database. Note that the principles illustrated in this simple example can easily be applied to numerous other situations.

Somehow this little gem eluded my gaze until now. It might not be the ultimate, full-featured reference mining tool, but Reference Miner performs a very specific job and it does it well. Reference Miner searches the Internet to find and display reference information from PubMed, Amazon (US, UK, Germany, and Japan), and the Library of Congress. If you or your institution has the appropriate journal subscription, Reference Miner allows you to click on a relevant reference and displays the full-text in your browser. The only downside to this application is the fact that it seems tied to another application produced by the same company called Bookends. Since Reference Miner is being given away for free its hard to complain, but it would be great if Reference Miner had tighter integration with other reference management applications such as iPapers or EndNote.

Hidden deep in the bowels of 10.4 is a private GraphKit framework that is currently only available to Apple's internal developers. This leaves most scientific application developers with the task of developing their own graphing frameworks if they plan to develop native OS X applications using the Cocoa Application Programming Interface (API). A crafty fellow by the name of Chad Weider saught to alleviate this pain for his fellow Mac developers and released a freely available graphing framework for Cocoa called GraphX. While the functionality offered in the first release is pretty basic, it should save developers a significant amount of time. The current features include:

• Graph mathematical functions (handles NaN, ±∞)
• Histograms
• Scatter Plots (just an enumerable set of points)
• Output as PDF
• Attributed Text (color, font, alignment, etc…) for Labels
• Uses the (inefficient, but nice) Cocoa-ish calls to DataSource

The next release is said to contain an expanded choice of graph types (Direction Fields, Pie Chart, etc) and an IB Palette for XCode integration. Example graph output can be viewed at the bottom of the GraphX homepage.

Impressed by the Terascale Computing Facility at Virginia Tech, researchers at Florida A&M are building a 128-node Infiniband cluster based on the XServe G5 hardware platform. According to Florida A&M's Dr. Lewis Johnson, "the types of matrix manipulations they’re doing lend themselves well to the G5 and its vector processors." The cluster, dubbed Laser Interactions with Materials for Identification Technology (LIMIT), is being funded by the United States Army Space and Missile Defense Command to develop tools and techniques to remotely detect hazardous materials.

Cell Culture Laboratory Information Management System (CCLims) - is boosting the productivity of Cell Culture Laboratories by 60%. Developed under sequential grants from the National Institutes of Health, the software has been validated by select cell culture facilities nationwide. The CCLims is available exclusively for Mac OS X. For speed, the CCLims leverages the incredibly fast SQLite engine now built into Mac OS X and the CCLims generates completely configurable reports with Apple's excellent WebKit engine.

The use of cultured cell models have been adopted as a valuable tool in applications in medicine and industry ranging from basic research to genetic analysis and prevention of bioterrorism. Until now, laboratories that focus on cell culture-related research lacked a comprehensive solution to track their cells through vast configurations of incubators, freezers and dewars through years of use. All too often, record keeping mistakes can result in wasted time, money, and effort spent growing the wrong cell lines.

Like it or not, PERL has become a staple scripting language among techies and bench-top scientists alike. Despite its abstruse syntax it seems that nearly everyone is capable of writing a bit of PERL, and the wealth of ready-made modules available through the CPAN archive network add to its allure. Every single copy of OS X comes with PERL pre-installed, but those unfamiliar with, or completely unaware of the OS X UNIX terminal may be oblivious to this resource. This is where Camel Bones comes in. Camel Bones is "bridge" between the PERL script interpreter and the advanced Cocoa Application Programming Interface (API) underlying OS X. Using Camel Bones it becomes trivial to create Beautiful Aqua graphical interfaces to your PERL scripts, giving it the same visual look-and-feel as any other native OS X application. The Camel Bones website provides a number of examples to get you started. If you've ever written a scientific application with Camel Bones let us know and we'll feature it on our site.

Apple's Keynote presentation software does a marvelous job of rendering text and graphics in ways PowerPoint could only dream of. However the lack of any significant functionality for creating and rendering complex mathematical equations is a shortcoming that prevents a large proportion of scientific presenters from ditching PowerPoint altogether. I recently came across this great tutorial that demonstrates how to use a program called "LaTeX Equation Editor" to import complex equations into Keynote in a clean and simple way. Tiger users might be able to pull the same stunt with the new Grapher.app application included in 10.4 but I've not verified this myself. One feature f LaTeX Equation Editor that I really like is the fact that when you export an equation to PDF it saves the actual LaTeX code inside the PDF file and can therefore be re-opened by the equation editor for further editing.

PCR can be one of the most tedious and boring aspects of biological lab work. A long day of oligo, primer, or siRNA design is painful and there exists a wealth of commercial and freely available applications to help alleviate this pain. As Mac users we expect be able to turn to our Macs and find applications that make tedious or painful tasks especially fast and easy. In the case of PCR the open-source and shareware communities do not disappoint. While several well-known commercial PCR applications exist to aid Mac users, we've done some searching to bring you the best PCR applications the open-source and shareware communities have to offer. If we've overlooked an open-source or shareware application in this area please comment on the story and let us know.

Open-Source and Shareware PCR Applications:

• Amplify 3
• AmplifX
• GeneRider
• BioAssistant
• OligoFaktory
• iRNAi
• GenomoRama
• ApE