by Dale Graham, Ph.D., DCRT (email@example.com)
Scientists are used to encountering one frustration after another as they pursue their research goals. However, computer-related problems have to rank high on the list of experiences that modern biomedical researchers find the most aggravating. We expect computers to solve our research headaches, not compound them. To help reduce "computer stress" at NIH, we offer solutions to some of the most common computing difficulties reported by intramural researchers.
Problem: An analysis has been performed using a Genetics Computing Group (GCG) program on the Helix computer, and after the files are transferred to the researcher's personal computer, the data, which looked fine on the screen, are so jumbled that they are practically uninterpretable.
Solution: The problem is that the analysis file from the mainframe is provided as a text file. When this file is opened with a word processor, it comes up in the "default font," which is usually a proportional font. This means that each letter will take up more or less space, depending on its size. However, for sequence analysis, you must use a monoproportional (or nonproportional) font such as Courier or Monaco for sequences to be shown properly. There also may be problems relating to document size and font size.
Here's what you should do:
Problem: Some of the analyses on the GCG, such as "squiggles" for RNA structure or "plot structure" for peptides, won't display properly on the screen.
Solution 1: The data for these kinds of analyses are presented in "plotter" format. The only way you will see such data properly represented on your screen is if you have a communications program that can "emulate" a Tektronix terminal. This is true whether you are using a modem or a network connection. The best solution, if you do a lot of these analyses, is to buy a communications program that can perform terminal emulation. DCRT recommends VersaTerm Pro (not just VersaTerm -- it must be the Pro version) for Macintosh users. Contact DCRT (phone: 594-DCRT) for the latest recommendations for PC users.
Solution 2: The second-best solution is to use a command that will "turn off" the plotter function and to save the file in a text format that can be manipulated with another program to produce output. To do this, you must add some information when you request the analysis from the GCG. That is, you need to type "-fig" on the command line after the analysis name. In addition, you need to provide a name for the output text file, such as "filename.out." Your command line should be patterned after the following example: "helix% squiggles -fig=filename.figure." After the analysis, the "figure" program can be used with this file to print the figure.
Problem: It can be very difficult to use the GCG suite of programs for restriction-enzyme analyses, simple peptide analyses, and other relatively simple analyses.
Solution: Personal computer users are far better off doing "simple" analyses on their computers, and not using mainframe solutions. Certainly, there are times when you must use a mainframe, but for simple stuff, using a mainframe is like using a sledge hammer to pound in a tack. Many programs are available for relatively simple analyses. Some of these are even free or cost very little. DCRT also offers a booklet on program options for sequence analysis for the Macintosh (see box, page 7).
Problem: What is the easiest way to get sequences from databases and perform homology searches? Do I have to use either the GCG or GenInfo computers?
Solution: If your personal computer is on the network and you are already using something like PC-Gopher or TurboGopher (Mac), you should be able to install and run a World Wide Web (WWW) "browser" such as Mosaic, MacWeb, or Netscape. These programs make it very easy indeed to retrieve sequences from databases on the NIH campus or all over the world. In fact, you can also use browsers to perform several different kinds of sequence analyses. A couple of useful addresses (or URLs, as they are called) are "http://www.nih.gov/," which will take you to the NIH Home Page and a treasure trove of information from scientific data to telephone numbers, and"http://mantis.dcrt.nih.gov:8000/ Publications/Internet_Talk/Tools.html," which contains a list of links, arranged by analysis type, for sequence analysis via the Internet.
Of course, this is far from a complete list of the wide range of computer problems encountered by the intramural research community. For help in solving other difficulties, from personal computing to mainframes, contact DCRT. We'll do as much as we can to help, even if it is just to suggest another avenue to explore. DCRT is also providing a lot of computer-related resources on its WWW servers and indicating links to other helpful sites so you will be able to have information and assistance at your fingertips if you are using a WWW browser.
DCRT has a dozen publications that explain how to perform scientific computing tasks and select appropriate types of software. To order these and other pamphlets, contact DCRT (phone: 594-DCRT; fax: 402-0537; e-mail: firstname.lastname@example.org).
"Comparing Alignment of Two Sequences Using the GCG" DCRT132
"Creating Internet Documents" DCRT124
"Getting Sequences and Homologies (From Mainframes)" DCRT103
"Guide to Cross-Platform Computing" DCRT111
"Guide to Preparing Posters Using the Macintosh" DCRT113
"Macintosh Options for Multiple Sequence Alignment" DCRT112
"Performing Multiple Sequence Alignments With GCG programs" DCRT105
"Preparing Figures for Publication on the Macintosh" DCRT106
"Searching for Patterns in Sequences: Regulatory Elements and Motifs" DCRT107
"Searching for Transcription Factors and Motifs Using Mac Software" DCRT108
"Sequence Analysis Programs for Macintosh: A Comparison of Features" DCRT110
"Using Macintoshes and the Internet for Sequence Analysis" DCRT112
NIH intramural researchers can get programs to "browse" the World Wide Web through a variety of avenues. Here are some suggestions from DCRT:
Macintosh computers -- You can get the current version of Mosaic or MacWeb from PUBnet by going into the Browser Software folder inside the WWW Browsers folder under Mac Software. These browsers are free. Netscape is a commercial product that can be purchased through Haven and Co. on the Business Purchasing Agreement list for $39 a copy without manuals and $60 a copy with manuals. All three browsers are supported by DCRT.
PCs running Windows -- You can get some browser software free to be used without support (that is, at your own risk) on PUBnet. Window users who want to use a supported product should purchase Netscape from Haven and Co. for $60 a copy (with manuals). Support will be provided through Netscape.