Research Computing News

Brief News Notes from The RCR:

The RCR puts FASTA 3 on the Web

The RCR has initiated a project to provide access to some components of our sequence analysis software over the Web. The programs will run on the RCR's Alpha server, but anyone can access the web pages from within the med.nyu.edu computer network without requiring an RCR user account or a password. The first program to get a Web interface is FASTA 3.0. This is a newer version of the FASTA sequence similarity program than the one which is included in the current GCG 9.1 package. FASTA 3 has been available to RCR users for about six months via a command line interface from a direct Telnet connection to MCRCR0, but it has not been widely utilized.

The RCR gets Windows site licenses for OMIGA and Sequencher

The RCR has purchased a site license for two new molecular biology programs for Windows computers. While we continue to recommend the use of Macintosh computers for molecular biology analysis, we have responded to the requests of users by purchasing licenses for two copies of OMIGA and one copy of Sequencher for Windows. These programs will be made available with a floating license so that users can install the software on their own computers, but will be limited as to the number of machines that can simultaneously use them. If high demand for these programs causes these floating licenses to be often unavailable, then the RCR will purchase additional licenses.

OMIGA, by Oxford Molecular Group, is very similar to the Macintosh program MacVector, except that it does not provide direct Internet connectivity to perform ENTREZ and BLAST searches. OMIGA functions include: sequence editing and translation, protein analysis (hydrophobicity, antigenicity, secondary structure, transmembrane helices), multiple sequence alignment, PROSITE motif searching, restriction analysis and graphical mapping, ORF detection, and PCR primer design.

Hoaxes, viruses and chain letters

If you have an e-mail account you'll probably have been the recipient of at least one, and probably several messages warning you about a virus on the Internet. The name of the particular virus might vary: "Good Times," "Win a Holiday," "Penpal Greetings," and "Join the Crew" are some common names. The warnings are all very similar: if you download an e-mail with a certain subject, various dire things will happen to your computer. At the end of the e-mail you'll be asked to send the warning on to as many people as you possibly can. As a result, these warnings spread like a rash around the Internet before dying down, only to be replaced by another.

First of all, lets deal with the bad news. It is possible to download a virus from the Internet, and it can be passed onto other people. There are two ways in which this may happen. The first is if you download a piece of software from a web site it is possible for it to contain a virus, and when you run the software your computer becomes infected. The second way is if you receive an e-mail with an attachment; when you open the attachment a macro may run that does nasty things to your system. The good news is it that it is quite rare for this to happen.

Let's look at this in a little more detail. Viruses usually spread in anonymous situations; someone may use a floppy disk on your machine and infect it. Someone else then uses a floppy disk on your machine, catches the virus and continues to spread it, without even being aware of the fact. However, when you download software from the Internet, you know the site that you've copied it from, and as a result, it is not difficult to trace the virus back to its source. Consequently, reputable companies try and ensure that all their software is virus free because it would be commercial suicide for them to do otherwise. If you're foolish enough to download "hacked" or illegally distributed software from a "warez" site or USENET newsgroup you have no such safeguard, but you shouldn't be using illegal software in the first place. Always use virus checking software when you download anything before you use it. You'll almost always find that your download does not contain a virus, but it's better to be safe than sorry.

If you receive an e-mail from someone that you don't know and it includes an attachment, exercise caution about opening it. Write back to the sender and ask them who they are and why they have sent something to you. If you have any doubts, just delete the e-mail with its attachment unopened. Please note here that the danger is in opening the attachment and NOT in reading the text of the e-mail itself. Just reading an e-mail is not going to infect your machine. Even if you do know the person who sent you the attachment it is still worth exercising caution, because it is possible that their machine has a virus and they are passing it on unknowingly.

If there are not that many viruses out there, then why are there so many warnings? People like to be helpful, and it seems like a nice thing to be able to warn friends and colleagues about potential dangers. Unfortunately, people are also very gullible, and are likely to take a virus warning on trust if it comes from a supposedly reputable source. If you receive one of these warnings yourself, its very tempting to just continue the cycle by passing it on, but this just compounds the problem.

Instead, you should run a quick search on the Internet for the name of the supposed virus, or take a quick look at a web site which lists hoax virus warnings (see the URLs at the end of this article). You'll probably discover that the virus warning is in fact a hoax. At this point either just delete the warning or contact the original sender and inform them that they've been hoaxed.

There is another category of hoax that is worth mentioning: the e-mail chain letter. E-mail chain letters are exactly the same as the old fashioned hard copy type, and they warn you that if you don't pass the chain letter onto at least 5 friends you will fall under a bus, your hair will fall out and your house will be hit by a meteorite or some other nonsense. While this appears to be rather ridiculous, it can be very upsetting to receive an email of this nature, and they prey on people's superstitions. Logically you should just delete and forget them, but I know that some people do find it difficult to do just that. However, all the advice that I can offer here is that they ARE nonsense.

A slightly different form of chain letter, but one which is just as annoying, are those that state that a small boy is dying of cancer and wants to receive a world record number of e-mails, that Microsoft will donate money to charity if a chain letter goes around the world a certain number of times, or even that if you send back old sneakers to a particular company they will send you a new pair, free of charge. Let me reassure you - there IS no small boy, Microsoft will NOT donate money to charity, and the sneaker company will NOT send you a new pair! So please, if you do get a letter of this nature, let your common sense take charge and delete it, don't send it onto other people!

• Run anti-virus software on all downloaded files
• Back up your system regularly
• Don't open e-mail attachments from people that you don't know, and be careful about opening them from those you do
• Take viruses seriously, but check out virus warnings before passing them on
• Do not be fooled into thinking that a warning must be true because it comes from a seemingly reputable source
• Don't send chain letters on to friends and colleagues.

Visit the following websites which provide lists of hoax warnings, tell you how to identify real viruses, and discuss many myths:

An iMac for the Lab?

The majority of the research laboratories of NYU Medical Center, and particularly those who use the RCR, have favored Macintosh computers over DOS/Windows based PCs. However, in 1996 and 1997, the Apple Computer company experienced a significant loss of market share across the personal computer industry and suffered serious financial, management, and public relations problems. Many researchers at NYUMC became worried that continued investment in Macintosh computers would become a hindrance in an increasingly "Windows only" computing world.

However, in 1998 Apple Computer has made a dramatic turn-around. Apple is now selling G3 computers at the rate of approximately 2.5 million per year. According to market research firm PC Data, Apple advanced to the third spot in the consumer market with 13.5% market share in August. Concerns about Macintosh computers on many campuses seem to have been assuaged as well: Dartmouth University has chosen the iMac as its recommended computer for incoming freshmen and Yale University's ITS Advisory Committee has developed a policy to provide equal support to both Windows and Macintosh computers.

This is good news for current owners of Macs and prospective buyers of new ones. The re-newed health of Apple protects the businesses of those companies that make software for it and provide support: without software your computer is little more than a dysfuctional boat-anchor. It is important for faculty to know that several of the largest software developers: Microsoft, Intuit, and Adobe have all made public statements of support for the Macintosh and have released new Macintosh versions of their primary programs (Office 98, Quicken 98, Photoshop 5.0, ImageReady, etc.).

More important in many ways is that Oxford Molecular Group, one of the key developers of molecular biology software, issued a press release in September of 1998 that stated:

"1998 installations of MacVector software for gene and protein sequence analysis on the
Macintosh were up 122% over the first six months of 1997... there is good demand for new scientific 
products on the Macintosh and renewed confidence in Apple in the scientific community." 

So, with all of this rosy Macintosh news, should you get a $1299 iMac for your lab or office? It depends on what you want to do with the computer. The iMac is fast (233 MHz G3), it has a big 4 GB IDE hard drive and built-in 10/100 MB ethernet and it takes up very little desktop space. The monitor is good quality, but only 15 inches. It does not have SCSI, so you cannot connect it to your existing scanners, external hard drives, or removable storage devices. The lack of a floppy drive is both inconvenient and a bene-ficial safety feature for a general use laboratory machine (reducing the chance of virus infection). The iMac would make an excellent web browsing and e-mail station, it would also be fine for word processing and moderate complexity graphics. It would not be a good choice for high end graphics, multimedia authoring, or sequence analysis since the monitor is relatively small and the hard drive is not the fastest.

In summary: A lab computer is purchased to support the research effort. An appropriate choice is one that can run the range of software needed and that fits into the lab's environment for management and service. The good news for Mac users is that "Macs are Back!" But the purchase of a Mac, if the best software is Windows based, isn't a smart move. Protect your investment with careful planning and by getting good advice before you spend your money.

Y2K just won't go away

Concerns about the Y2K problem continue. As of the time of writing, few of the ~4,500 desk-top computers in the Medical Center have been checked for Y2K compliance. Very few of those checked have been in the School of Medicine. While people with Macintoshes (the predominant platform for the research faculty) are probably correct in assuming that most Y2K problems will pass them by, there are many "gottchas" that are not yet emphasized. Specifically, major lab instruments and equipment are a possible source of trouble. Items like -70 degree freezers, cell counters, electron microscopes, sequencers, imaging instruments of various sorts and any other large/expensive/complex lab instruments are candidates for having an embedded processor with a vulnerable time/date chip. Time taken to check your equipment could be time well spent!

Establishing that an instrument is (or is not) Y2K compliant can be difficult. Some vendors refuse to provide information, fail to return phone calls, or provide deceptive or confusing information that sounds reasonable, but is actually meaningless. Others state that Y2K compliance is only guaranteed if the latest version of the hardware and software is purchased, something that a lab may not be in a position to do.

Individuals who are responsible for a piece of equipment and who have concerns about its Y2K status should contact the vendor and ask for a letter of certification for that item. If the vendor creates difficulties providing Y2K information, please contact the buyer in Purchasing who was responsible for placing the original order for the equipment. That buyer should be able to help get the information you need.

An important thing to remember is that the onset of the Y2K problem isn't going to be confined to midnight on the 31st December, 1999. The critical date change will sweep around the world over a 24 hour period and a failure effecting you may be a result of a change several time zones away. Many computer clocks run using GMT, which changes 6 hours earlier than EST. Many ISPs are based in California, which goes through the date change 3 hours after NY.

Some doomsday scenarios envisage disasters such as major power failures, the collapse of the city's traffic control system, gas pumps that won't pump, the list is endless.

Please be aware that some granting agencies have placed institutions and faculty on notice that if a Y2K problem is found to have hampered or compromised the ability to perform funded research projects, both the grant awardee and the institution may be penalized.

One thing is sure, it will be an exciting few days, even if very little happens. Do your best to make sure as little as possible of it happens to you...

Brief News Notes from The RCR

The RCR has hired two new staff members. Andrei Pavlof is our new System Manager for the Alpha. He will also be programming a new web interface to GCG programs. Gisella Walter is the new Associate Webmaster for the entire www.med.nyu website. She is supervising a complete renovation of the website including the homepages of every academic and medical department. The new School of Medicine homepage: