T H E   N I H    C A T A L Y S T      S E P T E M B E R  – O C T O B E R  1999



On Graduate Student Needs

I have one suggestion for the needs of graduate students at NIH. I am a graduate student who is finishing up a summer internship at NIH, and I have noticed one common desire among myself and the other summer interns I have met—centralized housing.

Centralized housing facilities (dorm, apartments, hotel, etc.) would facilitate interaction among students and allow for more frequent exchange of ideas. It would also provide an opportunity for weekly discussion groups, journal clubs, and lectures and seminars to be held. Many of the problems associated with renting in this area (lack of housing, high prices, transportation, and bad landlord-tenant relationships) would be eliminated, allowing the students to concentrate more on their research and learning experiences.

Michelle White, NIMH

—Centralized housing for students at NIH is one of the projects of the Foundation for the NIH. See story.—Ed.


On Interest Group Gaps

A cross-disciplinary suicide interest group would be useful.

—Michelle White, NIMH


Stephen Epstein

He may be "retired" from NIH, but former NHLBI Cardiology Branch Chief Stephen Epstein is still working about 60 hours a week as the director of vascular biology research at the Cardiovascular Research Foundation in Washington, D.C.

In the July–August issue of The NIH Catalyst, we reported that Science Watch had listed "retired NHLBI investigator Stephen Epstein" among the ten most-cited clinical investigators in their fields between the years 1980 and 1998.

"Most cited," he is. "Retired," he is not.—Ed.


Phage-Tech on Deck

The new Phage-Tech Interest group (PhTIG) was launched in September and will meet regularly .

The PhTIG looks at novel uses of bacteriophage, such as phage therapy of multidrug-resistant infectious organisms and phage-display technology to "dissect" single cells or a single mitochondrion.

Contact Steve Zullo by e-mail or at 435-3576

or Carl Merril by e-mail or at 435-3583.

Say What?

Need a special cell line? Or a line on a special technique? Want to know who’s working on a particular disease or gene?

Search rapidly through 2,603 1998 Annual Reports online to get this info. Any search combination will do: last names, institutes, a word in the title, other keywords.

Day Care Board

The NIH Day Care Board needs volunteers for a three-year term starting September 1999. Contact Lori Thompson at 496-1967 or Deborah Henken at 496-5541.

A WHALE of a Service for Sequence-Seeking Scientists


This week 77,000 new sequences were added to Genbank and about 3,000 to the major protein databases. A researcher with a new nucleotide or protein sequence would compare it with these databases right away, but few can afford to spend hours each week repeating the comparison with the new database sequences.

Some URLs


Citation and Literature Searching (Web of Science and Porpoise)

NIH Directory and E-mail Forwarding Service

NIH Molecular Biology Resources

Now, WHALES (Web Homology ALErt Service) will automatically keep NIH scientists informed of relevant new entries in these ever-growing DNA and protein sequence databases.

WHALES will be largely familiar to those who use Porpoise to keep up-to-date with the scientific literature. Like Porpoise, Whales is a web-based resource that allows NIH scientists to define profiles—in this case, text terms or sequences. Once a week, these profiles will be searched automatically against new entries in the Genbank, Genpept, SwissProt, and PDB databases; the results will be returned via e-mail.

WHALES has two profile modes: text mode and homology search mode. In text mode, you can define a text string such as "tyrosine & kinase," or an author’s name ("Wilson, I.A."), or even a protein size ("between 340 and 350" amino acids) or molecular weight ("greater than 60,000"). You can also specify an organism such as Mus musculus.

This search profile is compared against the text and reference data in the headers of new sequence entries. You can configure the weekly e-mail message to contain just sequence names, accession numbers, some selected fields, or even the entire sequence entry, at your choice.

In homology search mode, you enter your own nucleotide or protein sequence, which is then compared using Blast or Fasta with each week’s new sequences. Your sequence should ideally be in Fasta format, but most other formats will be converted automatically. Short peptides, such as those produced from mass-spec analysis of protein digests, can also be entered, and the Fasta program will then look for (potentially noncontiguous) matches of all the peptides in the database sequences.

Access to WHALES is possible only from computers on the NIH network and from Parachute. All search results are returned to the e-mail address associated with each person’s unique e-mail alias in the NIH Directory Service.

WHALES was developed by Helix Systems staff at CIT (Peter FitzGerald and myself). For more information, see the Whales help pages, or call GO-CIT, or e-mail to WHALES.

Susan Chacko


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