The Research Computing Resource
The Research Computing Resource
The RCR currently operates a UNIX server consisting of a DEC/Compaq AlphServer 4100-5/400 (MCRCR0) with 1024Mb memory, 4mm DAT, CD-ROM and 50Gb disk, connected via full-duplex FDDI to the Medical Center FDDI core ring.
The Research Computing Resource maintains generally accessible and regularly updated sequence databases and programs for molecular biology computing. At present, investigators at the Medical Center use the RCR for running the preponderance of their sequence analysis programs. With the networking initiative in the Medical Center, most faculty have lab computers and most of them are now connected to NYUnet. In fact, a network link is now the primary mechanism for the majority of investigators to access the RCR and the other Medical Center services. Computer terminals and printers connected to terminal servers on the NYUnet are generally available for users without their own networked computers. Lab PCs are used for most word processing and laboratory management programs.
The RCR sponsors a course entitled "Using Computers for Molecular Biology" which is offered as part of the graduate program of the Sackler Institute, but is open for auditing by all faculty and staff members. The course, taught by Stuart Brown, provides extensive instruction on the use of RCR computing resources and the World Wide Web for sequence analysis. The course notes are available on the RCR's Web site. The RCR Web site also contains other useful information about molecular biology computing including the complete GCG manual, links to molecular biology resources on the web, and a glossary of molecular biology terms.
Any faculty member may use the X-terminals, but individuals who are not RCR members should yield their seat should a member require it for his or her work. Use of the computers (Macintoshes and SUN) is restricted to authorized individuals who are members of the RCR, GCRC or the KCCC.
In the next few years the importance of molecular biology computing emerged as the principal use for the new computer. Accordingly, funding for the purchase of a VAX 6000-410 was obtained from the NSF to support molecular biology computing as the principal activity of the resource, and with the current administrative structure. The funds were provided under grant DIR-8908095 (to P.R. Smith, 35%), an equipment grant from Digital Equipment Corp. (to P.R. Smith, 35%) and with NYU-MC institutional funds (30%). Subsequently, NIH funds from the BRSG program (RR-05399) allowed significant upgrade of the disk storage of the system.
The RCR has received additional funding from the National Science Foundation under grant BIR-9318128 (to P.R. Smith) made possible by generous NYU-MC Institutional matching funds. Using these new resources, the RCR has upgraded the VAX 6000-410 to an AlphaServer 4100 5/400 creating a major computing resource supporting researchers throughout the Medical Center.
If you are a user of the RCR it is essential that you acknowledge your use of the RCR, and particularly the NSF's support of it. If you publish a paper, please include a sentence similar to the following in the Acknowledgements section: "The National Science Foundation is thanked for its support of the computing resources through grant BIR-9318128".
The RCR also maintains the SwissProt and PIR protein databases which have regular updates every 3 months. Between the regular releases, SwissProt updates are now deposited on the NCBI anonymous FTP server. We get these updates and make them available as a subsection of SwissProt. We also maintain the GenPept database of protein translations of all GenBank sequences as well as the TREMBL database of protein translations of all EMBL sequences (both are updated weekly). Special molecular biology related databases are also maintained. Among them are the Transcription Factor Database from David Ghosh at NCBI, PROSITE, a database of protein motifs from Amos Bairoch at the Université de Génève, and REBASE, the restriction enzyme database from Richard Roberts at New England Biolabs. We receive the REBASE updates via E-mail from the Roberts' lab; the others are obtained via anonymous FTP as new versions are released.
We also maintain a number of other public domain packages that we update as they are released. They include: ClustalW a multiple sequence alignment package and MALIGNED a multiple alignment editor. SEQUENCE Gary Olsen's multiple sequence editor, PHYLIP, a phylogenetic analysis software package, TREEALIGN, phylogenetic alignment of homologous sequences, PRIMER, a PCR primer selection software and LIGAND, Scatchard analysis software.
These packages are implemented in labs throughout
the country. With the exception of MDPP (which is much too big), all of these
packages are available from our MAILSERVer: click on the button for
instructions.
This team is far too small to provide one-on-one service on demand to all of the ~900 users of the RCR. The focus of the team is therefore on user education. Users find the team most responsive when they come with problems and are ready to learn: with extremely rare exceptions the team will not `just do it' for a user if there is no prospect that the user could not `do it' for themselves next time. The expectation is that the users are independent and self-motivated, two qualities necessary for the successful research scientist.
The RCR provides (amongst other things) a committment to maintaining the GenBank and other molecular biology databases and software at the state-of-the-art, help selecting a lab Macintosh computer and software, configuring basic network communications on that machine to access the RCR, guidance learning software needed for research, prompt responses to questions posted to the BULLETIN boards, small training sessions for groups of users, office-hours for drop-in questions and access to the annual comprehensive course for graduate students and faculty (who wish to audit).
The RCR does NOT provide a
`sequencing/GenBank searching service', help assembling/installing lab
computers, help running cables (network or otherwise), software/hardware
maintenance or service (excepting its own equipment), computer-basics or
office-automation training, or help with access to any systems other than the
RCR. People requiring help in these areas should contact either the MIS help
desk (x6864), the Educational Services
Department of the Ehrman Library or the NYU Computer Store/Repair shop where some of these services are offered.
What to do if you don't like something
The RCR
exists to provide services for its users. But this does not guarantee that
you will always get what you want, or have all your needs met. If you are
finding that the RCR people are not providing what you need, you have several
avenues to deal with the problem. First, contact the director of
the RCR, Ross Smith. Don't get put off: he has an obligation to respond to
the users problems. Try to find out whether this is something that the RCR
considers to be `your' problem, or whether there is some issue of policy or
security where the RCR is not free to help. Next, if this is
unsatisfactory, contact one of the members of the Advisory
Committee and explain your difficulties. Ask if there are issues that
that member knows about that may be at the root of the problem. The Advisory
Committee members are free to call a meeting of the committee to discuss your
problem and can escalate this issue to the Dean if this is appropriate.
Hopefully, nothing will get that far.
Finally, there is the annual `Users' Meeting'. Obviously this is not all that useful if a problem is urgent. It IS good for dealing with longer-range issues of policy and nagging issues that make life more difficult. Make sure you attend the Users Meeting if you are a user who has an investment in the quality functioning of the RCR.
The current members of the Advisory Committee are:-
Emeritus Members are:
Please note that we do not allow account
sharing! Since extra people do not cost a PI any more money, make
sure that everyone has an account and understands their obligation
NOT to share passwords. Your computer account should be private, or
at least as private as necessary to protect legitimate personalized use.
Note that account and password security is viewed as a very serious
issue by the institution: follow the link for more information about Security issues at NYU. Or,
better still, read the Security Acknowledgement form that you will have
signed! Please: don't mess up on this one!
Policies Concerning Groups and Fee Payment
The
following is the policy concerning user accounts which has been in effect for
the last five years.
Accounts are issued in the first instance to NYU faculty members (excluding those with the rank of `Instructor', unless they have independent grant support) who act as principal investigator for a group of users consisting of themselves and the students and postdocs working directly for them. An individual with an NYU faculty appointment can not be in the group of another faculty member: he or she must have an independent group. Each PI (faculty member) is responsible for the conduct of the members of his/her group on the computer and on the network.
Each PI is liable for the yearly fee ($500 for 1997) which covers all costs for the whole group. Accounts not paid up by the payment dead-line (March 1st, in each year) will be frozen, but they will not lapse until the beginning of the following year (you can't cancel your account in January, and then re-activate it in July for half price).
The `official' letter to the faculty concerning this issue can be down-loaded
(as a PostScript image) for printing on your computer by clicking here.
Adding a new user to an existing group
Adding a
users to your faculty group is simple also. The new user should bring a
memo, signed by the faculty head of the group, plus a copy of the New User form,
filled out in full, to the RCR Office (MSB 183). The memo should
request that the new user be added. The user should also bring his or her
NYU ID card so that the account can be activated immediately.
Removing/Modifying/Moving User Accounts
Removing a user, or modifying a user account is done by sending a memo
requesting that the user be removed or changed. If the user is moving to
another faculty member's group, he or she should co-sign the memo and request
the change. Please do not request deletion of an account if you know that
person is moving to another group: it is very disruptive to re-create their
account and recover their files.
Users, usually students and postdocs, who move from group to group, MUST let us know if/when they move (even though the move has to be authorized by the new group leader): we will pester the new group leader for the memo. People who have moved without notifying us run the risk of loosing their accounts if their old group leader disavows them (sadly, this has happened)
If an individual leaves the Medical
Center, they immediately loose access priviledges to the RCR equipment.
Please report the departures of students, postdocs (and faculty) so that
their accounts can be closed. We will allow a grace period for the finishing
off of work and for the orderly removal of files, if this is appropriate.
What to do if you forget your password
If you
forget your password you must bring your NYU-MC ID to the RCR office (183 MSB)
and request that the password be re-set. Passwords are not
reset over the phone! Ever! You must come by in person with your
ID. If you are at a remote location (e.g. Sterling Forest) you can visit the
local system manager who will verify your ID.
How to close a faculty group account
A
faculty group is closed by sending a memo from the faculty member responsible
for the group to a member of the RCR staff requesting
this action. The group and all the member accounts will be closed from the
date specified in the memo. Individuals, such as students in the group, who
wish to remain affiliated with the RCR will be given a grace period to
re-affiliate themselves with another faculty member agreeing to take
responsibility for them: the individual must show a reasonable reationale for
this new affiliation.
As pointed out above, closed accounts of faculty who remain at NYU-MC remain pending for one year. During this period the RCR will maintain E-mail pointers from the RCR machines to the new E-mail addresses of group members. Accounts of individuals who have left the institution are closed immediately and no forwarding addresses are maintained for them unless arrangements have been made otherwise. If forwarding addresses are established, these expire after a year or as soon as it is discovered that they have become inoperative.
Once a faculty group closes,
the files on the computers associated with the group's accounts will be
deleted by RCR staff. It is the responsibility of the group leader to ensure
that all data is removed and secured BEFORE the accounts are deactivated.
RCR staff will be happy to make special backups of the user areas before
deactivation: after the accounts are closed, this may nolonger be possible.
External Faculty Groups
In special
circumstances the RCR may permit faculty outside the NYU community to hold
(or continue to renew) RCR accounts. The basic mechanism for offering and
maintaining accounts is the same. However, there may be significant
restrictions on the services that can be offered to external users in order
that the RCR maintain the spirit of the license agreements for the software
it uses. The RCR therefore recommends that external faculty use the
resources of their home institutions.