Research Computing News
Volume 5, Number 1
August 1996
Contents
GCG v.9 Offers New Graphical Interface
Use the RCR Web Site as your WWW Homepage for Bioinformatics
Introducing the New RCR Molecular Biology Consultant
Course Update: Using Computers in Molecular Biology
Check RCR Newsgroup for Key Updates
Other RCR Services
GCG v.9 Offers New Graphical Interface
- Version 9 of GCG (Wisconsin Sequence Analysis PackageTM) will be available this November at RCR and we currently are evaluating a "Beta" version.In addition to some additional program options and minor algorithmic modifications, GCG v9 incorporates a totally new Graphical User Interface that will be known as SeqLab. This interface is based on the program GDE (Genetic Data Environment) developed by Steve Smith at the Harvard Genome Laboratory.
- Since the most frequently heard complaint about GCG is its cumbersome command-line interface and its steep learning curve, SeqLab should provide some very welcome relief Point and click operations are much more intuitive and the availability of GCG commands from menus greatly reduces the amount of memorization required to effectively run the program. However, the major drawback of SeqLab is that it requires an X-Windows environment. This means that users must either install an X-Windows emulator on their desktop computer (such as eXodus or MacX for the Macintosh) or else use the X-Terminals available in room 174 MSB.
- To try out the GCG v9 test release, just type gcgv9 at the $ (VMS) prompt on the mcrcr0 or mcrcr6 machine. To use SeqLab, you will need to use an X-windows teminal or X-windows emulator program.
- For a description and a glimpse of SeqLab, check our new GCG v9 Preview Web page (borrowed from GCG's own Web site) at: http://mcrcr0.med.nyu.edu/rcr/seqlab.html
- The SeqLab interface makes sequences the focal point of all analysis. Whenever possible, results will be represented in the context of the sequence or alignment.
- SeqLab offers powerful sequence editing capabilities:
- Enter new sequences, or edit existing ones on the fly, and then check them for accuracy using the checking mode.
- Align multiple sequences and group them to ensure that the alignment is maintained.
- Assign features to a sequence, allowing you to annotate your analysis.
- Highlight portions of your sequences or alignments with color for publication purposes.
- Select regions of a single sequence or of multiple sequences and analyze them with programs, such as PileUp or PlotSimilarity.
- Select regions of sequence based upon the feature table. This allows you to translation a set of exons for a gene, or to delete all introns.
Use the RCR web site as your WWW homepage for Bioinformatics
- We are in the process of totally re-creating the RCRıs website to provide more information to our users. http://rcr-www.med.nyu.edu/rcr/
- One of the most significant additions will be a page of links to Molecular Biology resources available over the World Wide Web. Use this page as your jumping-off point for exploration of the on-line biologistıs world. http://rcr-www.med.nyu.edu/rcr/molbiolink.html
- Another significant addition to the RCR website will be the complete notes for the course: Using Computers in Molecular Biology. Initially these notes will be similar to those used by Dr. John Hill in the Spring of 1996. However, the notes will be constantly revised and updated to reflect changes in the software and databases maintained by the RCR and to more closely reflect the new course being developed by Dr. Stuart Brown. By the Spring of 1997, the on-line notes will be identical to the notes used in the 1997 version of the course.
- We have also added the complete documentation for GCG and the new EGCG programs as part of the RCR web site.
Introducing the New RCR Molecular Biology consultant
Hello to all RCR users,
- I am Stuart Brown, the new Molecular Biology consultant at the NYU-MC RCR, filling the job previously held by Dr. John Hill. With this message, I would like to introduce myself and also continue a process of meeting with all RCR users in order to get acquainted, and to assess the current status of Molecular Biology computing at NYU.
- First, a bit of introduction. I am coming to NYU from a Postdoctoral position with the USDA-ARS Plant Genetic Resources Conservation Unit in Griffin, Georgia. (Yes, I am a Plant Molecular Biologist, but since coming to NYU, I have discovered that humans have DNA too!). At the USDA I developed microsatellite markers for sorghum, peanut, and other crop plants and used these markers to measure diversity and similarity in the USDA germplasm collection. In the course of this work I developed skills in automated DNA sequencing, analysis of raw sequence files, design of PCR primers, PCR, and automated DNA fragment analysis. I have also done a lot of library construction and screening, cloning, and other standard molecular biology lab work.
- Prior to my work with the USDA, I worked as a Postdoc for two years on expression of plant resistance genes at the University of Manitoba, in Winnipeg, Canada. I was involved in plant transformation, Northern analysis and RT-PCR. I did my Ph.D. work in Plant Molecular Biology at Cornell University in Ithaca, NY. My thesis research was on fungal genetics.
- For the second order of business, I will need help from all RCR users. I want to set up meetings with each research group that has purchased an RCR account. The topics that I plan to discuss at these meetings include (but are not limited to):
a) What is the general thrust of research in your lab - current and future
b) What computing resources are used in your lab including the RCR, Internet, or programs running on your own desktop machines?
c) What are your wishes for computational resources and support from the RCR -What do you use now?
What else would you like RCR to provide?
What can you imagine in your wildest dreams that computers can do to aid your research?
- Please contact me to set up appointments. I am also available to answer Molecular Biology or general RCR related questions by e-mail.
- My e-mail address is: browns02@mcrcr.med.nyu.edu
- I look forward to meeting with you soon.
- Stuart Brown
Course update: Using Computers in Molecular Biology
http://rcr-www.med.nyu.edu/rcr/molbio/syllabus-96.html
- The course, Using Computers in Molecular Biology (G16.2604), will be offered in the Spring of 1997.
- Dr. Stuart Brown will be the new instructor. The course notes are currently being updated and placed on the RCR web site so they can be used as a self-paced tutorial and reference. Check out developments at the course web page.
Check RCR newsgroup for key updates
- There are many different systems for communication within the NYU Medical Center. Printed notices can be posted on bulletin boards or sent by campus mail. Individuals can be contacted by phone, or just by dropping by their office for a chat.
- As the computer comes to play a larger role in our lives, computerized methods of communications have been widely adopted, but not everyone uses the same communication tools on their computer. Virtually everyone at NYU uses e-mail, but a mass e-mailing is not an efficient way to keep RCR users informed of important changes in RCR services.
- A better system is needed for disseminating information to RCR users, and users should also have the ability to post their own messages. Luckily, such a messaging system already exists within the Medical Center; it is the local USENET newsgroup: news:nyu.med.rcr. This newsgroup can be read from any terminal (or network connected computer) by typing news at the $ prompt, and then select nyu.med.rcr at the NEWS> prompt. VMS style help can be obtained by typing help but the VMS newsreader program is not warm, fuzzy, or user-friendly.
- Fortunately, there are some other, more user-friendly, ways to read USENET news. Netscape NavigatorTM (and most other Web browsers) can be configured to read USENET news. In Netscape, choose Mail and News Preferences ... from the Options menu at the top of the screen. Choose Servers from the tab-style menus at the top of the Preferences: Mail and News window. then type news.med.nyu.edu in the box next to News (NNTP) Server: toward the bottom of the window. You might also want to add mcrcr6.med.nyu.edu in the box next to Outgoing Mail (SMTP) Server: at the top of the screen, but do not put anything in the boxes below that govern incoming mail. Although it is handy to be able to respond to messages that you read in NEWS by sending an e-mail to the author from within Netscape, your Web browser is probably not a good choice as your primary e-mail reading tool. Towards the bottom of the Mail options in this window are two sets of buttons. Be sure that the following options are selected:
Messages are copied from the server to local disk, then:
- Left on the server
- Never
- When you are done configuring, double check that your Preferences: Mail and News window looks like the figure below, then click the OK button at the bottom right of the window.
- It is also necessary to fill out the information in the Identify section of Netscapeıs Preferences. From the Options menu again select Mail and News Preferences ..., but this time choose Identify from the tab-style menus at the top of the window. Enter all of the information requested, then click the OK button at the bottom right of the window.
- Now from the Netscape Window menu, select Netscape News. A new window will open on your screen. By default, you will have only a few newsgroups available in the left-hand half of the window, and each one of these groups will have a huge number of unread messages that will be listed in the right-hand half of the window. From the File menu, choose Add Newsgroup, then type nyu.med.rcr in the dialog box that asks you Type in a newsgroup to add to the list. Spend some time to familiarize yourself with the interface and read a few of the most current messages. Then you might want to delete all old messages so that the next time you look at nyu.med.rcr, you will only see new messages.
- It is worthwhile to browse around the wealth of other information that is available via USENET. From the Netscape Options menu you can choose Show All Newsgroups. This will create a nested list of over 3000 different groups where you can join discussions about topics ranging from HTML Editing to Alcoholism Recovery. Spend some time looking over the groups in the folder bionet, where you may find topics under discussion that are highly relevant to your own research. I particularly recommend bionet.molbio.methds-reagnts to everyone who does lab bench work in molecular biology.
- In addition to the NEWS capabilities of Netscape and other Web browsers, there are a number of small, free, applications that are dedicated exclusively to reading USENET. The Macintosh freeware program NewsWatcher by Peter Lewis is extremely good, easy to set up, and a pleasure to use. I highly recommend it, but I do not have space here to detail its setup and use. NewsWatcher can be obtained by anonymous FTP from mcrcr.med.nyu.edu and on the public AppleShare server NYU MC-RCR in the Apple Utilities volume in the News Things folder. It is also available from many shareware sites on the Internet.
Other RCR services ...
We have recently added some new molecular biology programs to the RCR's Alpha (VMS) server. The most significant of these is EGCG, a package of "Extensions" to GCG including alternate algorithms for standard GCG programs and many enhanced display options. Check out the EGCG manual at the RCRıs web site:
http://rcr-www.med.nyu.edu/rcr/egcg/
http://rcr-www.med.nyu.edu/gcg/
