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The new NIH forms are on the Mac IS server. PHS398 rev. 5/95 which are required for grants after 1/1/96.
Trouble e-mailing in Netscape?
11/21/95 I am working on the bug that crashes your machine when you print the oligo form. If this happens to you please
e-mail me
the type of computer you are on and the version of Netscape.(I'm blaming Netscape on this one). A quick fix is to "Submit" the order first and then go "Back" to "Print". This way we have the sequence even if it crashes.
11/17/95 The MBCF Open House will be on Thursday, December 14. At 1:30 pm invited speakers from Applied Biosystems Division/Perkin Elmer will be speaking in the Smith Family Room. "PCR: Optimization and Novel Applications" and "Fluorescent Sequencing: Template Prep and Editing." The seminars will be followed by a poster session of all services at the MBCF Dana 1030. This will be followed by food and refreshments until 7:00 pm. Hope you can make it.
11/17/95 The purified oligos ordered over the web our going through some growing pains. There are bugs to be worked out of the system. It's wonderful when you can pick up 48 purified oligos the next day. It's painful when we have to tell you that the 48 oligos synthesized fine but they're all floating in the waste container because of a line clog. Ouch. Bear with us.
10/23/95 The oligo order form is now functional. Order off the web site for $1.50 per base.
If you use paper the price is $1.85. As of today all 40 nanomole oligos are "ready to use". They have been
deprotected, purified, and quantitated.
10/10/95 New DNA sequencing price. DNA Sequencing will be adding a new sequencing service.
As of today, $22.00 per sequencing run will be charged if you do not require manual editing.
$30.00 per run will continue to be charged for all sequences that are manually edited.
Outside DFCI pricing will be $42.00 no edit, $50.00 Edit.
9/27/95 The new DNA synthesizer is now slated for arrival on 15 October. The annual MBCF open
house slash Christmas party is scheduled for Wednesday 13 December. If there is a conflict with any DFCI seminars or parties please e-mail me. We can move this date around. We will be offering several new enhancements to our current services at the open house along with door prizes. 2-4 pm science. 4-6 pm refreshments.
9/5/95 MBCF web site is upgraded to WEBSTAR 1.2.1. Should be much faster.
8/15/95 The network version of Sequencher 3.0 is now available in the MBCF folder on the IS server. Please read the installation instructions.
I add new information to the top of this file and leave the old information
untouched. I usually add something new at least once a month. Contact info and
computer vendor info at end of file.
-Paul Morrison web site url= http://mbcf.dfci.harvard.edu/
8/14/95 Sequencher 3.0 The Network Version is now in this folder. Please copy
the folder and follow the "Readme" directions. After you have it up and running
please return the hardware key.
8/3/95 BLAST E-Mail Help, BLAST Manual and BLAST FAQ have been updated.
Sequencher 3.0 "The Network version". In order to get rid of these
hardware protection keys I've just received the network version of Sequencher. I
will be asking for the return of the keys in a week or so and you will be able to
access the program with any networked Macintosh. 7/14/95 MBCF Web site URL = http://mbcf.dfci.harvard.edu Our web site is
officially open. Load this URL in your favorite web browser. Make it your home
page in NetScape or Mosaic. On October 1 or sooner you will be able to order an
oligo from the web page. Purified, quantitated and ready to use. Try Pedro's
Molecular Biology Tools.
6/1/95 Sequencher 3.0b12 Really the last beta. Your b11 copy expired at
midnight. Click install in the Sequencher 3b12 folder and follow the on screen
directions. If it says your EVE key isn't in the right place, just ignore.
5/30/95 SeqVu. Makes a pretty diagram of your protein alignment.
NewPowerPC 9400/PCI/132 Macintosh Computers. The 61, 71 and 8100 were just a
feasibility study of the PowerPC chip. On June 19,1995 you get to buy a real
computer.
5/10/95 Sequencher 3.0b11 If you downloaded 3.0b10 replace immediately with
3.0b11. This is really the last beta before the real 3.0 .
5/2/95 Sequencher 3.0b10 The last beta upgrade before final release of
Sequencher 3.0 If you want to know what the changes are just try it out or stop
by to check out the release notes. This version is "Fat Binary" which means it
has both native PowerPC and non native code. Some highlights: It screams on a
PowerPC.
It handles features in a new way.
2/9/95 Nentrez3.0 and nentrezcf Major upgrade. Faster,easier etc. Config to
EntrezBigMed.
1/23/95 Sequencher 3.0b2 Major upgrade to Sequencher. This is still a test
version. Wait a few more weeks for the release version unless you're dying for
heterozygote detection and chromatogram cleanup. It is also "non-native" code. If
you need the PowerPC version, contact me.
12/20/1994: e-mail Retrieve This a help file for using the e-mail Retrieve server
for DNA and protein sequences. This should be used for sequences that are brand
new. TurboGopher 2.05b Bug Fix.
11/29/94: TurboGopher 2.03b Much improved version of Gopher. Don't be swayed by
the glitz of MacMosaic. Supports "copy and paste" between main and bookmark
windows. TurboGopher can do a lot of thing faster, simpler and less wear and
tear on the network than MacMosaic.
Blast Client(1.08) Upgrade. Another way to do Network Blast searches. If you are
sending repetitive searches after viewing results, you might want to try Blast
Client. It shows results instantly in a new window.
Blast Manual, Blast E-Mail Help. Updates.
11/21/94: HyperBlast 1.10 upgrade Adds flexibility mimicking the changes that
NCBI has added to the Asn1 files. Also added is "Filter options". Short
description of what is filtered:The SEG program (Wootton and
Federhen, 1993) masks low compositional complexity regions, while XNU
(Claverie and States, 1993) masks regions containing short-periodicity internal
repeats. Note that neither SEG nor XNU is suitable for filtering untranslated
nucleotide sequences for use by blastn.
Nentrez Upgrade. If you use Squencher 2.0 and need an easier way to remove bad
sequence from the beginning and end of the chromatogram or need heterozygote
detection e-mail me and I will send you a copy of Sequencher3.0.
9/22/94: Phone numbers to get your 3 computer quotes are at the bottom of this
readme file. Some numbers have changed.
New Sequencher3.0 will be on the server by Dec 1. Heterozygote detection and
improved deletion of the junk sequence at the ends of the chromatograms. It is
also in native code. Beta versions that I have tried are 7 times faster. CLUSTALV
is now native.
MacMosaic 2.08 upgrade. Faster, better implementation of hotlist. I added a
few MolBio sites to the hotlist. This is the non native code. Native code is
available.
9/13/94:Multiple Alignment Construction & Analysis Workbench
(MACAW) is an interactive program that allows you to to construct multiple
alignments by locating, analyzing, editing, and combining "blocks" of aligned
sequence segments. MACAW incorporates several novel features. (1) Regions of
local similarity are located by a new search algorithm that avoids many of the
limitations of previous techniques. (2) The statistical significance of blocks of
similarity is evaluated using a recently developed mathematical theory. (3)
Candidate blocks may be evaluated for potential inclusion in a multiple alignment
using a variety of visualization tools. (4) A user interface permits each block
to be edited by moving its boundaries or by eliminating particular segments, and
blocks may be linked to form a composite multiple alignment.
7/11/94: Nentrez Release 3.0 There is no longer any reason to use Entrez
from Cdrom on a Mac that is on the DFCI network. This Network Entrez is much
faster and the databases are updated automatically. The entire DFCI is activated
to use the network databases. Take advantage of it.
If you have a PowerPC, be sure to use MacMosaic which is written in "fat"
binary. It is a speed demon.
7/05/94: MacPattern 3.2 update. MacPattern assists in finding putative
functions for new protein sequences by supporting pattern searches using the
PROSITE database, block searches using the BLOCKS database, and statistical
analyses (maximal segment score analysis). Please read the accompanying manual
and if you still can't figure it out, e-mail me.
6/24/94 MacMosaic2.0 and Sequencher 2.0 updates. Mail me if you
would like to try them out. They are Power PC and FatBinary. As soon as I have a feeling
that more then 10 people have PowerPC's I will start putting these programs on
the server. Entrez is already "FatBinary" which means it has the code in both
nonRISC and new Native code.
4/25/94 Location of MBCF printers has changed to MBCF zone. To send in
requests by sending them to our printers: The MBCF_IIg printer has moved from the
PTM zone to the MBCF zone.
3/30/94 : LaserWriter 8.1 Installer. This is an upgrade from 8.0 fixing some
bugs and speeding it up. 8.x is a huge improvement in printing speed. Also allows
printing of 4 pages on one sheet. Find it in "General Software" folder.
3/15/94 : Apple PowerMacs are in. The Power Macintosh 6100/60 is sitting on
the shelf over at Harvard TPC (495-5450) right now for $1,661.00, (no monitor).
This is the universal platform you've been waiting for. No reason to rush out and
upgrade because the "native" programs that will get a 5 to 10 times speed boost
are still being written. But if you are going to buy a computer anyway there is
no reason not to.
3/10/94 : Protein Structure Brush-up on your amino acids. MBCF photo Forget
who we are? Click on this.
2/28/94 :TurboGopher 1.0.8b4 TurboGopher upgrade. Color Icons. All known
bugs are fixed.
2/15/94 : GDB/Accessor 5.2 GDB/Accessor is called 5.2 to match the current
GDB version. Start-up and searching are faster.
1/5/94 : NCSA Mosaic 1.02 Bug fix upgrade. A little faster.
PowerPC's arrive on March 15. This week MacWorld Expo in San Francisco is
flush with programs that are already running in native mode. ( 10 times faster
then a Quadra 800. And don't tell me you don't need the speed. Or are you still
using a 128Mac with no hard drive?)
Has everyone got the message from IS that there is an easy way to dial in to
the network from home? You can access hard drives, read quickmail and print to
printers. (You have to be running Sys7 at home.) Any day they will upgrade it so
that TCP/IP programs will work from home too. Gopher, Blast, Telnet, Mosaic! Call
up the HelpDesk 23399 and scream " I want my TCP!"
11/22/93: NCSA Mosaic 1.0 Official release.
11/5/93: TurboGopher 1.0.8b3 Bug fix update.
10/25/93: NCSA Mosaic B5 Yet another way to navigate the internet.
9/20/93: GDB/Accessor Ä 1.0b A Macintosh program for accessing the Genome
Data Base (GDB) and related genetic databases on the Internet. No database
logins or e-mail addresses are required. This program has variations on retrieval
that complement TurboGopher. MacPattern 3.1 update. Changes: New statistical
analysis option: method of Eguchi & Seto to find the most "dissimilar" region of
a protein sequence, incl. graphical output; Support for GenBank format; Automatic
re-opening of index files on startup. Please rtfm.
8/30/93: NCSA GelReader 2.05 update. TurboGopher1.07 update.
7/23/93: Blast v1.6.1 update. FarFetch 1.1 update. Hyperblast is easier to
use but these programs have a little bit more to offer. Blast1.6.1 will complete
three-way searches.
7/09/93: MacPattern 3.0 update. MacPattern assists in finding putative
functions for new protein sequences by supporting pattern searches using the
PROSITE database, block searches using the BLOCKS database, and statistical
analyses (maximal segment score analysis).
Major changes in v3.0 are vastly improved pattern searches (search a 900 aa
protein against all of PROSITE in 6 seconds on a Mac IIcx), a new, faster
approximate block search method, and translations of nucleotide sequences in
three or six reading frames. Read the manual and then e-mail me.
7/01/93: Sequencher 2.0.10 update. Much nicer handling of the ABI
chromatograms.
6/10/93: A newer version of NIH grant templates. Take the time to try these
out and you'll never be trying to line up the photocopying again. Laserwriter 8.0
installer. This is Apple's new driver for the laserwriters. After running, go to
chooser and select LW 8.0 then hit the "autosetup" button. This will cut your
printing time in half. I put a copy in Software General use/Apple software.
6/2/93: New HyperBlast 1.09 This includes the ability to run your sequences
against KabatPro (sequences of imunological interest) and others. Also try Blast
1.4 one more time. With an ethernetted Mac you can see the search coming back in
real time and the built in help is good for fine tuning additional searches.
Authorin3.0 Submissions now are being handled by NCBI.
5/04/93: Sequencher 2.08 update. Disinfectant 3.1 update in public folder
from now on. Sequencher users make sure you update or you are losing out on some
great enhancements to viewing the chromatograms and editing consensus sequence.
You also get to hear Wally Gilbert read your sequence back to you.
4/12/93: Sequencher 2.07 update. Disinfectant 3.0 update
3/15/93: Sequencher 2.06b2 update and VecBase. This update does 2 new
things. 1) New parameter to "Auto strip" garbage off both ends of the imported
fragment. This is great for ABI files. 2) The ABI chromatograms are now reversed
in direction but the color is not changed. Also make sure you get a copy of
VecBase. This is the file that contains all of the popular vectors so that they
can be excluded when importing. If you tell it the vector and restriction site
the program will show you contaminating vector and ask you if you would like it
deleted.
Have you tried TurboGopher(1.06b3) lately? Use it to access the most up to
date Genbank and retrieve sequence with any kind of keyword.
2/08/93:
You may have noticed you can now log on to this server as "guest".
Learn a new trick: Make an alias of the server icon appearing on your desk
top and put it someplace convenient (like apple menu items folder). You can then
open it with a click.
MBCF now has a site license (as of 1/14/93) for Sequencher 2.0. For labs
that are sequencing and building contigs, this program is the way to go. If the
sequence is fluorescent then it is a must. You may run it in demo mode from this
folder. When you want to use it for real come get a hardware key. $50.00/month.
Directory of Tidbits in the MBCF folder
(Stuff that has been replaced by a better alternative gets moved to the
folder "Try an alternative")
Oligo Order Form To more easily order an oligonucleotide (especially from
Burlington) you can order electronically in several ways. Drag Oligo Order Form
to your Mac and fill it out Then do one of three things. 1) Print and fax to
632-4393. 2) Print to MBCFacility Laserwriter in PTM zone. 3) Attach the filled
out form and send by QuickMail to either Paul Morrison or Lori Wirth. Someday you
will be able to order directly to the synthesizer.
BIAcore Demo If you know what a BIAcore is then come talk to us. We have
one. If you don't then check out the demo. We will be introducing this service
shortly. (The demo turns color off, just go into control panel and turn it back
on after viewing demo.)
Entrez order form. Print this file, fill it out and fax in order form. For
$57.00 a year this is the first step in DNA and Protein sequence analysis. You
will need a CDrom player.
HyperBlast. A great program written by Mike Cherry at MGH,
(cherry@frodo.mgh.harvard.edu). (add: Mike is now at a genome type project at
Stanford, cherry@genome.stanford.edu). This will send Blast homology searches of
DNA and protein to the database at NCBI. The actual search in Washington takes
less than a second and the report is retrieved directly to your Mac. This is the
reason you just had that Mac ethernetted in your lab. You cannot use it on local
talk.
GopherApp: Don Gilbert's (IUBio) easy to use front end application for
accessing Gopher Servers. A fountain of information in front of you that has been
retrieved in seconds off remote servers on the Internet. If you have been waiting
for a painless introduction to the internet then copy this folder to your
ethernetted Mac and double-click.
Disinfectant 2.9 Today's latest and best public domain program to check if
your computer has been infected. You should also run some type of floppy scanning
for viruses. As of 7/6/92 there is a Mac virus that if infected you can kiss your
hard drive good-bye. LetÕs keep DFCI virus free. Be wary of any floppy that has
been across the river. Cambridge is infested.
The new NIH Grant templates to be used after April 1,1992 are in the folder
"NIH PHS398 as of 4/92".
Amplify is a Macintosh based PCR selection program in Amplify folder.
Fetch: A replacement for HyperFTP (see below) Much easier to use
and customize. A painless way to send IG formatted sequence to mbcrr so that
pro-search will run it. Also for retrieving the report.
HyperFTP: With this program you can get all the rest in their most current
version. HyperFTP will allow you to log on to Anonymous FTP from your Mac without
using a server. The programs go directly to your Mac. The program is probably
self explanatory if you read the header to "ftp-sites.txt" . The few things you
have to remember are: your name has to be "anonymous", your password should be
your e-mail address. If you don't know your international qmail address ask Chik
Tsiknas on qmail or 2-3399. You might already have an alias that is nice and
short. "firstinitial_lastname@farber.harvard.edu". When you log on a site first
read the "readme" file and the "catalog" file.
TurboGopher: An ftp and text display program for searching the net. This
type of program will be the preferred way to access remote ftp sites because the
connection is ÒstatelessÓ. The overhead on the server is much lower so that
multiple connections will not slow down. (New version 10/15/92 This may be the
best. Save your favorite site /directory as a bookmark.)
Once you get a program it will most likely be BinHex encoded (program.hqx).
Use Stuffit1.5.1 (on the IS server) to "Decode BinHex file" under the stuffit
menu and then "Open" the program.sit file that was just created.
CptExpand will automatically UNcompact a .cpt file.
GenBank Search. Extract sequences from genbank and they will be e-mailed to
you within 10 minutes.
Purchasing a Mac ? There is no reason to be stuck with the 6 to 8 weeks it
takes for an order to be completed through Harvard Tech. Prod. Center (495-5450).
For equivalent or cheaper price and a much speedier delivery check around.
ENTEX, Susan Russell 575-8212 , fax 2551590 << my current fastest cheapest
favorite.
JWP in Norwood (Paul Ghalani 575-8258) or Inacom (229-2190 in Burlington, ext 33
John Razado or ext31 Bob Chipman).
Paul Morrison Dana-1030
Molecular Biology Core Facilities
Dana-Farber Cancer Institute
1 Jimmy Fund Way
Boston, MA 02115
vox: (617) 632-3082 fax: (616) 632-4814 web site= http://mbcf.dfci.harvard.edu/ Qmail Paul Morrison at MBCF paul_morrison@dfci.harvard.edu morrison@mbcrr.harvard.edu
