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December 30, 1998
Make an interactive plan before you go to First Night.
Tenth Annual Molecular Biology Core Facilities Open House
Thursday, December 17, 1998
2:00 PM - 6:00 PM
Dana 830
The hot topics over appetizers:
What can Mass Analysis do for me?
What is high throughput DNA sequencing?
Where is MBCF going to be next year?
Thursday, December 10, 1998 POP mail
For those of you that are testing out e-mail using the Partners system the link POP on the very bottom right of the MBCF home page will get you there. Remeber to type in your short name in the first box. "PTM" for me. And then you are presented with a name, password dialog box. I type in "partners/ptm" for name and then my partners password.
Tuesday, December 8, 1998 Seminars In Oncology
Colorectal Cancer Genetins: Tumor Suppressor and Candidate Tumor Suppressor Gene Pathways
Eric Fearon, University of Michigan, Comprehensive Cancer Center
4:00PM
Smith Family Room
Dropping off peptides for synthesis or protein sequencing in August. Please contact us when you drop something off in August either by e-mail or phone. You should not expect delays because we are all caught up from the summer rush but you might drop off the day someone goes on vacation.
Wednesday, May 6, 1998
Auditorium, Jimmy Fund Building, Dana-Farber Cancer
Institute
1 p.m. Registration
1:30 "The Use of Multicolor Fluorescence
Capillary Electrophoresis for DNA Sequencing and Fragment
Analysis"
Paul Galgano, PE/Applied BioSystems
2:15 "The Role of Sequence-based Typing in
an Immunogenetics Laboratory"
Edgar Milford, Brigham and Women's Hospital
3:00 "ABI Prism 310 Applications in
Oncogene and Tumor Suppressor Gene Studies"
Jonathan Fletcher, Brigham and Women's Hospital
3:45 "Lung Cancer and Allelic Loss in Airway Epithelial Cells&emdash;Loss of Heterozygosity Analysis on the ABI Prism 310," Charles Powell, Boston University School of Medicine
The symposium is free of charge; however, space is limited and pre-registration is required. To register by phone dial 888/203-9868. For more information contact Chris Simollardes, 978/443-2960 or find more information on the web at <http://www.infolab.com/pe/310>.
cents a nucleotide inside the institute, one dollar outside.
This price is in effect if the oligo goes directly from the 3948 synthesizer to sequencing without researcher intervention. If you come by and ask for an aliquot, the price reverts to $1.50. Integration into a sequencing project and non interference by the researcher is the key to this fifty cent price.
"New Advances in Enzymology and Robotics: Towards Fully Automated
Fluorescent Genescanning,
Genotyping and Linkage Analysis," Dennis Gilbert, Perkin-
Elmer/Applied Biosystems
Advanced registration is required. For more information call 800/416-
8749.
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
4/28/98
Mitotic Motors in S. cerevisiae
The facility is working out the method in which we introduce the Biacore chip into the mass spec. Do a ligand fishing expedition and then identify the ligand by mass analysis. Stop on by and ask us how it can help you.
4/6/98 All MBCF servers are being changed over to Daylight Savings Time at 10:30 AM today. Avoid time conflicts and change your computer too. Just click ON Daylight Savings in your "Date-Time" Control Panel and SPRING ahead one hour. If you want an accurate system clock just download Vremya and aim it at "155.52.45.100". This should be the same IP address that is listed in your TCP/IP as "name server address".4/1/98 A new pricing schedule is now in effect for oligos ordered that will be going directly into MBCF DNA sequencing projects.4/13/98 On Monday, April 13, Lesley Stolz of BIAcore Inc. will be here from 1-4 PM to answer any questions about BIAcore SPR. She will be explaining the advantages of the recent upgrade as well as general questions of ligand kinetics.3/31/98
Mitogenic Signals and G1 Restriction Point Control3/24/98
Exploring the Virtues of DNA Alkylation Repair Using Knockout Cells and Mice3/18/98
How many times does the following happen to us: We find out third hand that a P.I. is angry about something; we're too slow, wrong sequence, peptide was garbage, and we call the P.I. up. We ask what the problem is and we get "you're too slow, wrong sequence, peptide was garbage". But when we ask for specifics and documentation of the problem we NEVER get it. So is someone telling fibs at the weekly lab meeting? Fibs of omission?
For example: "I don't have the sequence because the core facility has had them for three weeks". Instead of, "I don't have the sequence because the core facility has had them for three weeks because they have tried to sequence the sample several times and they say the sequence is 1) contaminated, 2) vector, 3) no DNA in the tube, or 4) all of the above.
I know that if no one was complaining then it means either we were faultless gods or we are doing something useful. We processed 49,000 samples/requests last year and are projecting 70,000 this year.
So, don't pass up the best reason for an on site core facility, (the ability to bitch directly at us), and stop by anytime. Officially we now have a "What's My Gripe" session every Thursday at 3:00 PM in the Dana 8 conference room.
Complain to your P.I. but bring the facts. And complain to us and bring the facts. This is your core facility and you can make it whatever you want.
3/2/98
Go to the
Women's Cancers Program Collaborative Research Grants page.Just get a letter of intent in by March 16. Or give Myles Brown a call at 617-632-3948.
3/3/98 "Mechanisms of Diffusion of Wnt and Hedgehog Morphogens," Norbert Perrimon, HMS
4:00 PM;Dana-Farber Seminars in Oncology, Smith Family Room, Dana 1620.
2/10/98 "The ATM Protein Kinase Family: Regulators of DNA Repair, Meiosis, and Cell Cycle Checkpoints," Merl Hoekstra, ICOS Corporation, Washington; 4:00PM;Dana-Farber Seminars in Oncology, Smith Family Room, Dana 1620.
2/10/98 We aren't moving! The facility is staying on the 8th floor of the Dana building. We just moved the Voyager DE-STR MALDI-TOF mass analyzer up to this floor! Watch this space for announcement of the Spring Open House in the MBCF in the same old place.
2/9/98 The "MBCF" AppleTalk zone is now "DFCI - MBCF" When using Sequencher 3.0 the "Sequencher Key Server" has moved to this new zone.
2/6/98 MBCF zone is DFCI-XRC Zone until Monday. This will only effect Sequencher network users. The Sequencher server will be found in zone "DFCI - XRC" until Monday. That zone will then be renamed "DFCI - MBCF". From then on Sequencher will find the key server in that zone.
The small print: The reason why this is occurring is that all of MBCF's computers, printers and servers are being moved on to their own more dependable network. The easiest way to do this was to buy the XRC's smart routers and move onto them as they moved to the Smith building. During the electrical shutdown on Saturday the zone will then be renamed.
1/16/98 MBCF Web site Upgrade. The MBCF Web site will be moving to a faster, more dependable network at 3:00 PM, Friday, January 16. Hopefully you should not notice much of anything but faster reloads in the coming weeks. If you do experience problems after 5:00 PM Friday, please notify me ASAP. paul_morrison@dfci.harvard.edu Paul @ 617 632-3082. For people outside the New England area it might take 24 hours before the new lookup tables propagate around the world.
1/12/98 HOTBOT web search. A search engine that for the moment blows AltaVista away is HotBot. Just as fast, better hits, ability to get 100 hits per page with short description. I put a link on the home page.
12/08/97 We're moving next year. The entire Molecular Biology Core Facilities will be moving upstairs to the Dana 14th floor in June, 1998. This will allow an expansion of services, especially DNA sequencing and Mass Spectrometry. We will be gearing up for this expansion before we move so we might experience growing pains before the move occurs.
12/08/97 New address The Dana and Mayer buildings have had their floors renumbered recently so they match the numbering system of the new Smith building. Therefore The MBCF present address is now Dana 830. (And instead of moving to the 16th in June we are moving to Dana 14.
10/21/97 The Perseptive STR MALDI/TOF mass spec is currently being installed in the facility. Come by and take a look, we will be asking for test samples to show you what it can do. More info later.
10/20/97 If you haven't used BLAST in a while check out PSI BLAST. Find it under the normal NCBI BLAST link. Brief Description:
The blastpgp program can do an iterative search in which sequences found in one round of searching are used to build a score model for the next round of searching. In this usage, the program is called Position-Specific Iterated BLAST, or PSI-BLAST.
9/12/97 Most of the DNA sequencing staff will be attending the Ninth International Genome Sequencing and Analysis Conference , Sept 13-17. DNA sequencing will continue through this time but keep the inquiries down to a dull roar. Thanks.
9/5/97, FRIDAY If you don't find us today it's because we're helping rename the street next door to "Jimmy Fund Way". Barbecue starts at 11.30 AM and the raffle is at 1:30 PM. Say hi to Yaz and Pudge Fisk.
08/29/97 The Human Genome Center at Baylor has reworked their "Batch Client v. 2.5 for BCM Search Launcher". It can be real handy for multiple file BLAST searches especially if you combine it with MacOS 8.
08/22/97 We have discovered that the 0.5 ml microcentrifuge tubes being sold in DFCI General Stores leak. 5% of the tubes will be empty after you have spun them. The tubes are:
USA/SCIENTIFIC PLASTICS, Cat#1405-000,Bulk pack 1000/unit
The QC# was 7113A2413 on the pack that leaked. When we notified the company we inquired whether they had any other complaints and they said they had.
My advise would be to not use any 0.5 ml tubes from USA/SCIENTIFIC PLASTICS and return the ones you have to General Stores.
ADDENDUM: 9/11/97 A company representative stopped by the lab. She actively tracked down the flawed tubes and replaced them from individual labs.
08/21/97 ABIView V.1.0 for displaying ABI trace and basecall data in Windows:
http://www.paranoia.com/~dhk/abiinfo.html
. If you want to keep your sanity, stay on the Macintosh OS and download
EditView. This program will allow you to view, edit, and print your DNA sequence chromatograms on a Macintosh.
07/30/97
The entire Facility will be closing at 12:15 PM today. The annual MBCF at the Red Sox Day Game is Wednesday, July 30 this year.
07/25/97
OK, now this is more like it. The National Library of Medicine as of June 26,1997 has made Medline (PubMed) free of charge. I type in tandom mass spectrometry, last 30 days and get mucho papers. After clicking on an interesting one I then click on the JBC link and get the full text with tables! And Mac OS 8.0 is on the shelves of the Micro Center on Saturday. Be still my beating heart.
07/24/97 Check out the US News and World medical report. It ranks the Dana-Farber Cancer Institute number four in the nation. Now if we could only tell US News that we had a real DFCI web site to link to. Every other cancer institute has a very informative link from the US News story. The DFCI link goes to the Dana Foundation! This site has not a scintilla of info about DFCI.
07/23/97 The Division of Immunopatholgy is testing out their new web site. This is a high end example of what each lab could have on the internet. The Immunology Seminar Series is the kind of helpful stuff that we need out there if it is kept current. I think they could catch the rat that runs across the page and add a big group picture of the division with names below.
07/18/97
BioTech's Life Science Dictionary
07/17/97 A new BLAST service for the recently released microbial genomes from
The Institute for Genomic Research (TIGR) is now available. You can do your protein against translated sequences that are being built into whole genomes but are not done yet. The question will be what happens when you get an interesting hit and now want the DNA sequence. Do you have to wait until completion of the contig or genome?
07/16-17/97 Visible Genetics will be giving demonstrations of their new automated DNA sequencing technology in the Dana 10th floor conference room on Wednesday and Thursday. If your lab would like to do high throughput molecular diagnostics by direct sequencing or variations on the theme you should stop by. Pour a gel and be ready to load in five minutes. DNA sequence data in less then 30 minutes.
07/15/97 The facility will be closed all day Tuesday in honor of BEACH DAY. Menu includes
Jack Daniel's marinated baby back pork ribs, German potato salad with sour cream, Greek olives and bacon,
home brew (a stout, a brown ale and a strong ale),
bocce ball and volley ball. Wayland Town beach and Paul's house.
07/01/97 Warren Gish has a new BLAST search which is called
WU-BLAST2. (He is at Wash U. now). The new version of BLAST which
includes gapped alignments is now available on the EMBL server. But check out the
BCM launcher page at Baylor. They have combined WU-BLAST2 with BEAUTY to make a lot more sense out of the alignments. BCM launcer has always been near the bottom of the MBCF home page.
06/19/97 OK, OK, by popular demand, the mbcf camera is back to auto mode. But if you don't have a life and sit there clicking on "reload" the picture will stop being refreshed. This is because if any file on the MBCF web server is hit a lot the file goes into ram cache.
06/16/97 The oligo problem (see 5/22/97) was not as bad as feared. There were some oligos that have been identified with deletions. These oligos have been identified and resynthesized.We have changed our protocols so that even this rare fluctuating valve failure will be spotted immediately and failed product will not ship to your lab. Besides never having it happen again we would like feedback as to how we could have notified users more effectively. It seemed like e-mail to all DFCI as well as putting notices on the web site was the fastest way.
And while you're thinking about it, ask yourself these two questions:
Do you think the commercial oligo suppliers have ever sent out a batch of suspect oligos?
Do you think they tried to notify all of their customers?
05/22/97 If you have used an oligonucleotide from us for cloning with run numbers between 29220 through 31395 please read this warning.
05/05/97 By reading this web site researchers at the institute can find out what goes on at the MBCF. But we would also like to know what you are doing. We have started inviting researchers from labs that are using us in their projects to speak at the MBCF lab meetings. This way we get to know why you are so anxious to get your data. We might even get excited about your project and work even longer hours. Or we may find an easier way to interact with your research. So if you would like to present in an informal way how the MBCF is being used in your project please e-mail me. Our lab meetings are at 2:00 PM on Thursdays. The slots are going fast.
04/04/97 Community of Science has gone to subscription only. So until someone figures out if DFCI paid the $10,000.00 you can't use them for Medline. But who cares? In the Entrez page NCBI has PubMed which gives you complete access to everything in Medline including not yet published. And if you want to download to Endnote just follow these steps. Paul Ferrigno in the Silver lab figured it out.
03/25/97 The Harvard Medical School and the Countway Library of Medicine has upgraded their web site with excellent links to electronic journals as well as medical area information. Click on the Harvard Med School Icon on the MBCF home page in the upper right. If you click on it in any other page at MBCF you go to the MBCF home page. The Nature and Science icons on the MBCF page will be replaced by something more interesting later because you can get to them from Harvard Med Web.
Your right, the MBCF live camera is not so live anymore. The color camera in live mode causes the site to hang once in awhile so I made it into a static photo that we can shoot anytime. If you want to be on the web for a day just come up and get your picture taken. Photo op is 11:30AM each day.
03/06.97 Be sure to check out "PubMed" listed on the Entrez page at NCBI. Another very slick way to interogate the entire Medline database. This seems to be as current as you can get.Why doesn't someone do a bunch of searches using this and Medline on "Community of Science" and tell me which one is better? C of S has EndNote download but PubMed has papers that are going to be published next week!
02/12/97 On April 19, 1997 TIGR is going to release 60,000 human cDNA's and 600,000 EST's. You will find them all deposited in Genbank. Pinch me.
02/04/97 RasMol 2.6 with Stereo view of Brookhaven PDB formatted protein files is in the MBCF folder on the MacIS Server. Or download here.
01/17/97 Non edited DNA sequencing reaches a new low price. As of the first of the year $20.00 will get you a non edited run. This is compared to $30.00 for an edited run. Save some money and learn to edit DNA sequence in your spare time. We have lots of easy ways to learn. Pick up a copy of Sequencher 3.0 and build the contigs yourself. And have you heard a rumor we are all going to have are Macs replaced at DFCI with PC's? As Nancy said, "Just say no." Even if it's free.
12/11/96 The turn-around-time for DNA sequencing is increasing. It's nice to be popular but results are taking at least two weeks. To alleviate this problem a fourth automated DNA sequencer will be installed later this month. We now need more space and more staff. Both are being resolved but it will take time. Please be patient.
10/23/96 Last Thursday, 19October the DNA synthesizer malfunctioned. That was 84 days of running without a failure. Today is day one of a new run.
10/4/96 No news is good news. 70 days of purified DNA synthesis without so much as a burp. Just ordered automated DNA sequencer number four to try to get the turn-around time from creeping past 1.5 weeks.
9/19/96 No if ands or buts, the DNA synthesizer has been operational for more than 55 days. 2.5 OD's has been the average yield for purified oligos. Turn-around-time has been always less than 22 hours. What more do you want? Same day delivery? On September 30 we will be upgrading so that 6 oligos, if sequence is in by 10:00AM will be ready by 5PM that day. The rest will go overnight. Procedures for identifying these fast track oligos will be put in place. Got any ideas? Should I charge more? Or should I allocate every P.I. an allotment of fast track chits that they can use or trade with their friends.
I would like to thank all of you who have put up with the transition to this new instrument. I would also like to thank the development team of the model 3948 DNA synthesizer at Applied Biosystems for making a fine instrument. If you read down this page you might find that it has not been a smooth road to get to this point. The way the instrument is running now I only see smooth road ahead.
8/5/96 OK, I know you're all going to say "Paul sure sounds like a broken record", but the DNA synthesizer is now working. In fact it has been working for 9 days straight! This is something it hasn't done since January. The yields are up and are now averaging 2.5 OD's for purified oligos. I'm not ready to say that everything is hunky dory but we have delivered all oligos in the last nine days the very next business day.
7/18/96 Check out the Community of Science Web Server that is listed on the MBCF home page. The DFCI has a subscription to this service so that Medline and patent searches are free of charge. Myles Brown tells me we should thank Bob Distel for this.
7/18/96 The replacement DNA synthesizer is nonfunctional. We are currently looking at alternatives for DNA synthesis. This problem will be resolved by August 1. Turn around time will be erratic until then. We apologize for the continuing problems with DNA synthesis.
6/14/96 The replacement DNA synthesizer is now on line. All of the oligos will again be purified.
6/4/96 Did everyone have fun during the power outage? Has anyone found out what happened? Did a squirrel fall off the exercise wheel? Shouldn't the lights work in the stairwells? Can Paul use a declarative sentence?
6/3/96 The new DNA synthesizer just arrived that will get us back in purification mode. It will be plugged in on Wednesday. A third automated DNA sequencer will arrive next week. Just a few additions to keep the expanding services from becoming backed up.
4/29/96 The continuing saga of the not quite released DNA synthesizer continues. We will not have the complete version of this machine until May 30, 1996. For all of you feeling the bumps of the beta test, just hold on a few more weeks.
4/24/96 The yeast genome is completely sequenced. The last 20% is not annotated so that searching with BLASTP will not find hits in these regions because the protein sequence is not there yet.
3/28/96 If your netscape doesn't work: Dialogue box says "Netscape was unable to create a network socket connection. There may be insufficient blah blah blah." This means that DFCI./IS has ran out of IP addresses to hand out again. Call 2-3399 And point this out to them. There is nothing wrong with my web site or your computer.
3/21/96
Down Load EditView. This program will allow you to view, edit, and print your DNA sequence chromatograms.
1:00-4:00pm, Wednesday, March 20
Auditorium, Jimmy Fund Building, Dana-Farber Cancer Institute
"Role of Polypeptide Sequence Analysis in Contemporary Health and
Life Sciences," Paul Tempst, Sloane-
Kettering Institute and Cornell Graduate School of Medical
Sciences
"New PCR Advances: Long PCR Applications, Novel Detection
Strategies, and a Hot New Approach to
Start PCR," J. Fenton Williams, Perkin-Elmer/Applied Biosystems
(They just want to know how many cookies to get.)
3/11/96 Printing the oligo form! The problem is resolved. When you submit a form now the response file includes all the information that you entered. Just print this out if you need a hard copy.
2/15/96 DNA Synthesis: A light at the end of the tunnel. Testing of the new synthesizer will be completed in 4-6 weeks. A note of appreciation for all who have been patient with us during this testing process. Let's hope the light isn't an oncoming train.
2/14/96 Netscape Navigator 2.0 (no beta) is available. Tell me when you want me to rewrite my pages so it uses the cool new menus.
1/25/96 We have been having continuous mechanical problems with the new synthesizer since 11/16/96. This has caused a large backlog as we switch back to the older machines. Please be patient.
Paul Morrison Dana-1030
Molecular Biology Core Facilities
Dana-Farber Cancer Institute
1 Jimmy Fund Way
Boston, MA 02115
The preceding comments are here to inform researchers at DFCI of recent changes in services at the MBCF. (Previous to 6/14/94 the comments were located on a local DFCI server and the comments pertained only to sofware used by the facility.) If your software is mentioned here it is because we use it extensively and you will only find update or bug list information. I will be posting "Paul's Review of Essential Molecular Biology Software" soon.
