This file is a compilation of MBCF News Update from 1995 when the original MBCF website was created to 2013 when the newest website was plugged in. I’m a pack rat and hate to throw things out. Useless to most, it can be used as a scattershot historical narrative of molecular biology updates through these years. I explain the problems and bugs that were a pain and also the seminars we attended.
Even before the 1995 website, there was an MBCF News Update blog that I wrote residing on an MIT DARPA net that was almost the internet. This file also captures postings from 1992 to 1995.
MBCF Late Breaking News 1992 to 2013, reverse chronology. There are many typos and HTML glitches embedded that I may or may not ever fix. Most links are broken or deleted. I may go through and activate the more interesting ones.
2013 to 2016 will occasionally be added from the limbo where they currently reside. Good ones will be separate files under the MBCF News menu or added to this file.
MBCF News Update
Tuesday, December 17, 2013, New MBCF Website will be plugged in.
The Molecular Biology Core Facilities which now includes Microarray, as well as Proteomics and Genomics, and a slew of other new services will plug in their new website this coming Tuesday, Dec 17. Hopefully, it will only be confusing for a short time as we combine and simplify three websites into one. On the left will be a simple jump off point which will be on every page to get to iLab, DNA LIMS, MiniLIMS, and Paypal. One stop shopping for entering data, interpreting data, finding out who moved your data, and paying for your data.
Saturday, November 23, 2013, Soft Opening of Advance Technology Core Jimmy Fund 408.
The Molecular Biology Core Facilities will be opening a satellite lab in Jimmy Fund 408 which will include MBCF instrumentation that is researcher operated. Right next to the flow cytometry core this lab will include MALDI/TOF/TOF mass spectrometry, Biacore 3000, Apollo 324 robotics for next-gen library prep, Agilent Bioanalyzer Tapestation, CLC Bio workstations as well as workstations for microarray analysis. We will move instruments in and out of this lab according to usage. After six weeks and no one is using it the service is moved out to be replaced by something new. Use it or Lose it. We will also allow vendors to set up long-term demos. They might sponsor a seminar then have their instrument available for six weeks. Nanopore, Nanostring will be doing this shortly. Our new website opening next week will have more details and a grand opening is planned for December. Anyone remember the MBCF Christmas parties?
We will also have office hours in this new ATC core. Currently, Zach Herbert 2-3PM Friday, Paul Morrison 3-4PM Friday although chances are you will find us there any afternoon.
Based on popular demand, we are pleased to announce another Galaxy training event for this year. BioTeam and the Galaxy Team are offering a training session that will focus on analyzing NGS Data using Galaxy. In addition to learning about the NGS related Galaxy features, you will also learn about what it takes to host your own Galaxy instance. This event is kindly hosted by Dana-Farber Cancer Institute. For more information about this training please visit the event website at Galaxy Training Registration website.
Date: Tuesday October 22nd, 2013 Time: 9:00am to 12:00pm
Location: Dana-Farber Cancer Institute
Smith Building Room 308/309
1 Jimmy Fund Way
REGISTER NOW: Galaxy Training Registration
Anushka Brownley Senior Scientific Consultant
SlipStream Appliance Galaxy Edition”
SlipStream Appliance White Paper
Tuesday, October 15, 2013, Big Changes to MBCF coming soon.
The Molecular Biology Core Facilities has been undergoing massive changes and improvements. Focus on what works, get rid of what doesn’t. This has been an ongoing process. Incorporation of Nanostring technology, NGS library prep, expansion of Next-Gen sequencing, incorporation of microarray, just a few of the numerous changes as we try to do more with less. You have to do the same thing with leaner RO1 funding and it is the same in the cores.
Mostly these changes have been word of mouth because we wanted gradual ramping up but now we need to open the doors a bit more. The lines have blurred between different genomic technologies and we want to make sure that Dana-Farber researchers know about all the choices they have on and off campus. If another core does it better or a commercial source, we’ll tell you about that too.
To that end we are announcing two changes:
1) A new MBCF website. Relatively unchanged since it was introduced in 1995 it is time to swap out the old technology and bring in the new with a more interactive website incorporating everything we now do. This site will ask your opinion about everything. Don’t be shy to tell us both anonymously and directly. This site will allow easier access to your data, your accounts, your billing, everything. As this site goes live we will ask again and again for your feedback. We are too close to the product so we might miss a glaring omission that impacts your research. Do not suffer in silence.
old mbcf stuff non bio bpc , currently residing at mbcf149
2) An Advanced Technology Core on Main Campus. Final details are being worked out but we have a slew of instruments that should be closer to researchers because they get the best use when they are researcher operated. This “ATC” core will also be home to vendor demonstrations of new technology. On average, this technology will be showcased for six weeks but if the demand is great we will find a way to keep it around. If you know of new technology that needs to be on campus tell us what it is and we will line up the vendor.
The website will be changing soon, the ATC core will go online later in the fall. We hope you bookmark the new website (which will still be mbcf149.dfci.harvard.edu) and watch us grow this fall.
September, 2013 New additions to MBCF
Really too many to list. Stop on by. Next Gen Sequencing Prep, Library prep on Apollo robots, new longer reads, both paired ends and single on Illumina MiSeqs. More reads per run.
January 29, 2013, Illumina MiSeq Now three machines
Sorry for no updates but we have been going crazy. Three Illumina MiSeqs now installed and updated. Paired-end 2×250, indexing, get your data the same day! Currently, we have for Q/C the Bioanalyzer Tapestation, QPCR, and an assortment of other tools. We will get your sample to work. We are testing am IntegenX Robot for TruSeq and other flavors of library prep. Sick of library prep? Talk to us.
Click on MiSeq Information at MBCF for more information. Check in often as this information will be updated often. Illumina has a ton of cool upgrades in the works for the MiSeq.
2012 Late Breaking News
May 30, 2012, Illumina MiSeq Next-Gen Sequencing out of Beta
We have run 27 different projects in the last few months. The MiSeq does well in various applications of Next Gen. Metagenomics, small genome, Epigenomics, targeted sequencing, indexed sequencing. The turn around time can be as fast as same day. Yes, a ChIP-Seq 50 or 2×35 and you get the data back the same day. 2×150 paired ends in three days. These times will continue as we just received our second instrument and will be installing a third when required to ensure you do not have to twiddle your thumbs like when you submit to the hulking behemoth Next Gen boxes.
We will be beta testing new 2×250 paired-end reads which can generate 16-19 million reads. That is 500 nucs times 19 million. Talk to us about indexing several samples into that one run, it’s easy. Click on MiSeq Information at MBCF for more information. Check in often as this information will be updated often.
Thursday, May 3rd, 2012: MBCF Open House in Dana 1620, the Smith Family Room, 1-4 PM New Genomics, Proteomics Services
Come check out all of the services available at the MBCF and meet the staff; Thursday, May 3rd from 1pm-4pm in the Smith Family Room, Dana 1620.
Learn about our Genomics and Proteomics cores, new DNA Sequencing services, Mass Spectrometry, Biacore, and more! Come discuss how we might be able to help you with your project.
Genomics Core Services:
New Illumina MiSeq service
Genotyping, Spectratyping, Cell ID,
Free Oligos (for sequencing)
Proteomics Core Services:
Mass Spectrometry: MALDI-TOF, ESI LC-msms, Post-translational modification analysis, mass fingerprinting, intact mass analysis
Biacore real-time interaction analysis
Amino Acid Analysis
Hands-on Tutorial Sessions
Did we mention there will be refreshments?
Here is a nice pdf to hang in your breakroom: CLICK
2011 Late Breaking News
Monday, December 19, 2011: Illumina MiSeq Next Generation Sequencing in a very short beta start-up phase
For the next thirty days we will be selecting samples for MiSeq next-gen sequencing. To validate the instrument on as many different applications we will be looking for variety, not volume. Small genome resequencing, indexed amplicon resequencing, de novo structural variants on small genomes, ChIP-Seq, QC library prior to HiSeq runs, etc.. Go to the Illumina MiSeq at MBCF page for further information. We are most interested in your sample if it is “different”. Contact Us for more info.
Monday, August 15, 2011: New Afternoon Sample Pick-up Time
Tired of rushing around to get your samples into the Fish room before noon? Stress no more. We’ve added an afternoon sample pick-up time. If you get your samples in before 3:15 pm (or 3:00 pm CLS building), you will get your data back the following day by 12:00 pm noon. The two current samples pick-up times remain the same with data returned the same day.
NEW! Sample dropped off 3:15 pm data in your folder NEXT DAY by 12:00 pm or sooner.
Sample dropped off 8:15 am data in your folder SAME DAY by 4:00 pm or sooner.
Sample dropped off 12:15 pm data in your folder SAME DAY by 8:00 pm or sooner.
The Power of Microfluidics: Enabling Genetics and Genomics Research
Jason T. McKinney, Application Scientist, Fluidigm
DATE: THURSDAY, JUNE 23RD, 2011
TIME: 11:00 AM Ð 12:00 NOON
LOCATION: SMITH BUILDING ROOM 308/309
Hosted by Thomas Westerling/Myles Brown Lab
Through the use of what is now the well-established field of Microfluidics (the handling and manipulation of nano- and picoliter fluid volumes), research in genetics and genomics is being revolutionized. The Fluidigm technology enables experimental design and execution previously considered impractical, if not impossible. Following a brief introduction to the core Fluidigm technology, we will introduce some of the more exciting work being done: SNP Genotyping with emphasis on economy-of-scale cost benefits (reagents and labor); traditional gene expression with a focus on Single-Cell studies; Digital PCR (limiting dilution quantitative mutant allele determination); and an exciting workflow for Next Generation Sequencing complete sample library preparation.
Please RSVP: email@example.com
PDF of talk to post in your hallway.
Friday, March 11, 2011: To Tweet, or not to Tweet. That is the question.
Scientists Connecting: Why Social Networking Matters
By Paul Morrison, Dana-Farber Cancer Institute
If you think you don’t have time in your day to create a LinkedIn page, or figure out how to Tweet, or even where there are good scientific blogs to read – you may want to rethink. You may end up with plenty of time because by not staying current, you are out of a job. (Click here for the rest of the story published in ABRF Communications.)
Monday, January 31, 2011: Advances in Genome Biology and Technology this week.
Registration was only open for a day so the lucky few get to go to AGBT on Wednesday. Twitter hashtag is #AGBT. The MiSeq is cooler than just a small HiSeq and Oxford Nanopore has a few exciting changes to their website just prior to the meeting. Wish I was there. Ah well, the dust will settle and the ABRF meeting on Feb 19-22 I can sit down and glean the wheat from the chaff.
Friday, November 26, 2010: All MBCF servers went offline for 30 minutes this morning, 9:30 AM
Don’t know why it happened. All data seem to be untouched. Backups to 6 AM are fine. We will be checking throughout the day but it could have been a network outage to the computer center at Burlington Avenue.
Wednesday, November 3, 2010: There is a reason to read Twitter
You couldn’t make it to the American Society of Human Genetics 60th Annual meeting this week. But you can read the headlines as they are spoken on Twitter. It’s easy. Take the acronym of the meeting and add the year to the end and a hashtag to the front. That means this meeting is #ASHG2010. Go to Twitter and search for that “hashtag”. (For the lazy just click the link.) You don’t need an account. Scientists in the audience are tweeting and “lukejostins” is a good example. Because not only does Luke Jostins tweet but he also has a blog called Genetic Interference which he then explains at the end of the day what his tweets meant. There are perhaps a dozen tweeters at ASHG doing the same thing. If you follow meetings and tweets you begin to learn who to read, who to follow, and who to disregard.
You do not have to sign in or create a Twitter account to do any of this but the Twittering gets easier if you do. You can save searches, follow the interesting people who tweet in /biotechnology and /sequencing. You do not, I repeat, do not need to follow me (MBCF) on Twitter.
Friday, October 8, 2010: CLC Bio at DFCI Pilot of Next Gen Software
Are you drowning in next-gen data or think you might be really soon? Not finding any decent solutions? There aren’t any! But there are some decent ways to slice and dice and visualize your data. CLC Bio is one of them. It can handle Helicos ChIP-Seq as well as that massive amount of data coming from your new Illumina HiSeq2000. DFCI and CLC Bio are currently working on a pilot of a server to move the demands of CPU horsepower off your poor underpowered desktop. Read this announcement PDF and contact Contact: Naomi Thomson firstname.lastname@example.org to sign up. Do it now.
Thursday, August 26, 2010: Bus Shuttle iPhone app!
To view the shuttle buses running around the Longwood Medical Area Click here. Since there are so many more buses the best way to catch a bus is to see where the next one is and then bolt from the lab. Even better, on that page lower left is a link to an iPhone app in the iTunes Apple Store which will give you an active map right on your phone. It works. I took the shuttle for the first time in months yesterday. Click this link to load it on your phone.
Tuesday, February 9, 2010: New Shuttle Schedule
Getting from the main campus to North Campus and MBCF at 21 Burlington just got a lot easier. All of the Institute Shuttles are now combined so a shuttle should be by every 6 to 15 minutes. (More shuttle in the morning and afternoon.) For now, CLICK HERE to get a new schedule and even view a map of where the shuttles are in real time. Make sure you copy the link to “Mobile Access” onto your iPhone or other internet devices so you can see exactly where the shuttle is.
Important: The drop off at North Campus is no longer on Burlington Ave but now goes to 20 Overland on the other side of the building. There are also plenty of stops right out on Brookline Ave at the corner of Overland and Brookline but also the bus stop in front of Harvard Vanguard.
Tuesday, December 15, 2009: New Longwood Area Shuttles
MBCF will be working through the holidays. Except for Christmas Eve and Christmas as well as New Year’s Eve and New Years Day we will be accepting samples. Go to the Bruins hockey game in Fenway Park instead.
Monday, November 23, 2009: Helicos Massively Parallel Sequencing
New Helicos Massively Parallel Sequencing answers here. The testing of this instrument has been working out very well. The project is now being opened to all interested labs. Informatics expertise dealing with large datasets is key but there are many avenues of help open to you and we will point the way.
Sunday, July 19, 2009: The MBCF LIMS Server is back online after a restart. The server failed on July 18. Thank you to all who notified us that the LIMS was unreachable. (The notification software did not work.)
Friday, May 29, 2009, Getting a computer fixed.
1) Harvard Technology Services will repair PC, Mac, or HP laser printers. Make sure when you call you indicate that it is departmental equipment or else they will tell you to drive it over.
2) If your Macintosh laptop or tower is acting up the first thing you should do is try the Apple Computer Store on Boylston Street. Just make a reservation at the Genius Bar. (OK to select “guest” than technical support.) Likely you can have an appointment within the hour. I did that Wednesday afternoon for a Mac laptop that had a screen not lighting up. It took all of 30 seconds for the genius to diagnose and they called me the next morning that the logic board was replaced and I could pick it up. Out of warranty, free of charge. Was it my winning smile or did my DFCI ID get me the white glove treatment? Not sure but it is worth a try when something needs fixing. He did not know how to quickly analyze ChIP-Seq data off a Helicos sequencer so there are limits.
Monday, April 21, 2009, Testing of Helicos 3rd generation DNA sequencing.
This summer the MBCF is testing the Helicos single molecule sequencer. Although this instrument sequences massive small runs of DNA like other “next-gen” sequencers it is really the third generation in that it is a true single molecule sequencer. In short, this means there are no amplification steps, sample prep is very easy, and the bias attributed to amplification is not present. These differences make it a very interesting protocol for ChIP-Seq and digital expression analysis. We are presently working with twelve labs in a test phase. These labs were selected because of their strong bioinformatics background with next-gen data. We will be opening up testing soon to another set of labs. If your lab is interested please contact Paul Morrison and Zach Herbert.
Wednesday, April 8, 2009, Pay Your Bill Entrez
We have made it easier than ever to pay for services ordered here at MBCF. If you are outside DFCI you can now use any Credit Card to pay for services when ordering to ensure that we start working on your project right away. Open an account, order the service and select the credit card option and follow the directions. If you need to pay a bill without ordering services just click here. Entrez
Wednesday, December 17, 2008, DFCI Research Computing now handles Sequencher completely.
For some time now Research Computing has taken over the contract of implementing Network Sequencher here at DFCI. It’s all good. Cheaper, one-stop installation for both PC and Macintosh and all completely up to date.
Go to Sequencher at DFCI page to get the latest version with very simple step by step instructions
nb: It would be smart to remove as much as possible of your current installation including anything that is connected with the key server, empty your trash, and restart before going to retrieve a new version.
Do you know that DFCI Research Computing has a full implementation of DNAStar right? Just click here.
Tuesday, December 9, 2008, Another Speed Boost to DNA Sequencing
We have made improvements in our servers so that MBCF staff can remotely slice and dice your DNA sequencing and get it to you at night and on weekends. Now all samples, even the 12:15 drop off, will get back to you the same day:
Sample dropped off 8:15 AM data in your folder same day by 4:00 PM.
Sample dropped off 12:15 PM data in your folder same day by 8:00 PM
Monday, November 17, 2008, New BLSC Drop off for MBCF Samples
Besides dropping off samples in the MBCF Fishroom on the 3rd floor of Smith building or directly with us in the lobby 4th floor Burlington we just added a third drop off on the 11th floor of the CLSB building on Blackfan Street. DFCI labs on the 10th and 11th floor now have an easy drop off as well as BIDMC labs or any other lab in that area.
Friday, September 12, 2008, Faster, Cheaper, Better DNA Sequencing
Have you noticed you are getting your DNA sequencing data delivered the very same day you drop your sample off in the Fishroom? Have you noticed the sequencing is cheaper? Spread the word. The more people who use us and the more samples coming in means it will get even cheaper. don’t worry that more sequencing will slow your results down. We have upgraded and built in large capacity.
Are the pickup times convenient? Tell us if they are not. Do you want an additional drop off spot? Tell us where.
Sample dropped off 8:15 AM data in your folder same day by 4:00 PM.
Sample dropped off 2:15 PM data in your folder next morning by 10:00 AM
Monday, June 9, 2008, MBCF LIMS system was offline Sunday.
Sometime in the early morning Sunday the MBCF LIMS system went offline. The Red Sox won but made the restart occur at 2 PM. No data were lost. Sorry for the inconvenience.
Monday, April 28, 2008, Transport Form for the Shuttle
If you are taking the shuttle with samples you need to print this form, fill it out, and tape it to the outside of the sample box. Don’t get caught without it. They will kick you off the shuttle.
Thursday, April 3, 2008, New Guidelines for DNA Sequencing
Check out the new guidelines for DNA sequencing. We now have three different services.
Primer Added Fast Track (you add primer) $8
Primer NOT Added Fast Track (we add primer) $10
Difficult Template $15
If you use the first service obviously it will be cheaper but you will also get the same high-quality data sooner.
Friday, January 25, 2008, MBCF 3 PM Gripe Session Cancelled
Paul has to go to his daughter’s piano recital. Individual appointments with the rest of the MBCF staff are still available.
Wednesday, October 17, 2007, MBCF LIMS Server down for twenty minutes.
The MBCF LIMS servers (click the fish) will be turned off for twenty minutes this afternoon. The start time of this outage will be approximately 3:30 PM. Go have a cup of coffee and we’ll be right back.
Tuesday, October 16, 2007, MBCF LIMS Server down for twenty minutes.
The MBCF LIMS servers will be moved this week. It shouldn’t take more than twenty minutes. I’ll note the exact time here before we do it so hopefully, anyone who is panicking comes here and is reassured. Go have a cup of coffee and we’ll be right back.
Tuesday, August 13, 2007, The Blais Proteomics Center is having the electricity turned on today.
Be ready for new additions to Mass Spectrometry. High throughput, high resolution, more data than you ever wanted to analyze.
Friday, June 15, What’s Your Gripe Session new day, new time.
Every Friday at 3:00 PM
Fourth Floor Conference Room
North Campus 21-27 Burlington Avenue
Monday, June 11, 2007, MBCF Web Sites Upgrade
The upgrade to the MBCF websites is completed. If you find anything wrong please e-mail email@example.com as soon as you can and point out the problem. Everything should load up faster than ever. All pages and software are now running on Mac OS X 10.4.9. If you have problems running Sequencher just read the next note.
Friday-Monday, June 8-11, 2007 MBCF Sequencher Server Switch
MBCF will be upgrading several servers this weekend. If all goes well on Monday morning we will be sending out an e-mail to all LIMS accounts. This email will deal with the only change that needs to be done on the client’s side.
Sequencher users after Monday morning will have to change the server IP address of our server which hands out keys for that software or else you will only run in demo mode. When this dialogue box comes up telling you the server is unavailable just follow the following simple steps.
To update Sequencher 4.5 key server
Quit Sequencher (demo mode)
Go to Sassafras K2 folder in your Finder Applications folder
Open Client folder
Double click KeyAccess Setup
Enter 220.127.116.11 in Connection: TCP/IP field
(This field should currently have 18.104.22.168)
You can now start up Sequencher.
Wednesday, April 25, 2007, MBCF Lab Merchandise
DFCI Coffee Mug MBCF Hoodies, Tee Shirts, Coffee Mugs, check it out.
Saturday, January 27, 2007, New Genotyping Strategies
Go to New Genotyping Strategies at MBCF to see how we might be able to help you design a better way to do microsatellite analysis, spectratyping, LOH studies, or multiplexed SNP analysis. The tools are constantly changing so this linked description was just written but is already old news. Talk to us. We might have the tool or we might tell you that the Broad Institute has the better tool.
Monday, January 1, 2007, MBCF Web site server outage
The MBCF server controlling the main MBCF web site crashed on 12/31/06 at 2:11 AM. The alarm system malfunctioned and no notifications were sent. This was not discovered and fixed until 1/1/07 at 1:11 PM. Fortunately, no data were lost. All primary services connected to the LIMS system continued to function during this time. Researchers may have only been stuck if they had not saved a direct bookmark to “Click the Fish”. We will be replacing systems the first week of the new year in order to keep the failures from ever occurring again.
Tuesday, December 19, 2006, MBCF Holiday Hours
The MBCF elves will be working on your samples throughout the holidays. But think ahead if you need 16-hour turn-around-time on those naughty or nice genotypes. Drop off in the Fish Room will be open 24/7 but if all else fails read the North Campus Shuttle Schedule and stop on by. It is only a five-minute ride. Faster than the Dana elevator.
Friday, October 27, 2006, Firefox Browser
As of today, I recommend Firefox browser for both Macintosh and Windows operating systems. The switch is painless and Macintosh now has Firefox 2.0 which is the cat’s meow. Intelligent Tabs, searchable history, wicked fast, as well as a slew of other improvements.
Monday, September 25, 2006, Running Windows XP Pro on your Macintosh
There are two pathways to do this easily. Run BootCamp made by Apple which allows the new Intel Macintosh to boot directly into Windows XP. The other way is to run Parallels to run Windows XP in a separate window under emulation. I have tried both and Parallels is the way to go. The emulation has no impact on the speed and you do not have to keep rebooting to switch operating systems. The installation is very easy. Make sure you install “Parallels Tools” which is right under the “VM” menu item. Stop by MBCF if you would like to see this work. I am editing this page and looking at the changes in both Windows XP Internet Explorer and Mac OS X Safari browsers at the same time on the same computer.
Are you worried that the new Windows Vista operating system will make this all obsolete? Vista is already running in Parallels. And anyway, Godot will show up before Vista does.
Sunday, August 26, 2006, Summer doldrums, what to do?
Buy a computer! Mac or PC? That isn’t a good question anymore. Purchase the fastest desktop computer on earth which can run UNIX, Macintosh OS X 10.4 as well as Windows XP all natively. That way you can run all scientific programs on the best platform for that particular program. Using BootCamp a quick restart will switch you from OS X to Win XP or use Parallels for simultaneous operating systems.
What computer is that you ask? There is only one computer which fits the bill. The Mac Pro.
Which Mac Pro to buy? Harvard TPC currently has on the shelf the 2.66 GHz model. The 3.0 GHz model is not worth the extra 800 dollars. One might only expect a 6% increase in speed. (This will change as more programs become universal binary coded.) Do not buy Apple’s expensive memory. Get it with 1GB and then go to Transintl for 1 and 2 GB sticks of RAM. They have to be purchased in pairs and the Mac Pro has 8 slots. A deal is two sticks of 2GB for $999.00. That way you can easily increase to 16GB of memory later.
Then there are the four bays which can be filled by cheap 7,200 RPM SATA hard drives from Micro center right over in Cambridge.
The 30 inch Apple LCD has also dropped in price so you do not have to feel guilty about this purchase. The Mac Pro video card can run a 30 inch and a 23 inch LCD screen side by side right out of the box.
That is a computer which can be on your desk before September 1 when the fall crunch begins.
Tuesday, May 16, 2006, MBCF CoreLIMS Calendar is down
The calendar program for signing up for DE-STR Mass Spectrometry and BIAcore 3000 time is currently not functioning. Just e-mail to sign up for time. It will be down for a day or so.
The rest of the MBCF LIMS system has recovered from the hard drive failure of May 13.
Friday, May 12, 2006, MBCF LIMS Server hiccups
On Wednesday the Click a Fish LIMS server started having difficulties. The main hard drive began a long slow death spiral. MBCF crew isolated the problem drive and started extracting ones and zeros to bring all accounts up to date. We did not want to fall back to a backup that was a few days old. Successful extraction and recovery were finished on Thursday afternoon and Click the Fish was back on-line at 4 PM. We will be upgrading the entire system next week to create a disaster recovery which will be automatic. We will take the system down from midnight to 6 AM a few times in the next week to complete this upgrade. We will tell you here and also out on the home page above the fish to warn you not to enter data that night.
If you experience any difficulties do not hesitate to e-mail us.
Do you know why this cow is in the Smith lobby? E-mail me the reason.
Tuesday, April 11, 2006, Apple Computer does Window XP
Apple computer announced on April 5, 2006, that Microsoft Windows XP could be installed on all Macintosh Intel computers. What does this mean? It means that Apple Computers can run Mac OS X, Windows XP, or the Linux operating system in native mode. There is no emulation so the operating system and applications will run as fast as the CPU will allow.
Today you can download Boot Camp from Apple and start using Windows XP. After installing you just hold down the option key then select the operating system you want to use.
OS X 10.5, Leopard, which will be out in June will have Boot Camp already installed. All you need is Window XP install disks.
So as of today, there is only one laptop which can run every operating system. The Mac Powerbook Pro. Why would you purchase a laptop which only ran Windows?
Tuesday, February 7, 2006, Just a fun fact.
Did you know that every header of every page at MBCF links to three different websites? Check it out. Click on the DFCI Flaming D and go to DFCI. Click on the Harvard Med School school shield and go to their site. Click on our facility name from any page and you are taken to the home of MBCF. It’s been that way for five years. Did anyone notice?
Tuesday, January 3, 2006, A Happy New Year for viruses and worms.
A major vulnerability has been discovered in the Microsoft Windows operating systems. A WMF (metafile) can be manipulated so that just viewing a graphic image on a website or in an e-mail can release a computer virus which infects your computer. This affects all Windows systems back to Windows 3.0.
All of your data at MBCF resides on MacOSX or Linux systems which are not affected.
Laymen update at Wikipedia WMF exploit.
Microsoft has announced it will release a patch for this weakness on Tuesday, January 10, but meanwhile, multiple viruses are showing up exploiting the flaw. This may be a problem for several weeks.
Monday, October 24, 2005, All MBCF Services are Electronic Ordered Only
All services at MBCF are electronically ordered. Go HERE to open an account or to log in to your existing account. In the future just go to the MBCF web page and Click the Fish. Samples can be delivered and picked up in the Fish Room sample drop off, at our Burlington Ave labs, or we can also FedEx.
Tuesday, August 23, 2005, MBCF Server is back in action
The MBCF Web server hard drive crashed on Monday morning. Sequencher was unavailable.As of 2:00 PM today it is now up and running. All services should be functional. Please e-mail me ASAP if you find something out-of-order.
Monday, August 22, 2005, MBCF Web Server has had a meltdown. No data lost.
The MBCF Web server has crashed and we are working for the moment on a June 2005 copy. All of your accounts and data are fine. You may find some links broken but this will be fixed within 24 hours.
Unfortunately, Sequencher will be unavailable until sometime tomorrow.
Monday, May 9, 2005, Sequencher works in Tiger Download latest version.
If you start up Sequencher and it only works in demo mode please contact us ASAP. (Call 617-632-3082) It is likely that the server key needs to be restarted. But we won’t know to restart unless someone tells us. The copy protection software is flaky. We hate it as much as you do.
Monday, February 28, 2005 FinchTV 1.3 Chromatogram viewer Update Get FinchTV!
Just click on the button and go to the bottom of the page to get a MacOS X, Linux or Windows chromatogram viewer.
Geospiza does it again and with FinchTV 1.3 makes an outstanding free viewer of DNA chromatograms better. Edit, print, view various ways. Now you can view the RAW data. If you want to improve your sequencing you need to look at the raw data. It shows the subtle changes that will be masked by the software. Improve your sequence length and take a look. Another new feature is directly going to NCBI BLAST services.
Monday, February 7, 2005, DNA Sequencing Primers are now free of charge.
Yes, free. All oligos ordered by Institute researchers for DNA sequencing primers are now free. How can we do this and make money? Simple. We aren’t supposed to make money. We are here to help you get the most science done possible. Charging you for services is just to keep you in check so we aren’t doing dumb science 24/7.
A note about common primers. If you submit a primer that you think someone else might find useful then, by all means, tell us and we will keep a supply and put it on the common primer list. Just give us a good name for it and a short description of why it would be useful. Then the next time you need it we already have a primer ready to go. They can also be not so common. The TLGZFEVP would be an example. “Tom Look Groovy Zebra Fish Expression Vector Primer”.
Saturday Night, December 18, 2004, MBCF moved today.
Six tons of scientific instrumentation was moved 1000 yards to the fourth floor of 21-27 Burlington Avenue today. I haven’t gone into detail as to how this would affect core services in the short term because I was unsure how long it would take to get the instrumentation back on-line. After firing up instruments tonight I can tell we are going to be up and running quickly.
DNA sequencing was shut down Thursday night and first runs should be done on Tuesday. Since switching to electronic submission we have seen a large increase in sample numbers but we should be able to clear the two-day backlog by the end of the week. We should be back to 24 hour turn around or less by next Monday.
DNA synthesis, peptide synthesis, amino acid analysis and all other services which use hazardous reagents may experience a one week delay. Primers for DNA sequencing will be given the highest priority.
Short Term: Expect delays of two to five days. All of our energies will be focused on getting services running.
Long Term: The New Year will continue to bring improvements to all services. A brand new Mass Spectrometer will be plugged in this week and we will unveil some unusual ways to analyze your protein. We have moved one thousand yards away but we will be even more accessible then we ever were. Surprises in the spring. If you want to meet Johnny Damon at our Spring Open House you may have to visit and use a core service before March 1. Tickets will have to be limited. Rumors that this Open House will take place at the Boston Beer Works are unfounded although they may cater the event. More later.
Monday, October 18, 2004, DNA Sequencing Electronic Submission
As of today, all DNA sequencing submissions should be submitted electronically. Check it out. Go there now and start an account. Everyone in your lab should have an account. All of your data will be in one spot and we can get it to you much faster than by e-mail. So sign up today and get the sequence fresh off the DNA sequencer. And try out Fast Track for even faster delivery of your sequencing data. Don’t be the last lab on the block to get data back in less than 18 hours.
Wednesday, April 28, 2004, FinchTV Chromatogram viewer Get FinchTV!
Just click on the button and go to the bottom of the page to get a MacOS X, Linux or Windows chromatogram viewer. This link will be copied to the software download page in a few days.
Monday, April 14, 2004, Sequencher Upgrades Are you having problems starting up Sequencher after April 14, 2004? That is because we had to shut down the old Sequencher Server and start up a new one. The fix is very easy.
1) Quit Sequencher, (likely you were only able to run in demo mode).
2) Go to “Chooser” under the Apple in OS 9.
3) Select the key icon in the top right window.
4) Select DFCI – MBCF “zone” in the bottom left window.
5) Select the “New MBCF Sequencher Server” in the window on the right.
6) Press the “logon” button.
7) You can now close chooser and restart Sequencher.
You are now over on the new server and nothing further needs to be done. In less than a week, we will have available the new version of Sequencher which is completely OSX native. This is the reason why we had to move to a new server. Next week you will be able to run OSX native Sequencher or the older OS9 Sequencher from the new server.
A bug that will be fixed: If you ever get a window saying “your network connection has been interrupted, please save your work and quit” you HAVE to do this. Then just start up Sequencher again. Please e-mail me if this ever happens. It should be a very rare event.
Monday, March 7, 2004, DNA Sequencing Delays
DNA Sequencing delays are now getting back to normal. There will be another week of turn-around-times hovering at 6-8 days but it will soon fall rapidly to the normal 1-3 days.
Monday, February 23, 2004, DNA Sequencing Delays
Due to a combination of unforeseen circumstances, we are experiencing problems in our ability to turn around the DNA Sequencing samples. The delay will, unfortunately, remain at 11-15 days for another week at least. Sorry for the inconvenience.
Tuesday, November 11, 2003, Sequencher Server access upgrade
Sometime in the next week or so the “Keyserver” for Sequencher will be upgraded. Hopefully, no interruption will occur. If when starting up Sequencher it responds only with “demo” mode just do the following: Mac OS 9 or prior operating system. Just go to Chooser. Select Key icon top left. Then go to “DFCI – MBCF” zone and select “Sequencher Server” and select “login” button. You are now back to normal. These upgrades are for deploying Sequencher which will run natively on Mac OS X. This will happen very soon. Stay tuned for details.
Friday, October 24, 2003, Mac OSX upgrade to Panther 10.3 at 8:00 PM tonight.
Macintosh OS X is being upgraded to Panther 10.3 this Friday night. Soon after we will be receiving the OS X version of Sequencher by Gene Codes for DNA Sequence assembly. Recent upgrades to our DNA sequencing protocols will routinely extend read lengths beyond one thousand bases. All of these changes will make DNA analysis much easier and cheaper. Do your lab a favor and go buy a Power Mac G5 dual processor, Get it from Harvard TPC then load it with memory.
Thursday, September 18, 2003, Harvard Technology Products/ New Computers
Harvard Technology Products has reformatted their website. Several ways to buy a computer. Specials viewed in PDF if you have a Harvard PIN number. One can also purchase directly from third party getting the educational discount. Check it out. The G5’s are selling like hotcakes and the Powerbooks were updated by Steve Jobs in Paris this Tuesday.
CANCELLED (Some speakers could not make it). CANCELLED Dana-Farber Cancer Institute Real-Time PCR User’s Meeting
CANCELLED Thursday, May 29th, 2003
CANCELLED 8:30 AM – 11:30 AM
CANCELLED Smith Family Room, 16th Floor. Rm. 1620 Dana Bldg.
CANCELLED E-mail Chris Simollardes so they can order enough food.
Tuesday, May 6, 2003, Apple Macintosh OSX 10.2.6 available
Macintosh OS X 10.2.6 is now available for update through System Preferences “Software Update”. Improved reliability of Address Book, Graphics, printing, OpenGL and especially USB hub devices. If you have had any kernel panics with 10.2.5 you should update immediately.
Monday, January 6, 2003, Apple Computer purchasing
The MacWorld Expo begins on Tuesday, January 7. So if you are about to purchase Apple Computer hardware you might want to hold onto the purchase order until you find out if the system just became cheaper or faster. You can watch Steve Jobs live at noon on Tuesday.
Thursday, January 2, 2003, MBCF in 2003
We are continuing to expand services which are in demand within the core facilities. We will be trying to double the DNA sequencing capacity in 2003 while expanding genetic analysis services. We also found out today that the Shared Instrumentation Grant for a new BIAcore 3000 was approved at 100% funding. We will aggressively get this instrumentation up and running to complement the existing BIAcore as well as integrate BIAcore with mass analysis. Other changes in services are expanding so quickly and are being used at 100% capacity that I don’t want to advertise them here. If you are an institute investigator you are just going to have to stop on by.
Tuesday, December 3, 2002, Macintosh Internet Browsers
There are many browsers to choose from. Unfortunately, Internet Explorer is the predominant browser on the Macintosh while also being the slowest. If you would like to try a faster browser check out Mozilla. Download the newest version from the right-hand side. Mozilla 1.2.1 is currently the newest in Mac OSX. If you really want speed you can even try the MachO version (currently 1.3a).
Wednesday, September 27, 2002, Seminars in Oncology
The Seminars in Oncology for October 2002, (and beyond when available), are now listed in both BioWeek and the HMS calendar.
Wednesday, September 18, 2002, Biology Week Seminars
The Biology Week Seminar postings just received a facelift. No longer PDF, it is now an interactive calendar.
Friday, September 13, 2002, Fall Seminars
The Harvard Medical School Calendar just received a facelift. Switch it to “View by Week”. The Whitehead “Biology Week” will be renewed on September 18.
Saturday, August 24, 2002, Mac OSX updates
Apple released Mac OS X 10.2 today. Get rid of your junk mail, connect to server hard drives effortlessly. It’s Jaguar and it purrs.
Friday, July 26, 2002, Mac OSX updates
On August 24, Apple will be releasing their newest update to Mac OS X which is 10.2, codename Jaguar. Early indications are that this version puts OSX over the top. If you have a packing slip for a new Apple computer purchased after July 17 make sure you keep a copy. This will allow you to get a copy for $19.95 instead of the full price of $129.00.
Friday, June 28, 2002, Genbank Explosion
Genbank growth continues a steep climb. 1.6 billion bases were added since the last full update (two months) which is equal to the total in June 1998. The protein Sequence “ELVIS” was present in the NR database 64 times last year. Elvis is now up to 150. Most everything is keeping pace but expect changes to database searches to accommodate this ever increasing search target.
Thursday Night, April 26, 2002, Power Outage
The transformer fire in Alston/Brighton knocked out power in the Institute for twenty minutes. All instruments recovered but many runs failed and were not completed. Expect delays especially in DNA sequencing.
Thursday, April 25, 2002, Navigation Improvements on MBCF web site.
While navigating all of the pages in the MBCF website a click on the Top MBCF graphic will get you out.
1) Clicking on “Molecular Biology Core Facilities” brings you back to MBCF home page.
2)Clicking on the “Flaming DFCI D” will bring you to the DFCI web site.
3) Clicking on the “Veritas Shield” will bring you to the Harvard Med School.
Monday, April 22, 2002, Harvard Medical School Research Rated #1 again.
For the thirteenth year in a row, U.S. News and World Report ranks research at Harvard Medical School the best in the nation.
Sunday, April 21, 2002, Cha cha cha changes
Just a few changes to the website this week. If you find something moved where you don’t want it or a link that doesn’t go anywhere just go down to the “suggestion’ button and send in a comment.
Friday, March 22, 2002, The CMS Molecular Biology Resource
The CMS Molecular Biology Resource is no longer mirrored at MBCF. This is a direct link to the San Diego home copy. If you have saved a link other than the MBCF home page just update your link for more up-to-date information.
Monday, March 4, 2002, cms The Glowing Knob
During the Science Fair, a lot of people wondered about the “knob” I was using to scroll and control volume. It is the PowerMate from Griffin Technology. If you think you are getting carpal tunnel it is worth the 45 bucks to check it out. Purchase it right from the site.
Wednesday, February 27, 2002, Science Fair
Dana-Farber Science Fair for Core Facilities in Smith 308-309. 1-4PM and a free lunch. Then it is off to the ice cream social in the cafeteria.
Wednesday, February 13, 2002, dfci phone
DFCI now has an online employee directory. This button is on the MBCF front page.
Monday, January 28, 2002, New Apple PowerMacs today.
Dual 1GHz PowerPC G4
2x256K L2 & 2x2MB L3
Forget the Linux farm, get a couple of these instead.
Thursday, January 24, 2002, Microsoft Office, Word/Excel/Powerpoint, for Mac OSX
Matthew Temple now has the CD of Office for OSX. e-mail him. Good stuff.
Friday, January 4, 2002, MacWorld Expo Starts Monday, Jan7-11
Apple, always secretive but usually low-key about what they have in store is flaming the rumors about Steve Jobs’ address on Monday, 9:00 AM PST. For the past week the Apple web site has said:
7 days to go, Monday: “This one is big. Even by our standards.”
6 days to go, Tuesday: “Count the days. Count the minutes. Count on being blown away”
5 days to go, Wednesday: “Beyond the rumor sites. Way beyond.”
4 days to go, Thursday: “It’s like a backstage pass to the future.”
3 days to go, Friday: “To boldly go where no PC has gone before.”
2 days to go, Saturday: “Full speed ahead: Lust Factor Ten.”
1 day to go, Sunday: “Just on more sleepless night.”
The iWalk rumor and movie is a fake. (I think). iPhoto sounds real. So does the LCD iMac. Maybe even a 1Ghz G4. But a G5?. Macs shipping with OS X as the default? Gigawire? An iProteome?
Wednesday, January 2, 2002, Seminars
Turning over that new leaf and you are going to attend all the good seminars? The Harvard Medical School Calendar is currently doing a great job at listing seminars in the HMS area. Click and find out where Steve West, Edward Benz, and Steve Gygi are speaking this month.
Monday, December 17, 2001, Microsoft Office v.X
The last impediment to using Mac OS 10.1 is now removed. Microsoft Office v.X is now available by an educational discount. Someone should find out why Harvard TPC does not have it listed yet. You need passwords for every copy in your lab. $59 a piece for each additional copy. Not too bad.
Biomarker Discovery: Advancing Clinical Proteomics
November 9, 2001, 9:00 am to 12:00 pm
Dana Farber Cancer Institute
Dana Building Room 1620 (Smith Family Room)
Refreshments will be served
9:00-10:00 am Ciphergen Biosystems~Pioneering Clinical Proteomics for Predictive Medicine
By Lisa Bradbury Ph.D. Senior Field Scientist, Director of Special Projects, Ciphergen Biosystems, Fremont, CA
10:00-11:00 am Case Study Presentation~Applications in Disease Research Using the ProteinChip Biomarker System
By Diane McCarthy Ph.D. Senior Field Scientist, Ciphergen Biosystems, Fremont, CA
11:00-12:00 pm Guest Speaker~ Brynmor Watkins, Ph.D. Associate Director of Proteomics, Lexigen Pharmaceuticals, Lexington, MA
Monday, October 29, 2001, MBCF website was down
The MBCF website was busted from 3:53 PM Sunday until 11:00 AM Monday. Can’t figure out why. Nothing was lost.
Wednesday, October 17, 2001, PDF Forms
The ordering forms on the PDF Forms page are now working again. Thank you for pointing out the broken link.
Monday, October 1, 2001, Price Reductions
Check out the new prices for services. DNA sequencing has dropped 30% from $20.00/run to $14.00/run. New instruments and new chemistry have allowed us to increase run length while charging less.
Friday, September 21, 2001, Website outages
The internet connection to the Dana-Farber Cancer Institute has been disconnected for the past several days. That is why you have been unable to reach this site. The internet “worm” NIMDA (admin spelled backward) was especially hard to eradicate.
Wednesday, September 5, 2001, DFCI New website
The Dana-Farber website has been completely transformed. It is now packed with useful information. If you are at DFCI and see an omission just send a comment in. They will get right back to you.
Friday, July 16, 2001, Servers UP
All MBCF servers are now up. Oligo ordering is back on-line. Because of multiple server failures, we have had to go to a Feb 29, 2001, back-up. You might find some out of date info on the servers until we can hunt down the last old bits and replace with new back-ups. Sorry for the inconvenience.
Friday, July 13, 2001, Servers down
That’s right. On Friday the Thirteenth all of the MBCF servers when down in a painful set of disk crashes. We are currently rebuilding past Feb 29. Oligonucleotide ordering will have to be done on paper through at least Monday, July 16. Sorry for the inconvenience.
Friday, January 26 to July 13, 2001, Missing News
This news will be replaced as soon as we grab it off the backups.
Monday, January 29, 2001, It’s a Boy!
Conner Bogle arrived 6:30 PM on Thursday. 6lbs. 11 oz., 19″. All are back home getting _lots_ of rest, (yeah right, waaaaah!!)
Friday, January 26, 2001, E-mail at DFCI
Do you have an e-mail account on the Partners system? If you are a researcher at DFCI you can get an unlimited size e-mail account. E-mail Matthew Temple to get one. It is IMAP reachable from anywhere in the world. This is a good feature.
An aqua button “@research” has been added to the bottom of the MBCF page.
Tuesday, January 16, 2001, Titanium Powerbook
Harvard TPC changed the layout of their online store. Go here to buy one of those titanium Powerbooks.
Tuesday, January 9, 2001, Titanium Powerbook
This is a _nice_ computer. 5.3 lbs, widescreen, 1 inch thick. And made out of titanium.
Tuesday, January 9, 2001
Steve Jobs MacWorld Expo Address is scheduled for noon today. Find out about the new Powerbook. Lighter, thinner, faster. Will he close the “megahertz” gap? (I know there is no gap since the RISC chip in the Mac can handle 3 to 7 times more instructions than the wimpy Pentium or Atholon.) find out what music is.
This link will give you streaming video.
Friday, January 5, 2001, DFCI Scientific Report 2000
The Scientific Report that you are just receiving in the mail is on-line. If this link remains active I will be moving it to an Aqua button. Easy to look up the 167 Independent Investigators with biography and a picture.
Wednesday, January 3, 2001, Seminar page updated.
Seminars in Oncology
Wednesday, November 29, 2000: Science Fair
Make sure you stop by Smith 308 to get your free lunch Noon to 3 PM. You can also find out about all the DFCI cores that are available to researchers at the institute.
Tuesday, December 5, 2000: Seminar in Oncology (note date change)
Speaker: Matthias Mann
Title: Novel Proteomic Methods to Map protein-Protein Interactions and Signaling Pathways
4:00 PM, Smith Family Room
Host: Stanley Korsmeyer
Tuesday, November 7, 2000: Genome Data
I have added a “genome” aqua button to the front page. I will try to list the top databases that contain unique eukaryotic genome data. The database might also be listed because it has a unique way of presenting the data. The access page for private database collections such as Celera and Incyte will also be listed. Unfortunately, if you don’t have an account these links will be useless. Harvard has an access agreement with Celera. It will still cost you to sign up. Hopefully in a year or so we will be back to searching one database.
Monday, October 2, 2000: Draft Human Genome Browser
One of the good examples for browsing the human genome. Send me your favorite link (Myles Brown found this one) and we’ll test them out. The winner gets an “aqua” button assigned on the MBCF home page.
Monday, September 18, 2000: Watch this space.
Summer is over and lots of new stuff. Sequencher 4.11 has many slick new features. Apple has released Mac OS X. Can it do some neat stuff for the molecular biologist? Yes. More news soon along with the Seminar in Oncology posting.
Friday, August 4, 2000: MBCF Closed for Inventory
The MBCF will be closed Friday. You may pick up oligos and drop off samples.
Wednesday, July 5, 2000: Internet News
Another small erosion of our rights to free speech. PETA, “People Eating Tasty Animals”, has lost the URL: peta.org. It seems another organization took offense.
Friday, June 30, 2000: MBCF Closed July 3 and 4.
The facility will be closed Monday and Tuesday. Why? Because:
Mostly sunny and warmer. High 80 to 85.
Mostly clear. Low 60 to 65.
Partly cloudy. High 80 to 85.
Partly cloudy and more humid. Low 60 to 65. High 80 to 85.
Fourth of July
Partly cloudy…very warm and humid. Low 60 to 65. High 85 to 90.
Wednesday, June 7, 2000: DNA Synthesis Problems
The synthesizer is fixed. We will wipe out the backlog by working non-stop through the weekend while you’re at the beach.
Tuesday, June 6, 2000: DNA Synthesis Problems
Monday, June 5, 2000: DNA Synthesis Problems
Since May 17 the facility DNA synthesis service has had repetitive mechanical problems. Please order DNA synthesis oligos from commercial sources until further notice. We apologize for this inconvenience. Service representatives have promised a working synthesizer by June 6.
Friday, June 2, 2000
Delaying Aging and Preventing Cancer with Micronutrients
Bruce Ames, University of California, Berkley
2:00 p.m. Jimmy Fund Auditorium
Thursday, June 1, 2000
Stop paying those big bucks for statistical interpretation of your results. Do it yourself at VassarStats.
Thursday, May 18, 2000
The CMS Molecular Biology Resource on the MBCF homepage has just been revised. The whole site has had a makeover. e-mail me if your favorite link is missing. The old 1999 CMS is here.
Monday, March 27, 2000
Internet Explorer 5.0 is available today from Microsoft. Faster, cheaper, better. It does some very helpful background tasks that you will never notice. I updated the protocol link on the MBCF homepage and it knew that something was changed and so refreshed.
Wednesday, March 8, 2000
Keeping current with upgrades is a pain. If you are migrating to OS 9 you might find it necessary to upgrade. Go to Version Tracker Web site to find every current upgrade available.
The DNA synthesizer is now functioning but may need an extra day to catch up.
Monday, March 6, 2000:
The DNA synthesizer malfunctioned on Saturday. Because of the lousy timing of this breakdown, it will not be serviced until Tuesday. Expect at least two days extra in turn-around-time. DNA sequencing primers are being outsourced but will be delayed because of shipping.
Thursday, February 17, 2000
Apple announced today at MacWorld Expo in Japan several new computers. A new PowerBook, 500mz G4, and a new Graphite iBook. The new Powerbook can be ordered at Harvard TPC. Two-week delivery.
Friday, February 11, 2000 Everyone like the new MBCF buttons? They are the superficial top layer of Apple’s new OsX. The more important features are hidden such as true multiprocessing and protected memory. These are the last vestiges of things that Unix people had that the proletariat did without. You can even run Red Hat without emulation if you really want Unix.
Advances in SNP Detection Symposia at Dana Farber Cancer Institute
Jimmy Fund Auditorium
Wednesday, February 9th, 2000
2:30 PM – 5:45PM
Sponsored By the Molecular Biology Core Facilities, Dana-Farber Cancer Institute & PE Biosystems, A Division of PE Corporation
2:00 PM – 2:30 PM Attendee Check-In and Refreshments.
2:30 PM – 3:30 PM
PE Biosystems and SNP Technology
Joe Olechno, Ph.D., Director of Planning
PE Biosystems, Foster City, CA
3:30 PM – 4:15PM
Robust Discrimination of SNP’s on The ABI Prism 7700 Sequence Detection System
Junko Stevens, Ph.D., Staff Scientist
PE Biosystems, Foster City, CA
4:15PM – 5:00PM
SNP Analysis Strategies For Genotyping & Mutation
Paul Galgano, Ph.D., NE Field Applications Specialist Manager
PE Biosystems, Foster City, CA
5:00PM – 5:45PM
High-Level Multiplex Genotyping and Mutation Detection
Larry Haff, Ph.D., Product Manager
PE Biosystems, Framingham, MA
Thursday, February 3, 2000
Want to make sure your search of the literature is exhaustive? Go to Searchlight run by the California Digital Library. Your favorite gene is cited and patented how many times?
Monday, January 24, 2000
Holding off until the last minute putting your sequence into NCBI? It’s easier than you think. BankIt 3.0 is even easier to use. Annotation is a walk in the park.
Friday, January 7, 2000
The Apple Web Site has gone through a major revision as well as announcing several new features. MacOS X (pronounced “ten”) is shown off. Get your free chunk of an Apple server now. You never know when it could come in handy later. (e-mail me at firstname.lastname@example.org).
Tuesday, January 4, 2000
The MacWorld Expo in San Francisco is this week. Steve Jobs is expected to announce on Wednesday a new PowerBook currently code named Pismo.
Monday, January 3, 2000
As of the new year, NCBI calculates that 1,012,190,000 bases of draft sequence are completed of the human genome. Over a billion bases is 31% coverage.
Tuesday, December 28, 1999
For viewing DNA sequencing chromatograms on a Windows or NT operating system download Chromas. It is now up to version 1.56.
Monday, December 27, 1999
The Electronic Journal Link on the MBCF front page has been changed.That link now sends you to a page where you decide whether to go to Hollis Plus or to Countway Library. Both have their advantages.
Thursday, December 16, 1999
If the oligo you’re ordering has the potential of being useful to other researchers in the institute we will make it for free. You get an aliquot and we post the sequence on the site. Other researchers get aliquots for free also. We’ll even name it after you.
Check with us before we make it. We might already have it synthesized. Check your Two-hybrid screening in yeast using the pBTM116 vector? We got ’em.
Tuesday, December 14, 1999
Find your vector contamination fast with NCBI’s new tool VecScreen This easily picks out and colorizes the early vector sequence in your DNA sequence run. It will also detect the vector downstream even if only a small fragment is showing and find the not so rare vector fragment inserted into the middle of your insert. Don’t be embarrassed by unsightly vector contamination in your publication. Use VecScreen today.
Wednesday, December 1, 1999
Time to click on OncoLink again. You can check out Stanley Korsmeyer in Real Player Video explaining “Bcl-1 Family and the Regulation of Programmed Cell Death”.
Save the date: Wednesday, December 1, 1999
DFCI Core Facilities Science Fair Smith 308/309, noon to 4:00 PM. All the core resources of the institute will be there. Raffles, food, prizes.
Wednesday, November 13, 1999
I am upgrading all of the pages on the MBCF website before December 1, 1999. If you have any suggestions for improvements please send them in now. I have already started to upgrade the “pricing” and “overview of services” pages. There will be a DFCI Core Facility Fair on December first at noon in Smith 308-309.
Monday, November 1, 1999
Mac OS 9.00 is now available and worth getting. Sherlock 2 searching and indexing of your hard drives work much better. Go to Apple-Donuts to download any of 300 internet plugins for Sherlock.
Thursday, October 21, 1999
Newly renovated CMS Molecular Biology Resource which MBCF mirrors is now in place. This very thorough resource for molecular biology on the internet can always be found on the lower half of the MBCF home page.
Tuesday, October 12, 1999
In case you get into an argument about how the Red Sox scored 23 runs, just click on the game score on this page. The page will also tell you where the Red Sox will be on Wednesday. Yankee Stadium But you already know that.
Monday, October 4, 1999
PubMed has had a facelift.
Friday, October 1, 1999
If you couldn’t make it to the Ig Noble Prize ceremony last night at Sanders Theater you can still check out the 1999 Winners. Fortunately, no one at DFCI won.
Tuesday, September 28, 1999
Seminars in Oncology every Tuesday.
Tuesday, August 31, 1999
Steve Jobs Keynote at Seybold today mentions the introduction of the G4. 1 Gigaflop sustained rate processor. 400 MHz G4 shipping at $1,599.00. 500 MHz G4 shipping in a few weeks at $3,499. And the 21 inch LCD “Cinema Display” monitor that ships with it look very nice too.
Phone Home If you leave your computer on overnight why don’t you have it work on something useful?
Wednesday, August 25, 1999
A new site for Molecular Biology On-Line Protocols. I used to compile this myself but these guys do a much better job.
Tuesday, July 27, 1999
The Macintosh iBook is a very slick computer for $1,600.00. And with the Airport, you go wireless.
Wednesday, July 21, 1999
Martin Hemler’s Lab has been added to the DFCI Lab pages. Martin whipped it up all by himself in one day.
Monday, July 19, 1999
Sequencher 3.1.1 is ready for installation from the MacIS Server. When upgrading you will need to also replace the copy of “Key Access” with the new version. To do a fool-proof install, delete “Key Access” and the Sequencher program from your hard drive (don’t delete any of your own files). Then follow the “Read Me Install Sequencher” directions that are with the program on the MacIS Server.
Wednesday, July 7, 1999
Genomics Another site which compiles Molecular Biology Tools.Software, Journals, and Genomes. It’s up-to-date today. Don’t ask me about the spelling.
Tuesday, June 15, 1999
Compendium of Biology Software
Tuesday, June 8, 1999
Cell and Molecular Biology Online Pam Gannon’s up-to-date Mol Bio site just got updated. Find it on the MBCF homepage.
Thursday, June 3, 11:00 AM, 1999
Radiation Oncology Seminar Series
Automated Screening for Single Nucleotide Polymorphisms (SNP’s) by DNA Chromatography
Karl Hecker, Senior Scientist, Transgenomic Inc, San Jose, CA
Mayer L104&B (next to cafeteria)
Tuesday, June 1, 1999
Seminars In Oncology
Kinase Cascades in Cancer Cell Growth and Death
Michael Weber, University of Virginia Medical School
4:00 PM Smith Family Room
Tuesday, May 25, 1999
E-Biomed Read Harold Varmus’s proposal for electronic publications in the Biomedical Sciences.
Tuesday, May 25, 1999
Seminars In Oncology
Hedgehog Signaling by the Patched-Smoothened Receptor Complex
Fred de Sauvage, Genentech
4:00 PM Smith Family Room
Thursday, May 20, 1999
Cancer Genetics site.A great site explaining cancer genetics to the lay person. Also a good refresher course for the oncologist.Their mission: “The purpose of this site is to provide an information resource to help you understand the genetic basis of cancer and to be able to interpret new discoveries in the field of cancer genetics. We have created the site in three sections that interconnect but offer different ways into both clinical and basic information on cancer, genetics, and the role of genetics in causing cancer. OR… just start anywhere your curiosity suggests.”
Tuesday, May 18, 1999
Seminars In Oncology
The Cdc14 Phophatase Restrains DNA Replication by the Opposing Cyclin E/Cdk2 Activity and Ubiquitin- Dependent Destruction of the Cyclin E/Cdk2 Inhibitor
Peter Jackson, Stanford University School of Medicine
4:00 PM, Smith Family Room
Monday, May 10, 1999
Apple computer releases MacOS 8.6. Click to update from 8.5.
Thursday, May 13, 1999
Molecular Genetics of Human Leukemias
Gary Gilliland, Brigham & Women’s Hospital
Noon, Smith Family Room
Wednesday, May 12, 1999
Structure and Function of the Human Immunodeficiency Virus (HIV-1) Envelope Glycoproteins
Joseph Sodroski, Dana-Farber Cancer Institute
Noon; Microbiology Conference Room, L-504
Boston University School of Medicine
Tuesday, May 11, 1999
Seminars In Oncology
Harriet Tischler Memorial Lecture
Role of Skp2 and Cdk2 in the Ubiquitin-mediated degradation of the Cdk-inhibitor p27
Michele Pagano, M.D., New York University School of Medicine
4:00 PM, Smith Family Room
Tuesday, May 5, 1999
Human Genome Resources at NCBI
Tuesday, April 27, 1999
Seminars In Oncology
Homologous Recombinational Repair as a Major Determinant of Chromosome Stability and Sensitivity to DNA Damage
Larry Thompson, Lawrence Livermore National Laboratory
4:00 PM, Smith Family Room
Dana-Farber Cancer Institute Seminars in Oncology presents
The Susan Swerling Lectures
Tuesday, April 20, 1999
Jimmy Fund Auditorium, Dana-Farber Cancer Institute, 35 Binney Street
“Signaling by Wnt Proteins During Development,” Roeland Nusse, Stanford University
“Patterning Dorsal Mesoderm in the Zebrafish,” Charles Kimmel, University of Oregon
“RNA-triggered Genetic Interference Mechanisms,” Andrew Fire, Carnegie Institute of Washington
For more information, please contact: Miles Brown, 632-3948.
Thursday, 6:00PMApril 22, 1999
Chemiluminescence in High Through-put Screening
Michele Palmer, Clinical Ligand Assay So6:00 PM
, Jimmy Fund Auditorium
Tuesday, April 13, 1999 Red Sox
I’m on the Red Sox bandwagon. Go to Today’s game.
Tuesday ,March 23, 1999
Seminars In Oncology
Identification of Components of the Cell Death Pathway
Vishva Dixit, Genentech
4:00 PM, Smith Family Room
Thursday, March 18, 1999
You probably already have an account at BioMedNet because it’s free. Go back and check out Extended Medline. This will bring up links to full text of many papers.
Monday, March 17, 1999
Description of various 3′ UTR’s.
Monday, March 10, 1999
Computer Retrieval of Information on Scientific Projects at NIH. Use this to figure out what everyone is doing, both past and present. With advanced search you can find all the NCI R01’s in Massachusetts.
Monday, March 1, 1999
NIH PHS 398 Form (4/98)
This form has been updated for Microsoft Office 98. Find it in the MBCF folder down on the MacIS Server, Ethernet zone.
Wednesday, February 3, 1999
Quickmail Servers Down
A large part of the DFCI Quickmail server seems to be down. NDM, CMB and other department zones are giving us back undeliverable messages. If you need your DNA sequencing data and expect delivery today, please stop by.
Tuesday, February 9, 1999
Seminars In Oncology
Broken Chromosomes: Checkpoints, Repair and Repeat Sequence Instability
Jim Haber, Brandeis University
4:00 PM, Smith Family Room
Tuesday, February 2, 1999
Seminars In Oncology
Regulation of T Cell Activation by Protein Tyrosine Phosphatases
Tomas Mustelin, Sidney Kimmel Cancer Center
4:00 PM, Smith Family Room
Monday, January 25, 1999
It may have been some time since you’ve ordered a computer from Harvard TPC . But try out their on-line catalog . They also now answer the phone! 495-5450 The G3’s are in stock.
Thursday, January 21, 1999
Current Trends in Hematopoietic Stem Cell Transplantation: New Stem Cell Sources
Mary Horowitz, Medical College of Wisconsin
12:00 noon, Smith Family Room
Tuesday, January 19, 1999
Seminars In Oncology
The Mrell/Rad50 Protein Complex: Linkage of Diverse Functions in the Cellular CNA Damage Response
John Petrini, University of Wisconsin Medical School
4:00 PM, Smith Family Room
Thursday, January 14, 1999
Anti-CEA Designer T-Cells for Cancer Therapy
Richard Junghuns, Beth Israel Deaconess Medical Center
12 Noon, Smith Family Room
Tuesday, January 12, 1999
Seminars In Oncology
Promoter Region Hypermethylation and Gene Silencing in Cancer
Stephen Baylin, Johns Hopkins Oncology Center
4:00 PM, Smith Family Room
January 5, 1999
Macworld Expo in San Francisco runs all this week. Steve Jobs live at noon today. And don’t miss any rumors.
Tuesday, January 5, 1999
Seminars In Oncology
Germ Layer Specification in C. Elegans Embryos
4:00 PM, Smith Family Room
January 4, 1999
Did someone ever tell you about the scientist who refused to send a competitor a phage ? And the competitor incubated the refusal letter in media and retrieved the phage? It’s an Urban Legend ! Send me the name of the scientists if you think it’s true.
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
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. Remember 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
Smith Family Room
Wednesday, December 2, 1998
Signaling to and Regulation of the p53 Tumor Suppressor Proteins
Carol Prives, Columbia University
Room SM308/309, Smith Research Laboratories
Tuesday, December 1, 1998 Seminars In Oncology
Estrogen Receptor and Antiestrogen Actions
Benita Katzenellenbogen, University of Illinois
Smith Family Room
Tuesday, November 24, 1998 Seminars In Oncology
Breast Development and Cancer/Oncogenes/Tumor Suppressors
Smith Family Room
October 15, 1998
This Saturday you can buy Macintosh System 8.5.Check out Sherlock which is the new “find” feature. Find it on the internet, on your hard drive or “in” your files.
October 8, 1998
Quackwatch Your Guide to Health Fraud, Quackery, and Intelligent Decisions. The town I live in is voting on a referendum next month on whether to fluoridate the town’s water. This site was a source of information to debunk the anti-fluoride contingent. Too bad the hysteria is high and the quackery is going to win in Wayland.
-update: fluoride passed in Wayland!!
September 29, 1998
We make high quality peptides that are purified by HPLC. It might not make sense for us to make a peptide for you that is going to be used to generate a polyclonal antibody. Why not? It doesn’t have to be as good as we make them if you’re going to just stick it in a bunny. And there are companies that will do it all and deliver antibody for a very decent price. Check out the Antibody Resource Page for more information about these companies. If you need a quality modified peptide (phosphorylated, biotinylated etc.), come see us. We can also QC the commercial peptide by mass analysis to make sure you are getting what you ordered.
September 29, 1998
HIV InSite is a new “gateway” to AIDS information. Compare it to Aegis HIV/AIDS knowledge Base which I’ve always had linked to the MBCF front page. Should I replace it with HIV InSite?
September 10, 1998
Biology Week Seminar Postings is back from summer break.
September 10, 1998
DNA Synthesizer All Caught Up Turn-around-time on DNA synthesis is now back to normal. Web the sequence to us by 2:00 PM and you can pick them up by noon the next day. We sent a bunch of them off-site last Friday and they say we will get them this Friday so some of you are still waiting. This is our first use of commercial sources. Are they all this slow?
September 3, 1998
DNA Synthesizer Failure.The DNA synthesizer recently had a software upgrade as well as the yearly replacement of many parts. Unfortunately this has put DNA synthesis intermittently out of business for the past two weeks because of new part and new software failure. As we put it back together you may experience a one week backlog of oligos. We are sorry for this inconvenience.
August 5, 1998
Outbreak is an on-line information service addressing emerging diseases.
August 4, 1998
Update 2.7 of the CMS Molecular Biology Resource mirrored at MBCF. (Listed on our front page). The newest list of biological tools listed by catagory and updated.
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.
July 16, 1998
The CMS Molecular Biology Resource mirrored at MBCF. That means this link is a local copy of all pages of the original west coast version. You should be able to load this more quickly from the east coast. I promise to copy the original at least once a month.
July 14, 1998
The CMS Molecular Biology Resource Bio-Web tools listed by “function” of tool. Pedro on steroids! Send them lots of e-mail that you love their site and you hope they keep it updated.
June 3, 1998
By now most of you are used to dropping off DNA sequencing templates at EXACTLY 0.2ug/ul and primers at EXACTLY 20ng/ul or 3.2pmol/ul. Read the specifics. If you want your data back fast you all need to stick to these guidelines.
June 3, 1998
Want a free oligo and do your good deed for the day? Give platelets. Read the specifics.
Tuesday, May 19, 1998
The Molecular Genetics of Hematopoiesis and Vasculogenesis
Alan Bernstein, University of Toronto
Dana-Farber Seminars in Oncology, Smith Family Room
Tuesday, May 19, 1998
Molecular Pathogenesis of Fanconi Anemia and Cancer Susceptibility
Alan D’Andrea, Dana-Farber CancerInstitute
12:00 PM, The Center for Blood Research, 800 Huntington Avenue.
Perkin Elmer/Applied BioSystems in association with the MBCF at the Dana-Farber Cancer Institute presents a symposium on
“Advances in Automated Fluorescent DNA Sequencing and Genotyping: Applications on the ABI Prism 310 Capillary Electrophoresis System”
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>.
4/28/98 Mitotic Motors in S. cerevisiae
Johns Hopkins University
4:00 PM; Dana-Farber Seminars in Oncology, Smith Family Room, Dana 1620
Speaker: Lesley Stolz Ph.D., Biacore Inc.
“What Biacore Technology Can Do For You”
Monday April 13
1:00 PM in Dana 821 Conference Room
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 “22.214.171.124”. 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.
Fifty 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.
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 Control
Martine Roussel, University of Tennessee at Memphis
4:00 PM; Dana-Farber Seminars in Oncology, Smith Family Room, Dana 1620
3/24/98 Exploring the Virtues of DNA Alkylation Repair Using Knockout Cells and Mice
Leona Samson, Harvard School of Public Health
4:00 PM; Dana-Farber Seminars in Oncology, Smith Family Room, Dana 1620.
3/18/98 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.
dot 3/3/98 “Mechanisms of Diffusion of Wnt and Hedgehog Morphogens,” Norbert Perrimon, HMS
4:00 PM ;D ana-Farber Seminars in Oncology, Smith Family Room, Dana 1620.
dot 2/10/98 “The ATM Protein Kinase Family: Regulators of DNA Repair, Meiosis, and Cell Cycle Checkpoints,” Merl Hoekstra, ICOS Corporation, Washington; 4:00PM ;D ana-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. email@example.com 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.
dot 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.
1) Download it and put it in a folder, call it “SearchLauncher”.
2) Open that folder and bring to bottom of screen to make it “tabbed”.
3) Now just drag as many protein files to the tab then drop them on the application.
4) Hit return if protein or type DNA seq for DNA and return.
5) Select search by number (e.g. “2” for WU-BLASTP+BEAUTY)
6) The searches are run and html file results are deposited in the SearchLauncher folder.
7) Open the results one by one in your favorite browser.
8) If this doesn’t make sense just e-mail me at firstname.lastname@example.org
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 advice 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.
dot 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 Immunopathology 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 than 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 launcher 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.
1) Display the references you want as Medline Reports.
2) Save the displayed references as text.
3) Import the file to Endnote using the Medline NLM Filter available in Enlink 2.0 in the NLM (Grateful Med) folder.
That’s it! All the standard Endnote fields, plus the abstract.
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.
You’re 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 website or your computer.
3/21/96 Down Load EditView. This program will allow you to view, edit, and print your DNA sequence chromatograms.
“Recent Advances in PCR, Genotyping and Polypeptide Analysis”
1:00-4:00pm, Wednesday, March 20, 1996
Auditorium, Jimmy Fund Building, Dana-Farber Cancer Institute
“New Advances in Enzymology and Robotics: Towards Fully Automated Fluorescent Genescanning, Genotyping and Linkage Analysis,” Dennis Gilbert, Perkin- Elmer/Applied Biosystems
“Role of Polypeptide Sequence Analysis in Contemporary Health and Life Sciences,” Paul Tempst, Sloan 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
Advanced registration is required. For more information call 800/416- 8749.
(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.
MBCF suggestions mail us site POP access
dfci phone dfci pager dfci faculty SiteSearch @research
orms 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.
dot 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.
The new DNA synthesizer is shipping from California on Sept 21. Hopefully the install and testing should not take more than a week or so… This machine will make 48 oligos that are deprotected, OPC purified, and quantitated. Get ready for fast, cheap, and clean oligos.
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.
Below this is old news (8/14/95 and older). It is the ReadMe file I kept in the MBCF folder on the IS server.
Warning! Make sure you take all comments past this point as an historical narrative of a “ReadMe” file that used to reside on a DFCI only Mac Server.
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. MBCF Web site. I’ve just upgraded
the site so that it carries a local copy of Pedro’s Molecular Biology Analysis
Tools. This will be helpful when the network is acting up.
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
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
It handles features in a new way.
2/9/95 Nentrez3.0 and nentrezcf Major upgrade. Faster, easier etc. Config to
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
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, 1993. 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 into
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!”
11/22/1993: NCSA Mosaic 1.0 Official release.
11/5/1993: TurboGopher 1.0.8b3 Bug fix update.
10/25/1993: NCSA Mosaic B5 Yet another way to navigate the internet.
9/20/1993: GDB/Accessor 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
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
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
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.
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,
(email@example.com). (add: Mike is now at a genome type project at
Stanford, firstname.lastname@example.org). 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
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. Let�s 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. “email@example.com”. 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 �stateless�. 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.
dotCptExpand 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
JWP in Norwood (Paul Ghalani 575-8258) or Inacom (229-2190 in Burlington, ext 33
John Razado or ext31 Bob Chipman).
Paul T 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
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 software 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.