MBCF Late Breaking News


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
Boston, MA

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 , new mbcf new mbcf 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 on-line 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 2x250, 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 2x35 and you get the data back the same day. 2x150 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 2x250 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
Sanger sequencing
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
Peptide Synthesis
N-terminal Sequencing
HPLC purification
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 pror 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

TIME: 11:00 AM 12:00 NOON
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: chris.simollardes@fluidigm.com
PDF of talk to post in your hallway.

Friday, March 11, 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 Nanaopore 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, 9:30AM-10:00AM
Don't know why it happened. All data seem to be untouched. Backups to 6AM 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 off 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 nthomson@clcbio.com 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 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 device so you can se 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 Years 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 on-line 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" then 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.
mail us

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 for 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.

You do 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.
mail us

Sample dropped off 8:15AM data in your folder same day by 4:00PM.
Sample dropped off 2:15PM data in your folder next morning by 10:00AM

Monday, June 9, 2008, MBCF LIMS system was off line Sunday.
Sometime in the early morning Sunday the MBCF LIMS system went off line. The Red Sox won but made the restart occur at 2PM. 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 3PM 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 aproximately 3:30PM. 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 Masss 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 web sites is completed. If you find anything wrong please e-mail paul_morrison@dfci.harvard.edu as soon as you can and point out the problem. Everything should load up faster than ever. All pages and software are now running in 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 in Connection: TCP/IP field
    (This field should currently have
    Click Logon
    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 multi-plexed 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 1:11PM. 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.

    Tuesday, September 7, 2006 A problem with Sequencher hogging your CPU off campus.
    When you are on the DFCI campus your computer is behind the DFCI firewall and Sequencher, as well as the network copy protection software (KeyServer made by Sassafras) is happy. But if you run your laptop off-site, even if you are only running a PowerPoint presentation for a job seminar, you may end up with a sluggish or unusable Macintosh. The software attempts to connect to the MBCF server and cannot but never gives up until it is using all of your computer processing power. I have detested the copy protection software that Sequencher uses for ten years and now doubly so. If you are having problems with your Macintosh off site and you have Sequencher installed please e-mail me "paul_morrison@dfci.harvard.edu" and I will find a fix. Meanwhile if you want to send angry e-mail send them first to Sassafras, the makers of the copy protection software and then to Gene Codes, the makers of Sequencher.

    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 with 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 was 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 6AM 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 Windows 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 install 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 web sites? 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 web site 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.
    CERT advisory.
    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 2:00PM 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.

    Thursday, May 5, 2005 Sequencher doesn't work in Tiger Sequencher 4.2 or 4.5 will not work in Macintosh OS 10.4 Tiger. Watch this space for news on a fix for this.

    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 back log 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.

    Tuesday, June 22, 2004 Sequencher Key Server Problems
    Sometime on Friday night the Server for the Sequencher Key decided that the license had "expired". Anyone using Sequencher during the weekend was not allowed to use Sequencher in anything but "demo" mode. We figured it out when we couldn't use it Monday morning. The server was restarted and this seems to have cleared up the problem. We don't know why this happened so it may happen again. If you have any problems please call or e-mail us so we can fix the problem.

    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.

    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 in 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 if 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 web-site. 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 hot cakes 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 in 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.

    1999 - 2002 MBCF News
    1996 - 1998 MBCF News
    1992 - 1995 MBCF News


    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.

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