Archive for: December, 2011

My favorite Christmas song...Christmas in Hollis!

Dec 13 2011 Published by under Uncategorized

I forgot how good this was...

3 responses so far

Scibloggers Fantasy Football: Week 14

Dec 13 2011 Published by under Uncategorized

Finally JadeBio reasserts her dominance over the pack.  I forgot my picks again this week, I'll have to get better about this.  As far as the top 3 overall its JadeBio (113), PLS (107), and Odyssey (102).

#1.  JadeBio

#2.  Odyssey

#3.  Namnezia

#4.  SugarScientist

#5.  Alyssa

#6.  GertyZ

#7.  PLS

#8.  Hermie

#9.  Chall

#10.  Dr. O

2 responses so far

Databases Gone Wild...Unigene

Dec 13 2011 Published by under Database

Unigene is a fun little database that you can use to mine expression of the transcriptome throughout tissues and cells.  And in conjunction with Unigene you can use Homologene, an additional database that allows you to look at the specific transcript to see homology in various species.  It even links you to the GEO microarray database so you can search relevant experiments.

If you want to give it a whirl, here is some sample data from Ataxia Telangiectasia Mutated (ATM) gene.


No responses yet

If you were thinking about getting me anything for Christmas...

Dec 12 2011 Published by under Uncategorized

I wouldn't mind the following:

-X-men:  God loves, Man Kills graphic novel.
My mom tossed out my comic book collection when I went to college and besides this book does a good job of drawing parallels to some of the crazy religious whackaloony today.

-iTunes Gift Cards
The more the merrier, how else am I going to finish my Cowboy Mouth compilation?

-Chef's Tables Stand for iPad
Would be very helpful as Genomic RepairWife and I use it to look up recipes in the kitchen.

-Garde Manger Cookbook.
I have a huge mancrush on Chuck Hughes and his cooking show, Chuck's Day Off. My wife is cool with it.

-Johnnie Walker Blue Label
If you get me nothing else, get me this. Feel bad for the poor bastard in the video below, what a waste of great alcohol.

2 responses so far

Databases Gone Wild...again...Flybase

Dec 12 2011 Published by under Database

Reaching back into the depths of scientific history, we have been working with fruit flies (Drosophila melanogaster) since the early 1900s.  We've all read about the exploits of Thomas Hunt Morgan and the white eyed flies in our basic biology textbook during our formative undergraduate years.  Drosophila has proven itself through the following century of research to be an invaluable model organism to study genetics and development.  Over the years of research a mountain of mutants have been made and phenotypes observed, thus necessitating the need for a storage repository for this wealth of knowledge.

If memory and records serve correct the genesis of Flybase was in 1992 by Dan Lindsley, a researcher at UCSD, who at that time was sort of a curator for all things Drosophila.  Prior to Flybase Lindsley's Genome of Drosophila melanogaster was the holy gospel of all fruit fly researchers.  Lindsley a septuagenarian at the time said to hell with keeping track of all of this, and the Flybase consortium was formed and led by Bill Gelbert at Harvard.  What made Flybase was so remarkable is that you had to think back at the time, the database was taking off at the same time as the internet was.

So check out Flybase to search for information on different mutants, gene ontology, GWAS, all 12 sequenced Drosophila genomes, etc.

3 responses so far

Grinding away your mental edge...take some time to think

Dec 10 2011 Published by under Mentoring

I think a serious misconception amongst trainees is that the only thing that matters in grad school is racking up a huge body count of hours at the lab bench.  I see them grinding away at the bench hour after hour only to go home too exhausted to do any critical thinking.  You have to partition out some of your time to read, write, and more importantly just to think.  I've asked these lab bench workaholics how often they are reading and the answers are quite frightening.  In my opinion (and for what little it is worth) you need that precious time to just sit and process your own research, your subfield, and what is going on around you in science.  This is what sustains the flame of intellectual curiosity and keeps you mentally sharp and focused.  At least for me anyways.

Does this sound like utter bullshit?

9 responses so far

Are you a Labguru

Dec 08 2011 Published by under Database, LIMS, Review

As we move to a much more technology based research infrastructure I am seeing plenty of people dumping the good old hardbound laboratory notebooks for electronic notebooks. Instead of paper based archives of samples, freezer storage, and to do list, we are slowly gravitating to works database systems, excel spreadsheets, or FileMaker Pro databases. At some point why not combine these databases with your data storage in addition to your research and literature notes that some research groups are stashing in individual lab wikis. Why not use an all encompassing system to house your entire electronic research infrastructure including your data, literature searches, sample storage locations, and supply inventory in lieu of being spread across the technological four corners of the Earth?

This is what Labguru can do for you. Labguru is a project management browser-based software commonly referred to as “software as a service” that safely and securely stores your data in the cloud. The fine folks at BioData, makers of BioKm software, gave me a free trial to play around with their system for a little while. I have to say that I’m quite impressed with it, especially since I have been quietly shopping and testing electronic laboratory notebook (ELN) systems for our lab, and this is as fine of one as there is on the market. And I’m being honest about this; I’m running a free trial, which I will terminate after this post, is published.

Labguru would be an ideal piece of software for new PI’s that are starting up their labs or ones that have to manage a horde of undergraduates. Labguru allows you to set the tone as far as the way you record and report your research which is invaluable when you have a slew of transients passing through the doors of your lab. You don’t need to be trying to decipher data from the arcane shorthand of an undergrad from two summers ago that fell off the face of the earth once they left your lab. Instead, drill down into their annotated your way project files and open up the excel file and snag the data you need.

I’m still working my way through the software but find it very interesting if you are in the market for this type of software. It is not without fault, I have found a few minor issues that I have communicated to BioData but I think they can iron out these before they roll out the software. Also they are receptive to suggestions so why not kick the tires on the thing and if you find something you don’t like, let them know so they can get to work on it. The cost of Labguru isn’t too bad considering how much you can do with it and the fact that it is a software as a service, you don’t have to worry about all the data clogging up your computer’s hard drive.  So take the tour and see if you like it.

Labguru - Tour from BioData Ltd on Vimeo.

Note: This is an unpaid and unsolicited review. I have received no compensation for this, even refused the free T-shirt. If you would like me to review your products let me know and I would be happy to.

12 responses so far

Texts From Bennett

Dec 07 2011 Published by under LinkLove

is hilarious, you have to go visit this site.

No responses yet

I want to interview someone...

Dec 07 2011 Published by under Uncategorized

Seriously, I'm going through a dry spell on stuff to post and wouldn't mind interviewing anyone in the sciences.  If you know of someone or want to be interviewed yourself, leave me a comment or send me an email (contact information in the about tab).

Oh yeah and I'll be doing another week of databases next week at the urging of readers.

4 responses so far

Scibloggers Fantasy Football: Week 13

Dec 06 2011 Published by under Uncategorized

Oh Crap!  Alyssa just jumped into the top spot and PLS is going to turn the season into a battle with JadeBio.

#1.  Alyssa

#2.  PLS

#3.  Odyssey

#4.  Chall

#5.  SugarScientist

#6.  JadeBio

#7.  Dr. O

#8.  GertyZ

So as you can guess several of us were so taken aback by #Burzynski last week that we forgot to make our picks.  I for one pledge to do better next week.

One response so far

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