Leave me some suggestions of stuff to cover next week and I'll look it up...
Until then, enjoy some 311. See you Monday.
Archive for the 'Database' category
Leave me some suggestions of stuff to cover next week and I'll look it up...
I am a subscriber to the NCBI newsletter that comes out monthly to see what is shaking over in NIH land to get a better idea as what new databases are coming online, which ones are being mothballed, and what these databases are being used for. Take at look at the latest news here and if you like it below are the instructions for subscribing to the NCBI newsletter so that you don't have to go find it, they'll just email you when the new one comes out.
Send email to firstname.lastname@example.org with Subscribe in the subject line.
MitoCheck is a database built off of RNA interference (RNAi) screens to identify all proteins that are required for mitosis in human cells. It includes:
-affinity purification and mass spectrometry to identify protein complexes and mitosis-specific phosphorylation sites on these
-small molecule inhibitors to determine which protein kinase is required for the phosphorylation of which substrate.
MitoCheck is also establishing clinical assays to validate mitotic proteins as prognostic biomarkers for cancer therapy.
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.
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.
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.
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.
So I'm going to be a homer for my own subfield today and present to you folks the DNA Repair Database run by the University of Pittsburgh Medical Center. If you ever wanted to know what proteins were involved in DNA repair, which specific pathways, and various orthologs this is the website to go to. It serves as a nice landing spot for you to look up information on these genes (links to GenBank, etc.). And not to call you guys out any but I think you are missing a few proteins, but overall its a fun little database.
So if you folks liked the database content I can keep this going for another week, or if you can think of some cool databases to look at, drop me a comment. Thanks
Day 4 of 5. We're closing in on hotel motel time now folks.
So lets take a look at the Kyoto Encyclopedia of Genes and Genomes, which was created by our friends at the Japanese Human Genome Project in the mid 1990s. KEGG allows you to search for genes and create pathway maps (you know those ones that are so pervasive in glamour mags these days. You can also look a variety of chemicals and obtain pertinent information in addition to structure (including jmol files). Sadly not all of the features of KEGG are free, apparently now they want you to kick in a few bucks to tap the keg once in a while. But there is a lot of good free stuff on there, so fire up the google machine and check it out.
Day 3 of 5
I'm talking about the Allen Brain Atlas, named for the Microsoft co-founder and philanthropist Paul Allen. I picked this database because of all of the neuroscience douches that hang around here at Scientopia. If you ever wanted to know whether a particular gene was expressed in the brain and where at, this is the database for you. Thanks to Allen's patronage, this database does a fantastic job and integrating genomics with the neuroanatomy of the mouse.
So go ahead and toss in your favorite gene and see where it lands.
Day 2 of the 5 day database series...
No, I'm not talking about crazy Brenda that lives down the street, I'm talking about BRENDA, functional enzyme data collection repository developed and run by the fine folks at the Institute of Biochemistry and Bioinformatics at the Technical University of Braunschweig in Germany. Want to know a particular Km value for a specific enzyme substrate? Ask BRENDA.