Tag Archives: YeastMine

Tip of the Week: Yeast genome? There is an app for that!

GBrowse navigation basics tutorial from yeastgenome on Vimeo.

The Saccharomyces Genome Database (SGD) has several short video tutorials that introduce basic navigation (shown above), expression data and more.  Each of these tutorials are short, 1-2 minutes, and there are 21 of them (15 on yeastmine alone). If you want to go further in depth, we have a tutorial on the Saccharomyces Genome Database (SGD) (subscription)also that is about an hour long, modular and includes exercises. We have also done tips on Yeastmine and other SGD related tools (open access). You can also find a tutorial at OpenHelix on GBrowse, which is the browser used at SGD. And there is this short 5 minute GBrowse video tutorial.

So, a yeast researcher has no lack for video training on using SGD.

But, today I wanted to introduce you to SGD’s new app for the mobile researcher: YeastGenome App. The app has some pretty decent functionality. As their FAQ enumerates:

yeastgenome-3-newipad

“Saccharomyces Genome Database by gene name or keyword to find fundamental information about your favorite gene. Browse the database by feature type and quickly view fundamental information, sequence information, Gene Ontology, interactions, phenotypes, and references associated with the terms.

Does the app have any other special features?
Yes, you can use the app to save your favorite genes in a convenient list. You can also e-mail yourself or your friends and colleagues any information you find about yeast genes in the Saccharomyces Genome Database.”

I’ve had a go at the app for a bit, and it makes browsing and searching yeast genome data pretty convenient and easy. The app was reported in this year’s Database issue at NAR and it gives a good rundown of the app. Don’t need convincing? Then you can go right to iTunes and get it now.

But this reminds me, I did a feature on mobile apps for genomics research last year that reviewed GeneWall, Wowser and MyGenome and the year before that introduced an app for “moving molecules”. THis new app and several I’ve seen in the interim since those posts suggest that perhaps it’s time to do a new post on mobile apps available for genome research.  Perhaps that will be the next tip of the week from me in a few weeks.

Tip of the Week: A year in tips III (last half of 2010)

As you may know, we’ve been doing tips-of-the-week for three years now. We have completed around 150 little tidbit introductions to various resources. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

Here are the tips from the first half of the year, and below you will find the tips from the last half of 2010 (you can see past years’ tips here: 2008 I2008 II2009 I2009 II):

July

July 7: Mint for Protein Interactions, an introduction to MINT to study protein-protein interactions
July 14: Introduction to Changes to NCBI’s Protein Database, as it states :D
July 21: 1000 Genome Project Browser, 1000 Genomes project has pilot data out, this is the browser.
July 28: R Genetics at Galaxy, the Galaxy analysis and workflow tool added R genetics analysis tools.

August

August 4: YeastMine, SGD adds an InterMine capability to their database search.
August 11: Gaggle Genome Browser, a tool to allow for the visualization of genomic data, part of the “gaggle components”
August 18: Brenda, comprehensive enzyme information.
August 25: Mouse Genomic Pathology, unlike other tips, this is not a video but rather a detailed introduction to a new website.

September

September 1: Galaxy Pages, and introduction to the new community documentation and sharing capability at Galaxy.
September 8: Varitas. A Plaid Database. A resource that integrates human variation data such as SNPs and CNVs.
September 15: CircuitsDB for TF/miRNA/gene regulation networks.
September 21: Pathcase for pathway data.
September 29: Comparative Toxicogenomics Database (CTD), VennViewer. A new tool to create Venn diagrams to compare associated datasets for genes, diseases or chemicals.

October

October 6: BioExtract Server, a server that allows researcher to store data, analyze data and create workflows of data.
October 13: NCBI Epigenomics, “Beyond the Genome” NCBI’s site for information and data on epigenetics.
October 20: Comparing Microbial Databases including IMG, UCSC Microbial and Archeal browsers, CMR and others.
October 27: iTOL, interactive tree of life

November

November 3: VISTA Enhancer Browser explore possible regulatory elements with comparative genomics
November 10: Getting canonical gene info from the UCSC Browser. Need one gene version to ‘rule them all’?
November 17: ENCODE Data in the UCSC Genome Browser, an entire 35 minute tutorial on the ENCODE project.
November 24: FLink. A tool that links items in one NCBI database to another in a meaningful and weighted manner.

December

December 1: PhylomeDB. A database of gene phylogenies of many species.
December 8: BioGPS for expression data and more.
December 15: RepTar, a database of miRNA target sites.

Tip of the Week: YeastMine


For this week’s tip I would like to take you over to the Saccharomyces Genome Database (SGD) & from there try out the beta release of YeastMine. YeastMine is based on the InterMine open source data warehouse system. We’ve featured other incarnations of InterMine, such as RatMine from RGD in this tip and modMine (associated with the modENCODE project) in this tip, so you’ve already seen some of its capabilities. The aspect that I want to focus on when we look at YeastMine is the interoperability of InterMine resources.

Mary noticed the beta YeastMine release notice first & mentioned it to me. When I got over to SGD, not only did I see the notice on YeastMine, but also noticed that they are now linking to GeneMANIA in some of their interaction resources. I think that’s cool because soon we will be releasing a new GeneMANIA-sponsored tutorial. I’ll head back over to SGD & maybe do a tip on that too, some other day, but for now enjoy today’s tip on how to make a gene list and then link to gene homolog information on FlyMine, the FlyBase/Drosophila version of InterMine.