Tag Archives: iPad

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: one iPad app to rule them all

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There is none.

Ok, so that is the simple answer. The complicated answer is this: my ideal genome browser iPad app would have the flexibility to go from a mass market browser to look at an individual’s genomic variants in a genomic context with information about the research, genes, etc presented in such a manner so that any thoughtful person or doctor could understand, to a full fledged UCSC genome browser type research tool.

So, that’s not feasible. Instead, I’m going to look at three genome browsers for the iPad, two for research, one for the mass market. The former are GeneWall by Bioskoop and Wowser by the Children’s Hospital of Philadelphia, the latter is MyGenome by Illumina (links take you to iTunes app store).

The iPad and other touch tablets are perfect research assistants and the day is fast approaching, if it’s not already here, where most researchers will have one on the lab bench for entering and accessing data.

So what am I looking for in a iPad genome browser?
Navigable: it should have a very intuitive, iPad native navigation. I should be able to pinch and swipe my way through the genome with finely controlled ease.
Comprehensive: I should be able to access my genome of choice, past assemblies, and a huge range of annotations.
Flexible: I should be able to upload my own annotations with ease.

Why not just go to the UCSC Genome Browser? You could, but it fails the first test. It’s definitely usable, but many features available on a computer are not available on the iPad and navigation is obviously not iPad native.

20120509-091620.jpgGeneWall works nicely on the first criteria, but zooming in and out takes several (sometimes many) pinches of the fingers. There is no simple way to zoom in and out or walk the chromosome in a more fine tuned manner. On the second, though it comes with a single genome (human) with only a few annotation tracks so it’s not very comprehensive to start, you can easily add annotation tracks downloaded as bed files. So it has some flexibility. The pathway search and gene list function are nice too. A quick YouTube intro here.

20120509-091959.jpgWowser is somewhat different in that it is an iPad interface to the UCSC Genome Browser. It works natively with the iPad and so is easy to navigate. Zooming and walking was intuitive. On a few different wireless networks it was slow to load, but not excruciatingly so. It is quite comprehensive, including the latest human reference sequence and many, but not all, of the UCSC tracks. The tracks are simple to hide or add in. Future updates are said to be including other genomes and more tracks. I could not find a way to add your own custom tracks or data, so on flexibility GeneWall wins out.

Both apps are great, if not quite “there” yet. I think either would be useful if you are looking at the human genome for research.

20120509-092126.jpgMyGenome is a different beast. From Illumina, it’s audience is not the researcher but the medical professional and patient. It’s a beautiful app with a nice interface. Easily navigable, it was simple to get to the information wanted. There is a lot of information there, but it is still quite limited. I took several variations that effect propensity for prostate cancer and other diseases and was unable to find information on them either because the variation is listed but no information, of variation was in an intergenic region which seemingly isn’t included. A user can not yet upload their own data,or other annotations, which is understandable since by Illumina’s own account this is only the beginning. Currently it’s a great educational tool (though I was a hung for more gene information), in the future it will be a good way to browse your own data.

So the bottom line for all three of these are that they are useful as they stand and for their stated purpose, but I’m looking forward to the future of browsing genome data like I was on an Avatar set :). It’s coming.

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

  • Special hot topic item Friday morning: RT @dgmacarthur: Joe Pickrell’s discusses potential artefacts in the Science RNA-editing paper at @genomesunzipped: http://bit.ly/jUVz6t [Mary]
  • Nice–appears to be the new BioMart interface: RT @yokofakun: A rudimentary semantic-web support in #BioMart . Test-server: http://central.biomart.org [Mary]
  • McKinsey says “big data” is…er, big: RT @westr: “Big data: The next frontier for innovation, competition and productivity http://bit.ly/kVEXAZ” -via @ahier #pm101 [Mary]
  • Tox Town: Environmental health concerns and toxic chemicals where you live, work, and play” – a simple-to-click interface that links out to some interesting info & reports from throughout the NLM’s collections. [Jennifer]
  • Fascinating research area, cool new database and data sets: RT @CHOP_CBMi: Our AudGenDB Project is announcing the public beta release of its web app today. Check it out! http://ow.ly/4TgQg #audiology #audpeeps [Mary]
  • Links to an Italian page, but you’ll get it–new iPad app: RT @mobimed: Genome Wowser – The Children’s Hospital of Philadelphia: Genome Wowser The Children’s… http://goo.gl/fb/hsDrS [Mary]
  • Bwaaa-haaa-haaa! Best literary reference about telomere studies EVAH! RT @NatureNews: RT @dr_krystal From orphanages to epigentics by @marianlturner “Please, sir, I want some more telomeres” http://bit.ly/jybGfj in @naturenews [Mary] (PS: if it does turn out that this relationship holds, it will be a sad consequence of neglect. I’m just not all there on the strength of the link….)
  • That’s a disorder? Sounded like grad school to me… Meh. {note–contains cuss word} RT @bengoldacre: An excellent and admirable image on normal. http://bit.ly/kBYS2s [Mary]
  • Found it on Nature.com Blogs: Biocomicals, “Where science meets with fun” [Jennifer]
  • Brent is right, this is interesting: RT @brent_p: very interesting! http://bit.ly/ktrQPh Sequence-specific error profile of Illumina sequencers [Mary]
  • Free disease cards that compile info from OMIM & more: Clinical Utility Gene Cards, “Bringing together information regarding a specific disease and providing clinicians with guidance on genetic testing for hereditary conditions in real settings of clinical genetic services.” from the European Journal of Human Genetics and Nature.com. [Jennifer]
  • RT @ncbi: New! BioProject DB: a collection of genomics, functional genomics & genetics studies and links to their datasets http://1.usa.gov/lYGKmW [Mary]

iPad app for moving molecules

Found this from Wired on Friday, iPad Lets Scientists Drag, Pinch and Swipe Real Molecules . It’s an app that allows scientists to manipulate molecules with an optical tweezer using the iPad as an interface. Quite a fascinating app and the video is interesting.

Got me to thinking, how is and could a tablet computer be used in biological science (bench or otherwise)? I wrote about iPhone apps before.

I have an iPad, and I use it a lot for reading news, reading books, catching up on email, watching movies. I find it’s potential though much more intriguing than what I’m using it for.

There are some great biology research-related apps I use. I use Papers (opens iTunes) to read and annotate research papers, and I have the Nature and PLoS reader apps, but it feels to me that developers have only mined the surface of what one could do with a handheld touch-screen tablet (be it iPad or Slate or…). Or at least what it seems you should able to do based on Star Trek movies :D.

I can see an app for keeping a lab book (there are notebook apps, but I want something geared towards lab notes. I can see an app for manipulating multiple sequence alignments (kind of like JalView) or even a game like Fold It on the iPad for multiple sequence aligns. In fact, why not Fold it on the iPad or tablet. Thought he UCSC Genome Browser can be viewed using the browser on the iPad, I can see a suped up GenomePad for the tablet. How about a personal genomics app?

Have any ideas or apps that you use for research or would like to see?

At Experimental Biology conference next weekend!

I’ll be at the Experimental Biology conference next week. We’ll (OpenHelix of course) will have a booth where we’ll be presenting UCSC Genome Browser Training.

So, come by OpenHelix booth 562 for:

  • a brief demonstration on the features and functionality of the UCSC Genome Browser
  • answers to questions you may have on using the UCSC Genome Browser
  • a free CD with the UCSC Genome Browser tutorial suite, including self run tutorials, PowerPoint presentations and exercises.
  • Quick Reference Card on the UCSC Genome Browser and UCSC Table Browser.

We’ll also will also be presenting its new Genomics Search and Learn Portal. The portal directs scientists to the most relevant publicly available bioinformatics and genomics resources on the web, and then gives them immediate access to tutorials, training materials, and useful tips and information developed by OpenHelix.

Hey, and if nothing else, stop by booth 562  to pick up your free “puzzle” pen (always a popular item).

And of course in our socially networked world, Experimental Biology is on Facebook and interestingly, they’ve got an iPhone/iPad app… guess there always is ‘an app for that’.