Tag Archives: iPhone

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…

  • If you are in the Boston area: RT @larry_parnell: RT @NatNetBoston Day one schedule for the upcoming #Cambridge, Mass. #sciencefestival, and more http://bit.ly/hRcNN5 [Mary]
  • miRBase 17 was released April 26th – check out all the new features! (I’m updating our miRBase tutorial now) [Jennifer]
  • RT @dgmacarthur: Nice. MT @akhomenko: “Genetics, whether the high priests like it or not, is going to be crowd-sourced” http://on.wsj.com/f6Huta [Mary]
  • Well, technically it is genomics. Of a sort… RT @mjrobbins: Indeed RT @noodlemaz: *Titter* RT @krishgm: hilarious and terrifying. sex education from the guardian http://bit.ly/gAxfoI [Mary]
  • interesting: RT @kshameer: Pfam annotation is now beginning to be co-ordinated via Wikipedia: http://bit.ly/eSM9uT #Bioinformatics [Jennifer]
  • There’s a new iPhone app for EcoCyc (via mailing list):  “An iPhone application is now available for EcoCyc, and may be downloaded through the iTunes store.  EcoCyc-Mobile provides a streamlined mobile interaction for EcoCyc, a bioinformatics database that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655.  Use EcoCyc-Mobile in the laboratory, in the classroom, at a conference, or in the library.” [Mary]
  • RT: @phylogenomics: Next-Generation Sequencing & Genomic Medicine – 8/1-3 in SF http://ff.im/-Ch0LM [Trey]
  • RT @kshameer: GTEx (Genotype-Tissue Expression) eQTL Browser: http://1.usa.gov/fG8LTs #genomics #bioinformatics [Mary…I feel a tip-of-the-week coming on…]
  • From the lab of Peer Bork and a Carl Zimmer article: Bacterial Ecosystems Divide People Into 3 Groups [Jennifer]
  • Biggest chuckle of the week: Meatomics! RT @SCEdmunds: Trying to learn about the genomics of meat production in this talk, but can’t stop thinking about a juicy steak. Mmm, #Meatomics! #BITWDD [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?

Tip of the Week: BioGPS for expression data and more

This week’s tip introduces BioGPS, or Gene Portal System. We get a lot of questions about two things that BioGPS can help you to tackle: what do I do with a list of genes to find out what they are? And the next question people have after that is: and where are they expressed? BioGPS can help you with both of those problems. It is a tool that integrates and displays many types of data that researchers would be interested in. It also allows you to customize your display with the types of data that are most relevant to you–using their extensive plug-in collection. And it can do so from your browser, or access the basic portal from your iPhone!

Recently there was a question at BioStar about ways to quickly access some human gene expression data. The top rated answer over there was BioGPS, so we thought we’d provide a look at the kinds of things available to users via BioGPS. This 5-minute movie introduces some of the features.

Basically you can search for a gene or a list of genes, you can search with various types of IDs, you can search by keyword, or you can even search by genomic intervals. Your resulting list will quickly link you to all kinds of information from expression data, to annotation details and wikis, and more.  The results are provided in a handy default view with panels of information which may offer what you are looking for.

But you can go further with BioGPS using their customization and plug-in features. You aren’t tied to the default view. The system offers plug-ins: other tools can pipe their information over to BioGPS so you can use it within that framework. You can  register/create a login and then store views that are suited to your research needs.

At the time they wrote the paper provided below, they already had over 150 plug-ins available. As I write this today there are nearly 400 things you could bring in to supplement the views of the genes you are interested in. And the range of plug-ins is tremendous: interaction data sets, SNPs, phylogenetic data… The Figure 2 in their paper gives a partial list of the plug-ins at that time, and the categories they highlight include: literature searching (such as PubMed, iHop, patents, more), gene portals (such as Entrez Gene, UniProt, Gene Cards, more), genetics (dbSNP, HapMap, HuGE, more), pathway tools (KEGG, Reactome, STRING, more) and even reagent providers. But there are more now, and it looks like more will continue to be developed and added. It really depends on what you need and want to display for your searches. You can browse around or search the plug-in collection to explore what’s available to view.

There are other tools you can use to explore expression data specifically. We like the UCSC Gene Sorter for some types of queries. Of course the large repositories of GEO and ArrayExpress can offer expression data as well. But for some users the BioGPS portal may offer integration and customization features that will suit their research needs. Go over and check it out. Register, set up some views, and you’ll be finding all sorts of useful annotations for your genes or regions of interest.

Just to also quickly mention: you can do searches from your lab bench, or from seminars, with the iPhone version of BioGPS as well. I didn’t have time to cover that in the movie but there’s more information over at their site about the tool. I’ve got mine installed and I’ve found it handy during talks!

Quick links:

BioGPS homepage: http://biogps.gnf.org/ EDIT: has moved: http://biogps.org/

BioGPS iPhone app: http://biogps.gnf.org/iphone/

Reference:
Wu, C., Orozco, C., Boyer, J., Leglise, M., Goodale, J., Batalov, S., Hodge, C., Haase, J., Janes, J., Huss, J., & Su, A. (2009). BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources Genome Biology, 10 (11) DOI: 10.1186/gb-2009-10-11-r130

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…

  • NWChem for High-Performance Computational Chemistry has recently gone Open Source. (HT GenomeWeb) [Jennifer]
  • DIYGenomics relates an iPhone app that compares consumer genomics collections. [Mary]
  • A poster on BridgeDB, a resource for ID conversions. Hat tip to Chris Evelo. [Mary]
  • Sanger has done a very nice site for personal genomics and general background on the human genome, aimed largely at the general public and at teachers. http://www.yourgenome.org/ [Mary]
  • Nice phylogenetic analysis site for building protein phylogenies and structure predictions: PhyloBuilder [Trey]
  • Wired magazine had a fun take on some metagenomics from the Galaxy team. [Mary]
  • Via tweet: RT @dgmacarthur: 50% of UK respondents would take free genetic testing, but only 5% interested at current DTC prices: http://bit.ly/b7tDvx [Mary]
  • I completely missed World Statistics Day. No fireworks. No cake. Nuthin’. Sigh. [Mary]

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…

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’.

Friday SNPpets

Welcome to our Friday feature link dump: 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…

Tip of the Week: GenomePad

feature_gpI discussed iPhone apps that would be useful for biology earlier this year and we’ve added one or two since. There is a new one now that I’m definitely putting on my iPhone, GenomePad. This is an iPhone app that creates an easy-to-use interface to the UCSC Genome Browser. Today’s tip is a quick introduction. Since I don’t have iPhone screencast capability, I’m going to quickly describe the basic functionality of the app below in a few screenshots. The GenomePad people also have a short video with an video introduction.

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BioGene: iPhone app for NCBI searches from MSKCC team

iphoneI can’t remember how I got on this email list–but I like it :)  Today I was notified that there was a handy iPhone app to quickly get gene info out of the NCBI resources.  I wish I had this last week at the ASHG meeting.  You know what happens: you catch a gene name or see a symbol in a talk, it’s just one of several on a slide…but you must know what that is right now!!  This handy-dandy quick interface will let you search for the symbol and links you to Entrez Gene info, which also links to references in PubMed.

I like it.  I expect to use it.  The first reviewer over in the iTunes store says it has already expanded their conversation.  I wish it also covered OMIM, but I haven’t used it too hard yet, maybe I’ll get there.  That also would have been a help last week.  I was hearing about a disease and I wanted some information.

Check out the MSKCC team page here for more details, and download it from the iTunes store (for free) if you like the sound of it.

BioGene: http://cbio.mskcc.org/tools/iphone_ipodtouch.html

For other iPhone apps we’ve come across, check out our earlier post on the iPhone and research.

iPhone and research

Ok, so I just got my new iPhone 3Gs. I couldn’t resist. Anyway, my contract on my first generation iPhone was up. So, it was time to reconfigure and explore the huge number of apps out there for the iPhone.

I use the iPhone for a lot of things, directions, finding out what stores are in the area, keeping my grocery list, listening to music, watching shows, browsing the web, keeping my calendar and contacts and a bunch more. Oh, and to make and receive phone calls :).

I’ve read past posts on other blogs about scientific apps for the iphone, I decided it was time to check out what apps there are now.

I’ve found a few I like, some that might work (I do computational genomics now, so I haven’t tried the ones for the bench), and one that has nothing to do with biology (directly anyway), but I am in love with. Follow me below the fold.

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