The OpenHelix Blog

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…

• A great list of bioinformatics analysis algorithms and tools. [Trey]
• BMC has a new journal entitled Mobile DNA (and one of the editors-in-chief was my Ph.D. advisor, Thomas Eickbush). Some excellent first papers you should check out. [Trey]
• Interesting study on genetically engineered plants: “The impact of transgenes is basically limited to their immediate function” for the interview, paper is here. [Mary]
• Speaking of BMC, BMC Biology now incorporates the Journal of Biology (they had a ‘relaunch’ of the journal at the Experimental Biology conference, across the aisle from where we were.. cake, champagne and t-shirts! . Hey, check out the site for the free iPad giveaway. Funny, I counted 3 iPad giveaways in the exhibit hall.. [Trey]
• Found this as I was writing an article on informal education in bioinformatics for a special issue of Briefings in Bioinformatics. It is from NatureNews: “US seeks to make science free for all“   [Jennifer]
• Xenopus!  I always liked that name.  In fact, am now kicking self that I haven’t used that for some online persona….Anyway, Xenopus tropicalis, first amphibian sequence now available, see Science.  [Mary]

I am happily the lucky scientist here at OpenHelix who has been selected to create a full tutorial on a network resource named GeneMANIA, but I just couldn’t wait to share some of the details about this resource’s great features. GeneMANIA stands for Multiple Association Network Integration Algorithm. Users can either input a single gene and see interaction networks associated with the gene, or (more powerfully) to enter a list of related genes and use GeneMANIA’s ’state-of-the-art analysis algorithm’ to quickly and easily find additional related genes.

GeneMANIA allows a  scientist with no prior training in computational bioinformatics to easily use their gene list of interest to search a customized list of published functional genomics publications, as well as a wide variety of public databases, and receive the results of their analysis in an easy to interpret PDF report. Users can even upload their own important datasets and affect how the algorithm scores each gene and dataset. I  cannot cover all this functionality in this short tip – you’ll have to see our tutorial for that – but here I will show you how to do a basic search and some of the display features of GeneMANIA.

GeneMANIA stands for Multiple Association Network Integration Algorithm. For more information about it, please see this 2008 GeneMANIA publication, or the GeneMANIA documentation.

Innovative technology allows researchers to quickly find and effectively use publicly available genomics and bioinformatics resources on the web.

I don’t write code.  There.  I said it.  Yes, I have been a bioinformatics professional for over a decade and I don’t write code.

I’ve taken the classes and I own the books.  I’m down with the philosophy.  I get the need. But writing code makes me cranky and miserable.  Chasing a stray comma or semi-colon for 45 minutes makes we want to pull my hair out.  I have the ultimate respect for the people who have the patience for this.  But I’m not one of them.

Personally, I’m interested in finding the leads, and answering the biological questions.  That’s what drives me.  I’m essentially a super-end-user.  And that’s what I really like.

Recently we did a training on Galaxy and we were working with some grad students/post-docs who shared my phenotype.  They had been trying really hard to write some scripts to accomplish what they needed to do.  They also reported that comma-crazies affected them too.   After we showed them Galaxy, they were ready to put down those scripting books.  In fact, one of the comments to us was {paraphrased}, “We’ve been trying to teach ourselves programming.  I think that’s over.”  They said it would be more worth it to them to spent time learning Galaxy than learning programming.

That’s what I think, too.  Learning to use Galaxy is worth your time.

Now, I’m glad I know something about programming.  Probably the best back-end thing I ever learned was writing SQL statements. (Thanks, Rick At the Jackson Lab I shared an office with a very patient programmer who helped me with that.) Both of these have helped me to converse with professional programmers.  I know what to ask for in development projects better.  And I know enough that when handed some code I can sometimes get it to do what I need (or, ah, find someone who can help me locally….).

Galaxy is developing a user community that is doing that now–bridging the people with the questions and the people who like to build the bridges.  Across the mailing list the other day came word from Ido Tamir about a very helpful series of blog posts he’s going to do that offers help with Galaxy tasks.  The first one is importing data into Galaxy.  (There are some built-in import strategies already, Ido just created one that offers a bit more customization for additional features.)

Visit Ido’s Adventures in the galaxy Pt.1 to learn more–and see the code.  But spend some time learning Galaxy.  Our free tutorial (sponsored by the Galaxy team) will get you started.  We provide an overview of what Galaxy is, and the fundamentals of the interface and how and why to use it.   The great screencasts the team does that address specific tasks will really get you further.

And if you are like me, you can skip the scripting and go right to answering the biological questions. If you are developer helping people like me in your local group–get them using Galaxy and you can build stuff that they can use, and stop bugging you.

Use Galaxy.  It’s worth your time.

Genome-wide association studies (GWA/GWAS) generate a lot of data that needs to be viewed and analyzed. There are some software tools out there to do that, including UCSC’s Genome Graphs.

I haven’t looked at it in detail yet, but this new downloadable, java viewer was recently developed and reported in Bioinformatics: AssociationViewer (download here). I’m passing it on to you. As I said, haven’t had a chance to give it a test drive, but as the title of the article states, it’s a ” scalable and integrated software tool for visualization of large-scale variation data in genomic context.” At first glance, it looks interesting.

If, like us, you were not able to go to sunny, warm Florida last week to the Advances in Genome Biology and Technology conference, well… never fear, that’s what blogging is for . Several bloggers who attended have given some interesting and informative overviews and highlights of the conference. Anthony Fejes gave a live blogging blow by blow, Daniel MacArthur of Genetic Future writes about the battle lines being drawn at sequencing companies (and some highlights), Dr. Robison discusses a new company planning to offer $5,000 dollar genomes (but only Human) this year (that $1,000 genome isn’t far away!). So, if you want to know some of the goings on at the conference, those are good places to start. The “Complete Genomics” story seems to be a big one.

OpenHelix today announced the free availability of tutorial suites on model organism databases and resources used extensively in research. The first tutorial suites available are GBrowse, Rat Genome Database (RGD), Mouse Genome Informatics (MGI), and WormBase. To be added in the coming weeks are Zebrafish Information Network (ZFIN), FlyBase and Saccharomyces (Yeast) Genome Database (SGD).

The tutorial suites, funded in part by a grant from the National Human Genome Research Institute of the National Institutes of Health, include a self run, narrated tutorial introducing the resource and how to use its feature and functions. Each suite also includes PowerPoint slides, handouts, and exercises that can be used for reference or for training others.

One of the first tutorials available is on GBrowse, developed by the Generic Model Organism Database (GMOD) project, a popular tool used by researchers to develop genome browsers for model organisms, species of interest, and particular topics. By learning how to use this “generic” genome browser, you can leverage that knowledge to use dozens of resources devoted to a wide range of research areas.

“The OpenHelix GBrowse user tutorial is very well done and will be an excellent resource for the many research communities that use GBrowse to visualize genomic data,” said Dave Clements of the National Evolutionary Synthesis Center who runs the GMOD help desk.

Model organisms, such as yeast, mouse, rat, flies, and many others, have long been used by researchers to expand our understanding of biology and to assess the effectiveness and safety of therapies before going to human trial. Many of the genomes of these organisms have been completely sequenced, giving the scientific community even greater insight into the organisms and their relation to human biology. The genome data is now available and searchable on publicly available online databases and resources.

You can view the Model Organism tutorials at http://www.openhelix.com/model_organisms.shtml. OpenHelix provides over 60 other tutorial suites on a number of genomic databases and resources through an individual, group, or institutional subscription. Further information can be found at www.openhelix.com.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

So, last week we listed the first half of the year’s tips of the week, 3-5 minute movies introducing useful tips and tools for genomics. This week we’ll list those tips from the last 6 months. That’s 51 short video tips! Listed in the continuation…

Recently Mary pointed me to this journal that came out this year, I thought I’d pass it on to you: BioData Mining. The journal is open access and housed at BioMed Central and the focus:

…all aspects of data mining applied to high-dimensional biological and biomedical data, focusing on computational aspects of knowledge discovery from large-scale genetic, transcriptomic, genomic, proteomic, and metabolomic data.

There are some interesting articles in there, for example, this one on a new software developed gene ontology based  clustering for microarray experiments. They publish papers on resources, methodologies and scientific results from mined data. Could be a journal to keep an eye on.

Comprehensive tutorials on the model organism databases ZFIN, SGD and PlantGDB and GBrowse, a model organism genome browser, enable researchers to quickly and effectively use these invaluable resources.

Seattle, WA September 15, 2008 — OpenHelix today announced the availability of new tutorial suites on several model organism resources including Zebrafish Information Network (ZFIN), Saccharomyces Genome Database (SGD) and the Plant Genome Database (PlantGDB) and also a tutorial using genome browsers with GBrowse. These four tutorials expand OpenHelix’s model organism database training which now also includes tutorials on MGI (mouse), FlyBase (drosophila), Gramene (grasses), RGD (rat), WormBase and more to come soon. Model organisms are integral to our understanding of basic biology and modern biomedical research. ZFIN is a collection of data, tools, and resources on the zebrafish (Danio rerio), a popular model organism for developmental biology and genetics research and SGD is a collection of data, tools and analyses centered around Saccharomyces cerevisiae, commonly known as bakers’ or budding yeast. PlantGDB is the primary resource for plant comparative genomics.

Additionally, OpenHelix has added a tutorial on GBrowse, a web application that allows you to explore genomic sequences together with annotated data. GBrowse is rapidly becoming the genomic browser of choice amongst model organism databases, because the browser is both universal and yet customizable.

The tutorial suites, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contain a narrated, self-run, online tutorial, slides, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:

ZFIN

• to perform effective searches and understand the displays
• to access advanced searches enabling multifaceted queries
• to use the various databases of genes and markers, expression data, mutant genotype/phenotype details, ontologies, and more
• to investigate many related resources associated with ZFIN

SGD

• to navigate the SGD site, locate Basic and Advanced Search options, and use the site map to access additional search tools
• perform the two Basic SGD Quick and Text Search types and understand the displays
• to navigate the SGD Locus Page and access data from a variety of tools, tabs, and links
• to investigate many related resources associated with SGD

PlantGDB

• to perform quick searches and navigate sequence pages
• to conduct BLAST searches across several plant species of your choice
• to create exon/intron gene predictions and sequence alignments
• to construct tables displaying highly varied information from many datasets

GBrowse

• the basic layout and search methods at GBrowse
• how to access detailed annotation data tied to genomic sequences
• how to select and customize annotations using Tracks
• how to upload and incorporate your own data or other external data sources
• take a tour of different GBrowse installations at model organism databases

To find out more about these and other tutorial suites visit the OpenHelix Tutorial Catalog and OpenHelix or visit the OpenHelix Blog for up-to-date information on genomics.