The OpenHelix Blog

We had a tip last week on converting genome coordinates using Galaxy. This week I’d like to introduce you to the Galaxy interface. This screencast was actually done by one of the developers of Galaxy and is a quick introduction to the interface. We are currently working with Galaxy on a longer introduction to the tool, but thought I’d give you taste of it here. Galaxy is an excellent analysis tool. It’s not a database, but rather a tool to analyze data you can obtain from other sources and allows you to save your workflows and many other tools that help you analyze and collaborate. (if the movie to the left doesn’t load, try this link to view the movie).

Comprehensive tutorials on the ASTD, Entrez Protein, and MMDB databases enable researchers to quickly and effectively use these invaluable variation resources.

Seattle, WA September 24, 2008 — OpenHelix today announced the availability of new tutorial suites on the Alternative Splicing and Transcript Diversity (ASTD) database, Entrez Protein and the Molecular Modeling Database (MMDB). ASTD is an European Bioinformatics Institute (EBI) resource for alternative splice events and transcripts for the human, mouse, and rat systems. Entrez protein is a comprehensive database of protein information brought to you by the National Center for Biotechnology Information (NCBI). MMDB is another NCBI resource which contains an extensive collection of three-dimensional protein structures with detailed annotation that can be used to learn about the structure and function of many proteins. Together these three tutorials give the researcher an excellent set of resources to carry their research from transcript to 3d protein structure.

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 with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:

ASTD

• to perform Quick and Advanced searches
• to navigate gene and transcript report pages
• to predict intron/exon boundaries and likely regulatory protein binding site
• to search manually curated data regarding alternate splicing

Entrez Protein

• to perform basic and advanced searches utilizing the many available tools and options
• to understand the protein records and exploit the many internal and external links you are provided with
• to explore some of the resources provided by the NCBI network of databases, such as “My NCBI”

MMDB

• to search MMDB using both basic and advanced query techniques
• to understand the detailed results you obtain
• to visualize and manipulate structures using NCBI’s Cn3D structural viewer
• to locate and view structurally aligned homologs

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.

About OpenHelix
OpenHelix, LLC, provides the genomics knowledge you need when you need it. OpenHelix currently 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.

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.

Today’s tip of the week is introducing dbRIP, a database of Retrotransposon Insertion Polymorphisms in Humans. The dbRIP database, as you can tell from the title, is a focused resource on one subject: Retrotransposons in humans. Though focuses, retrotransposons are an important aspect of the human genome comprising 40% of it. They have an effect and a useful branch of study. This databases uses a local installation of the UCSC Genome Browser annotated with the RIP data. The tip movie (click the graphic to start) introduces you to the database. If it is something that interests you, you can learn more about how to use this database from the free UCSC Genome Browser tutorials at OpenHelix, since this database uses the same software.

One of the reasons we started this blog (and company) is because not only are the number of genomics databases, analysis tools and resources rising dramatically, they are in constant flux. New resources are born constantly (the graph on the right shows the rise in the number of resources listed in the annual NAR database issue), current resources are continually being updated and changed, resources merge (UniProt) and some just fade away.

I bring that up because Ensembl actually is not undergoing an update, having a major update and part of it is fading away… all at the same time.

Ever wanted to adopt a pet? Perhaps you’ve thought of donating to a zoo by “adopting” a zoo animal, well, you can do even more. The Encyclopedia of Life (which I’ve written about before) needs someone to adopt a species as an ‘authenticator/curator’. The EOL has a lot of potential, but it’s going to require some volunteer work. This week’s tip introduces the EOL, what kind of data is there in the ‘model’ pages and shows you how to sign up!

I love my job, databases intersect with my personal interests often. “A blog around the clock” reports on a new open access Sleep Journal and a “Sleep Database.” As someone with sleep apnea (and whose CPAP machine changed his life), I am fascinated by the entire subject. So I’ll be keeping tabs on the journal, and the database (Phylogeny of Sleep) is fascinating. The database’s purpose, as the homepage states:

Today’s tip of the week introduces you to Gramene, a great database of grass genomes including rice, corn, oats, millet, wheat and others. The database is full of serious data and genomic analysis tools for the grasses, but today we are going to show you something fun you could do with Gramene… plan your dinner. After quickly showing you that there is a wealth of data on a large number of species, we’ll point you to some information on how to cook those genomes.

Speaking of Genbank’s 25th, a few weeks ago Science had a news piece “Proposal to ‘Wikify’ Genbank Meets Stiff Resistance.” Apparently, those in the Mycology research community have found many inaccuracies in the Genbank records and wish to see a change that would allow annotations to be made by the community:

a scheme like those used in herbaria and museums, where specimens often have multiple annotations: listing original and new entries side by side. It would be a community operation, like Wikipedia, in which the users themselves update and add information, but not anonymously.

But the idea is meeting resistance from Genbank’s Managers:

I was perusing the new PLoS Computational Biology just now, with my hands gripped to my coffee mug. I spotted this article:
Genes and (Common) Pathways Underlying Drug Addiction by Li et al. I was wondering if the genes that direct me to coffee each morning were identified. But it doesn’t look like they covered coffee. The list of Addiction Related Drugs from their site has other plants. Alas.

To visit the new database, go here: KARG.