• From BioMed Central article alert: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models (highly accessed, on my to-be-read list) [Jennifer]
• P-ter at Gene Expression shows the utility of a good genome browser by finding processed pseudogenes in a region that a study identified as a ‘short, novel, unspliced transcript’ using a genome browser. [Trey]
• Semantic Medline Prototype? [Trey]
• Interesting Nature article & I think access is free: Citizen science: People power [Jennifer]
  

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.

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.

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. Ensembl undergoes a periodic update and was due for one in April, but they have postponed that update till July as per this Ensembl blog post. So, they are not undergoing an update.

But in July there will be several updates, Ensembl 50!, including an update to the web interface. We’ll keep you informed as to what the particulars of that update are and how the interface change might affect your usage of the site (and a review of course .

Also, at the end of their post, the mention the demise of SSAHA which you are now able to access through the BlastView:

Last but not least, please note that from Release 50 we will no longer be providing the ‘ssaha’ sequence search. If you wish to run your own ‘ssaha’ sequence search you can download the files to generate the search hashes from our FTP site.

SSAHA, is a quick tool for sequence matching, as you can see from the Ensembl Help:

SSAHA (Sequence Search and Alignment by Hashing Algorithm)
SSAHA is a very fast tool for matching and aligning DNA sequences. It is most useful when you are looking for exact or ‘almost exact’ matches between two sequences. In Ensembl, you can use it to search against genome sequence assemblies.

So, I assume as of July it will be dead.

Of course, as they mention in the blog post, a similar search you can use for quick genomic sequence searches is the BLAT tool at the UCSC Genome Browser. Of course you could also download and install SSAHA yourself from the SSAHA homepage and obtain the hash tables from Ensembl’s FTP site.

This database contains what are known as sleep quotas for 178 separate references, on 127 different species (as of June 29, 2007), in 46 families, across 17 orders, with additional sleep data on other species being added to the database as they become available. Sleep quotas are essentially time spent in each of the two major sleep states (REM and NREM) per day.

So, it is a very focused database to be sure, though they do have some larger projects in mind such as a comparative analysis between mammal and bird taxa (The author of the post linked above is correct, they should include many other taxa, sleep is ubiquitous in animals beyond mammals and birds).

Interesting.

Couple other sleep resources, articles for your reading pleasure:

1. Allen Brain Atlas Sleep Study data: “Microarray data is available for seven brain regions collected from five experimental conditions: sleep deprivation, recovery sleep, and three time-of-day controls.”

2. Interesting blog post and article on function of sleep. From “A blog around the clock”.. always an interesting read

3. American Sleep Apnea Association

4. Sleep Research Society. (they have some slide sets on sleep research and information for use)

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:

GenBank’s managers are dead set against letting users into GenBank’s files, however. They say there already are procedures to deal with errors in the database, and researchers themselves have created secondary databases that improve on what GenBank has to offer.

But would this work? In Francis Collins’ talk at the GenBank anniversary he mentions the proposal though isn’t sold (video, at 2hr 22min). But Steven Salzberg suggests in an opinion piece in Genome Biology last year that the current solution isn’t working and one possible solution is to add a layer of ‘wiki’ to the database.

“Wikifying” a genome database or Genbank would be one more step beyond even what TAIR is doing. TAIR hopes that authors will curate the database and save on time and money spent on curators. But there is some concern that this might not work as planned.

Though wikis have been quite successful in some instances (of course wikipedia being an example), the internet is littered with dead wikis that never got the community support to keep them going successfully. It is also littered with wikis filled with inaccuracies, spam links, bad information and turf battles. If a wikified GenBank went the way of a lot of other wikis, the solution to fix inaccuracies might be worse than the original problem.

The wikification of GenBank would be allowing only credentialed editors make changes I suppose, but in reaction to a suggestion for academics with research credentials to enroll as identifiable editors of Wikipedia (in order to increase the accuracy of those articles), one blogger writes:

There’s nothing nastier or more tenacious than credentialed scholars squabbling about their area of research.

He might have a point, though this is GenBank and sequences, not the minutiae of population genetics (I’ve seen some quite acrimonious discussions there!) . Perhaps a way could be made for a ‘wikified’ layer of genbank and I can definitely see the usefulness. Wikis can be a great tool for the right community and subject.