Well, we now have our own. As many of our readers know, we have a genomics and bioinformatics search engine that helps the researcher find the database or analysis tool that best fits their need. Type in a term and you get a list of genomics resources that are queued in rank of relevancy. In addition, you are shown where in context (the resource web site, or in our tutorials or blog if there) where the term was found. Additionally, you’ll find tutorials we’ve created on nearly 100 of them, about a dozen free to the user like PDB, SGKB, UCSC Genome Browser, and another 80 or so by subscription.

Anyway, you can now put the search (which of course is publicly available) on your blog or web site using one the widgets we’ve just had created (by the same people who helped create our database search). We have three sizes and you can find them and the code for them at this page.

You’ll also see I’ve put the smaller widget on the right column here on the blog. You can put a term in there and test it out. It will open another page with the results of our search. Try it out!

Thanks to Mary for running a Tip of the Week – “CHOP CNV database” a couple of months back. CHOP CNV database is a high-resolution genome-wide survey of copy number variations of a large number (2,026) of apparently healthy individuals. It is publicly accessible and has been widely used by a large number of research groups world-wide. I am now pleased to announce the public release of our software system behind it: CNV Workshop. CNV Workshop is a suite of software tools that we have developed over the last a few years. It provides a comprehensive workflow for analyzing, managing, and visualizing genome copy number variation (CNV) data.

It can be used for almost any CNV research or clinical project by offering the following capabilities for both individual samples and cohort studies:

CNV identification
Implements a modified circular binary segmentation algorithm that reduces false positives
Fully configurable parameters for sensitivity/specificity management
Annotation
Individual locus-specific annotations such as position, type of variation, call metrics, and overlap with CNVs of other data sets, including the Database of Genomic Variants.
Functional gene annotations such as genes affected and known disease associations
Accepts user-provided annotations
Presentation
GBrowse-enabled visuals for querying, browsing, interpreting, and reporting CNVs
Export of results into Excel, XML, CSV, and BED files
Direct links to public resources such as the UCSC Genome Browser, NCBI Entrez, Entrez Gene, and FABLE
Project and Account Management
Authentication and permission scheme that is especially useful for clinical diagnostic settings
Analysis result sharing within and between projects
Simple Web-based administrative interface
Remote access and administration enabled

CNV Workshop currently accepts genotyping array data from Illumina’s 550k, 610- and 660-Quad, and Omni arrays, along with Affymetrix’s 5.0 and 6.0 arrays, and can be easily configured to accept data from other platforms. The package comes preloaded with publicly available reference data from more than 2,000 healthy control subjects (the CHOP CNV Database). CNV Workshop also allows the user to upload already processed CNV calls for annotation and presentation.

The software package is freely available at http://sourceforge.net/projects/cnv/. It is also described in more detailed in our recent paper on BMC Bioinformatics.

-Xiaowu Gai

Additionally, if you are a developer or provider of an free, publicly available genomics or biological resource, database or analysis tool and would like to post in our guest feature, be it an introduction to your tool, updates or upcoming features or even an opinion about the current state of genomics research and data, please write us at wlathe AT openhelix DOT com. We would love to put you in the queue for the next guest post.

Our first guest post next Tuesday will be from Inna Dubchak , principal investigator at the LBNL/JGI group, developers of the VISTA comparative genomics resource (who sponsors a tutorial, free to the users). She’ll discuss some new tools at VISTA and give you a quick preview of some new upcoming features.

Let me state first, I completely agree with their premise, that databases and resources have become imperative. The earlier model of “publication of experimental results and sharing of the reated research materials” needs to be extended. As they state:

It is however no longer adequate to share data through traditional modes of publication, and, particularly with high throughput (‘-omics) technologies, sharing of datasets requires submission to public databases as has long been the case with nucleic acid and protein sequence data.

The authors state, factually, that the financial model for most biological databases (we are talking the thousands that exist), has often been a 3-5 year development funding, that once runs out, the infrastructure needs to be supported by another source. In fact, this has lead to the defunding of databases such as TAIR and VBRC (and many others), excellent resources with irreplaceable data and tools, that then must struggle to find funding to maintain the considerable costs of funding infrastructure and continued development.

The demands of scientific research, open, shared data, require a funding model that maintains the publicly available nature of these databases. And thus the problem as they state:

If, for financial reasons, BRCs are unable to perform their tasks under conditions that meet the requirements of sceintfic research and the deamnds of industry, scientists will either see valuable information lost or being transferred into strictly commercial environment with at east two consequences: (i) blockade of access to this information and/or high costs and (ii) loss of data and potentioal for technology transfer for the foreseeable future. In either case the effect on both the scientific and broader community will be detrimental.

Again, I agree.

They discuss several possible solutions to maintaining the viability of publicly available databases including a private-public dual tier system where for-profits paid an annual fee and academic researchers have free access. They mention Uniprot, which underwent a funding crisis over a decade ago, as an example. Uniprot (then Swissprot) went back to complete public funding in 2002. There are still several other databases that are attempting to fund themselves by such a model. BioBase is one where several databases have been folded. TransFac is one. There is a free, reduced functionality, version that is available to academics through gene-regulation.com and the fuller version for a subscription at BioBase. This former version allows some data to be shared, as one could see at VISTA or UCSC. I am not privy to the financials of BioBase and other similar models, and I assume that will work for some, but I agree with the authors that many useful databases and resources would be hard-pressed to be maintained this way.

Other possibilities include fully  including databases under a single public institution funding mechanism. The many databases of NCBI and EBI fit this model. In fact, there is even a recent case of a resource being folded into this model at NCBI. Again, this works for some, but not all useful resources.

Most will have to find variable methods for funding their databases. Considering the importance of doing so, it is imperative that viable models are found. The authors reject, out of hand, advertising. As they mention, most advertisers will not be drawn to website advertising without a visibility of at least 10,000 visitors per month. There might be some truth to this (and I need to read the reference they cite that use to back that up).

But the next model they suggest seems to me to have the same drawback. In this model, the database or resource would have a ‘partnership of core competencies.’ An example they cite is MMdb (not to be confused with MMDB). This virtual mutant mouse repository provides direct trial links to Invitrogen from it’s gene information to the product page. They mention that though 6 companies were approached, only one responded. It would seem that this model has the same issues as directly selling advertising.

They also mention that, at least for their research community of mouse functional genomics, “Institutional Funding” seems the best solution for long-term viability and open access. Unfortunately, until institutions like NIH and EMBL are willing or able to fund these databases, I’m not sure that’s thats a solution.

As they mention in the paper, the rate of growth of the amounts and types of data that is being generated is exponential. I am not sure that government or institutional funding can financially keep up with housing the infrastructure needed to maintain and further develop these databases so that all the data generated can remain publicly and freely accessible.

Information is should be free, but unfortunately it is not without cost. It will be interesting to see how funding of databases and resources evolves in this fast growing genomics world (and imperative we figure out solutions).

PS: On a personal note, the authors use their resource, EMMA (European Mouse Mutant Archive), as an example in the paper. I like the name since it’s the name of my daughter, but it just goes to prove that names come in waves. We named our daughter thinking few would name their daughter the same. When even databases name the same name, you know that’s not the case.

Chandras, C., Weaver, T., Zouberakis, M., Smedley, D., Schughart, K., Rosenthal, N., Hancock, J., Kollias, G., Schofield, P., & Aidinis, V. (2009). Models for financial sustainability of biological databases and resources Database, 2009 DOI: 10.1093/database/bap017

New-technology DNA sequencing provider Complete Genomics will provide near-complete genome sequences of 100 individuals to the Institute for Systems Biology, driving the first ever association study for a complex trait using whole-genome sequencing. Here’s the press release, and GenomeWeb has some additional information

This study was done by Complete Genomics, and as Daniel mentions, does indicate some changes and advances to come. Read the entire post, he mentions some things learned at ASHG about how these studies will look in the future, and particularly, this sentence…

Now the real challenge - coming up with ways of handling the massive volumes of data generated by these technologies

goes to the heart of something I see as a very important question. Not only the right tools but funding them.

An embarrassment of riches.

Models for financial sustainability of biological databases and resources — Chandras et al. 2009 (0): bap017 — Database.

I will be writing up a longer review and some thoughts about the article. I’m having a bad blog week, and kind of lost some stuff I was writing. But I would like to point out the article for now, post my thoughts soon (later this evening?)

There are now thousands of databases and analysis tools for the researcher to use when doing research in biology and genomics. The first problem the researcher has is just finding those resources, finding the right one. In another step toward helping that happen, we’ve put together a highly relevant, curated database of genomics and biological resources available to the researcher and a search engine to find them based the context of the keyword found at the resource site, tutorials and even our blogs posts that mention the database. You will find that your searches will lead you to resources relevant to your needs. Today’s tip introduces this new search.

We strongly believe this is the best method available now for the researcher not only to find relevant resources, but to find training on how to use those resources. And check back, our database of resources will be growing, as will our features.

The URL is the same: http://www.openhelix.com. Though we also now have http://www.openhelix.eu for our European users. They’ll both go to the same place of course! (though in the next couple days as our domain moves to the new servers, the first will be our old site, the latter will be our new one).

We have a new site and functionality! OpenHelix will now have a great new search engine (free and publicly available) to search through hundreds of genomics resources to find exactly what you are looking for. We believe this will be a great boon to finding your data. A large number of those (approaching 100 now) will have links to our tutorials for you to view and learn how to use those resources, some are sponsored and free to the user, others have reasonable subscription cost.

Our blog will have a new look and a new URL: http://blog.openhelix.com. Of course, if you use http://www.openhelix.com/blog, you’ll be easily redirected.

We have lots of exciting plans for the search, for the site, for the blog and for our tutorials over the next few months and into the future, so keep an eye out! And please, if you find a feature you want or hit a snag, let us know!