Tag Archives: search

New feature, research articles, on OpenHelix site

If you go over to the OpenHelix home page, you’ll start to notice some differences. Our tutorial landing pages have an added new feature. We now have a section on each landing page that shows the most recent research in the BioMed Central journals. For example, the screenshot here is for our GeneMANIA tutorial suite. At the bottom left corner you’ll see the 5 most recent research articles that have used GeneMANIA from the BioMed Central catalog of research journals. This will be useful to users to get an idea of what kind of data  a resource has and research that is done using the resource. This will also be helpful to find other resources that might be of use (often a related-resource will be mentioned in conjunction with the resource of interest).

This is the beginning of a series of new features we hope to add to the landing pages that will enhance the ability of researchers to learn all they can about the data and tools available to them. We will be adding a “recent video tips” section and more.

And, if you are a publisher of research literature and would like to get a ‘recent research list’ like this on our landing pages for your journals (will need access to full text of articles), please contact us and we’d love to work with you to do so for the benefit of your journals, the resources, the researchers and yes, OpenHelix :).

In our continuing effort to maintain and expand our search database and engine, our tutorials, our blog and more, you will also notice we have added advertising to our site. The ads are a top banner ad, a side skyscraper ad and a small ad on tutorial landing pages. Please consider viewing these sponsors if they interest you. Ads will not be on sponsored tutorials such as UCSC Genome Browser and PDB, and others, nor will they be visible for any subscribers to the catalog of tutorials.

If you would like to sponsor a tutorial so that it is publicly available, whether you are the developer of the tool or a company, please contact us about the opportunity to get training and outreach to a large number of researchers.

Also, though we have a dozen sponsored tutorials that are publicly available, we do have a large catalog of over 90 additional tutorials available for subscription. You can subscribe to access these as an individual, department or institution.


We’ve got widgets

I’ve mentioned others’ widgets before. They can be very handy tools on websites and blogs to add content and useful interactive searches, etc.

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!

Tip of the Week: Ratmine

Ratmine is a ‘data warehouse’ that allows the user to construct queries across different areas of biological knowledge from SNPs to Pathways. It’s developed by the people at RGD and uses Intermine a project developed for Flymine and as part of a project between RGD, SGD and ZFIN to implement Intermine for these databases and ” develop new methods of interoperability for cross-organism research.” We’ve mentioned Intermine before and it’s also used in ModEncode Intermine is going to have to be a subject of a later post I think :).

This tip is actually a video done by the RGD group and one of those gems I’ve found at SciVee in our attempts to integrate our tips at SciVee (which will be coming). We occasionally will highlight a short tutorial done by someone else here at our tips (occasionally) and since I’ve found this gem and just got back from vacation in Florida :)…
Btw, while you are at it, you might want to check out this interesting set of tutorials on biomedical ontologies.

OH Launches Genomics Search and Learn Portal

OpenHelix today announced the launch of the new www.openhelix.com web site, a first-of-its kind portal that assists researchers in conducting breakthrough research.  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.

“There are now thousands of databases and analysis tools for the researcher to use when doing biological research,” said Scott Lathe, CEO of OpenHelix, “The first problem researchers have is just finding the most relevant tool.  There are catalogs of resources on the web, but they are cumbersome to use and using a keyword search on them more often than not delivers irrelevant results. The OpenHelix portal solves this problem”

The OpenHelix portal searches a highly relevant, curated database of genomics and biological resources, OpenHelix tutorials and training materials, and tips and information on the resources on the OpenHelix blog.  The portal delivers a list of relevant resources for the user using a proprietary relevancy system developed by OpenHelix scientists. Once a user finds the most relevant resources in the results, they can immediately go to training on the resource.

Searching for the most relevant resource is free to all users.  Some of the tutorial suites are also free, as they are sponsored by the resources themselves, such as the UCSC Genome Browser.

“The second, and possibly most significant problem a researcher faces is learning how to use these often complex and changing resources”, explained Lathe “Since OpenHelix has multiple trainers all having PhDs in biological sciences, intimate knowledge of the resources, and having years of experience with on-site and online training, we have a unique ability to provide the solution to this problem.”

With an OpenHelix individual or institution subscription, users can access the complete catalog of OpenHelix tutorial suites, over 80 currently, in categories including pathways, expression, variation, literature and general databases. These tutorials are continuously updated each month with new tutorials added frequently. (For a complete catalog, go to http://www.openhelix.com/cgi/tutorials.cgi)

With a subscription, scientists quickly learn how to use the tools they need when they need them. The online narrated tutorial, which runs in just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders. The 30-60 minute tutorials highlight and explain all the features and functionality needed to start using the resource effectively. The tutorials are used to introduce a new resource, to view new features and functionality, or simply as a reference tool to refresh a users knowledge on a resource.

In addition to the tutorials, subscribers also receive useful training materials including the animated PowerPoint slides used as a basis for the tutorial, suggested script for the slides, slide handouts, and exercises. This can save a tremendous amount time and effort for teachers and professors to create classroom content.

The new portal was partially funded by NHGRI grant 3R44HG004531.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web.  More efficient use of the most relevant resources means quicker and more effective research.

Tip of the Week: Finding the right genomics resource

ohsearch_thumbOpenHelix just opened our new web site. We will still be offering the tutorials we’ve always offered (80 and growing!), but now we have a new search engine and database of many more resources. And it’s publicly available and free.

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.

Blog and Site are moving

We’ll be having a bigger announcement later, but we are moving!

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 URLhttp://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!

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.

Continue reading

Tip of the Week: Subscribing to journal updates with NCBI

NCBI RSSTwo weeks ago, I showed you how to use HubMed, an alternative search interface to PubMed, to subscribe to a feed for a specific journal, allowing you to stay up-to-date on new articles and issues of that journal. As mentioned earlier, many journals have feeds to their updates, but using PubMed and HubMed are good alternatives if you can not find a feed, want to customize it a bit or just like a single place to go to for all your feeds. This week, I’m going to show you how to do the same thing, subscribe to a feed for a specific journal, using NCBI as suggested by a commenter in the Tip of the Week a couple weeks ago.

Tip of the Week: eTBlast

etBlasteTBlast is a great tool for searching the literature, not only PubMed, but also CRISP (a database of federally funded biomedical research). Unlike PubMed or CRISP, you don’t use a few well chosen (hopefully) keywords, you can just paste in an entire paragraph or abstract and eTBlast will search and find papers similar to the entire paragraph. It saves you the time and effort of trying to narrow your search down. Just wrote that amazing research up and need to find citations for it? or granting agencies, experts in the field or the best journal to submit it to? eTBlast can help you with that. Want to do some boning up on a new field? eTBlast can help you create that reading list. This 5 minute tip shows you quickly how to use eTBlast and obtain some relevant results.

The eTBlast server site at Virginia Tech also hosts the handy ARGH search tool, allowing searches for acronyms used in biomedical contexts.

Tip of the Week: One search to rule them all

Ok, well not exactly (wouldn’t that be nice). What do Ensembl, Gramene, Reactome, Wormbase, HapMap and RGD databases all have in common? (other than “.org” ;)) They all have a search mechanism powered by the same software, BioMart. [link fixed; Mary] In this week’s tip we take a real quick look at these and other databases use of BioMart and briefly show you that the steps are the same (choose dataset, filter dataset, list attributes to show) and you can search some of them all at the same place.