The OpenHelix Blog

Researchers, faculty, students and staff at Washington University can now efficiently and effectively learn to use bioinformatics and genomics resources with the extensive tutorial suite catalog from OpenHelix.

Bellevue, WA (PRWEB) April 26, 2010 — Bernard Becker Medical Library at Washington University School of Medicine has purchased a subscription to OpenHelix (www.openhelix.com) giving faculty, students and staff access to over 90 tutorial suites on bioinformatics and genomic resources.

With OpenHelix tutorials, Becker Library offers the Washington University community a quick and effective way to learn about the most powerful and popular genomics and bioinformatics databases and resources. These tutorials cover many types of resources including protein databases, bioinformatics analysis tools, model organism databases, SNP databases, comparative genomics, pathway and interaction resources and much more. “We’re thrilled that we are able to provide such a fantastic suite of resources to our research community,” said Kristi Holmes, PhD bioinformaticist at Becker Medical Library. “These tutorials are the perfect compliment to the instruction and consultation services offered by our Bioinformatics@Becker program.”

These tutorials are the perfect compliment to the instruction and consultation services offered by our Bioinformatics@Becker program

The online narrated tutorials, which run in just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders. The approximately 60 minute tutorials highlight and explain the features and functionality needed to start using the resources effectively. The tutorial can be used by new users to introduce them to a resource, or by previous users to view new features and functionality, or simply as a reference tool to understand specific features.

In addition to the tutorial, users also have access to 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 of time and effort for teachers and professors creating classroom content.

“It is difficult, and certainly cost prohibitive, for university Libraries to create and provide training on the many critical genomic resources available,” said Scott Lathe, Chief Executive Officer of OpenHelix. “With an OpenHelix subscription, Washington University provides an efficient and effective training solution for their researchers.”

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) 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. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

Greetings! OpenHelix Blog is instituting a new semi-weekly feature. Every Wednesday we have our “Tip of the Week,” on Thursdays we have our “What’s Your Problem,” and now on an occasional Tuesdays we are going to have our “Provider Guest Post.” These will be posts from providers of genomics tools and database and will be opinions, updates and upcoming features of the resource, whatever the provider of the resource would like to convey to users. We have several lined up for the coming weeks, so keep checking back.

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.

We’ve introduced Galaxy (http://www.usegalaxy.org) before in the Tip of the Week section, have showed you one thing useful you could do with it, and now we also have a free tutorial and training materials that introduce you to the basic use of the tool. In today’s tip of the week, I’m going to show you workflows. Workflows was in beta until recently, so it isn’t in the first version of our tutorial (though it will be in the second). It’s a great feature, so I wanted to introduce it here. Workflows allows you to set up an automated process that takes your data through a preset series of manipulation and analysis steps. This can be very useful if there is a process you are doing a lot and you don’t want to have to do each step every time, or if you create a analysis process you’d like to share with a colleague. (and I’d like to point out that Galaxy has a good number of other short screencasts of tasks you might want to check out after doing the tutorial )

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

{I’m closing comments here since a fresh thread is up–Mary}

A question we get asked all the time–and I see on mailings lists with about a twice/year frequency–is where can I look at the restriction sites in my sequences? I’m going to mention a few that I know about, but if anyone has other favorite tools or spots, do let us know in the comments.

UCSC Genome Browser: if you look in the browser in the “Mapping and Sequencing” Track groups area there is a menu called Restr Enzymes. I have turned this track on, and turned off some other default tracks, and created a “Session” to show you exactly how this can look. I picked a small gene for the example. Load my session: http://genome.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Mary%20Mangan&hgS_otherUserSessionName=restriction_enzymes

You can see the sites in Ensembl, too. From that UCSC session I provided you can click the link in the blue navigation area at the top of the UCSC page to go to the exact same region in Ensembl. In the “Detailed View” section at Ensembl you can see menus for “Decorations” and other display features. In Decorations you can check the box for Rest. Enzymes to see them on your viewer.

However, there may be times where your sequences is different from genomic, or not available in a species browser, and sometimes you just want another type of viewer. You might try PlasMapper (http://wishart.biology.ualberta.ca/PlasMapper). I took the same sequence from the browsers (the Casp-1 gene) and put the FASTA sequence in, and created a really quick map. It also gives text output if you prefer. It can add a display for some handy features that you might have on plasmids or constructs like promoters or affinity tags. Takes only a few seconds, a very handy little freely available tool for you to know about. I know it isn’t new, but it is such a common question for us that we thought we would mention it.

Dong, X., Stothard, P., Forsythe, I.J., Wishart, D.S. (2004). PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Research, 32(Web Server), W660-W664. DOI: 10.1093/nar/gkh410

A call came from RGD this week across their mailing list. They are doing a “white paper” to accompany a group of research papers are coming out in Nature Genetics. You can read the paper and become a signatory on this paper, demonstrating your support for rat genome research. There is a podcast right on their homepage that explains this in more detail.

If you think you might like to show your support as a signatory, please:

1. Go over to the RGD homepage. Listen to the podcast. (Ignore that dreadful music at the beginning, it goes away).

2. Download and read the white paper that is there. If you can support it, email the team.

3. Put your requested information (name, title, affiliation, etc) in an email to Tim and Howard–their address are right below the podcast.

If you think others in your department would be interested, please mail out a call to them. The RGD team needs this by Thursday February 28.

EDIT: bumped back up because today is the deadline.

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.